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Rodríguez-Aguilar ED, Gutiérrez-Millán E, Rodríguez MH. Accurate Recapitulation of Chikungunya Virus Complete Coding Sequence Phylogeny Using Variable Genome Regions for Genomic Surveillance. Viruses 2024; 16:926. [PMID: 38932218 PMCID: PMC11209212 DOI: 10.3390/v16060926] [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: 05/03/2024] [Revised: 06/03/2024] [Accepted: 06/05/2024] [Indexed: 06/28/2024] Open
Abstract
Chikungunya virus (CHIKV) is transmitted by mosquito bites and causes chikungunya fever (CHIKF). CHIKV has a single-stranded RNA genome and belongs to a single serotype with three genotypes. The Asian lineage has recently emerged in the Western Hemisphere, likely due to travel-associated introduction. Genetic variation accumulates in the CHIKV genome as the virus replicates, creating new lineages. Whole genome sequencing is ideal for studying virus evolution and spread but is expensive and complex. This study investigated whether specific, highly variable regions of the CHIKV genome could recapitulate the phylogeny obtained with a complete coding sequence (CDS). Our results revealed that concatenated highly variable regions accurately reconstructed CHIKV phylogeny, exhibiting statistically indistinguishable branch lengths and tree confidence compared to CDS. In addition, these regions adequately inferred the evolutionary relationships among CHIKV isolates from the American outbreak with similar results to the CDS. This finding suggests that highly variable regions can effectively capture the evolutionary relationships among CHIKV isolates, offering a simpler approach for future studies. This approach could be particularly valuable for large-scale surveillance efforts.
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Affiliation(s)
| | | | - Mario H. Rodríguez
- Center for Infectious Disease Research, National Institute of Public Health of Mexico, Av. Universidad 655, Cuernavaca 62100, Mexico; (E.D.R.-A.); (E.G.-M.)
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Wang W, Dong Z, Du Z, Wu P. Genome-scale approach to reconstructing the phylogenetic tree of psyllids (superfamily Psylloidea) with account of systematic bias. Mol Phylogenet Evol 2023; 189:107924. [PMID: 37699449 DOI: 10.1016/j.ympev.2023.107924] [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: 05/17/2023] [Revised: 09/05/2023] [Accepted: 09/09/2023] [Indexed: 09/14/2023]
Abstract
Psyllids (class Insecta: order Hemiptera: superfamily Psylloidea) are a taxonomically and phylogenetically challenging clade. Recent studies have largely advanced the phylogeny of this group, yet the family-level relationships among Aphalaridae, Carsidaridae, and others remain unresolved. Genome-scale phylogenetic analysis is known to provide a finer resolution for problems like that. However, such phylogenomics also introduces new problems: incorrect trees with high confidence yielded due to systematic error (bias). Here we addressed these issues using hundreds of single-copy orthologous (SCO) genes in psyllid transcriptomes and genomes. Our analyses revealed conflicts between the nucleotide-based and amino-acid-based phylogenetic trees. While the nucleotide-based phylogeny strongly supported the (Aphalaridae + Carsidaridae) + Others relationship, the amino-acid-based one recovered Aphalaridae + (Carsidaridae + Others) with 100% support. Further inspection revealed significant compositional heterogeneity in nucleotide sequences for 67% of SCO genes, but not in the corresponding translated amino acid sequences. We then used different strategies to combat this compositional bias, and found that using the RY-coding strategy (coding the standard nucleotides as purines and pyrimidines) the nucleotide-based phylogeny became consistent with the amino-acid-based one. We further applied RY-coding to a published concatenated nucleotide dataset and recovered the Aphalaridae monophyly (which is refuted by the original literature on non-recoded sequences) at the base of psyllid tree. Moreover, it was found that variations in evolutionary rate could lead to errors in nucleotide-based phylogeny. The fast-evolving Heteropsylla cubana (Psyllidae: Ciriacreminae) was incorrectly placed within the subfamily Psyllinae. This bias can be avoided by using data removal or RY-coding strategies. Together, our results strongly support the family relationship of Aphalaridae + (Carsidaridae + Others), and show that the amino-acid-based concatenation analysis is more robust than nucleotide-based one. Future phylogenomic analysis of psyllid nucleotide sequences should take into account methods such as the RY-coding scheme to address potential systematic biases arising from composition and rate heterogeneities.
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Affiliation(s)
- Wei Wang
- State Key Laboratory of Integrated Management of Pest Insects and Rodents, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Zequn Dong
- State Key Laboratory of Integrated Management of Pest Insects and Rodents, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Zhong Du
- State Key Laboratory of Integrated Management of Pest Insects and Rodents, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Pengxiang Wu
- State Key Laboratory of Integrated Management of Pest Insects and Rodents, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China; University of Chinese Academy of Sciences, Beijing 100049, China.
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Niu Z, Lin Z, Tong Y, Chen X, Deng Y. Complete plastid genome structure of 13 Asian Justicia (Acanthaceae) species: comparative genomics and phylogenetic analyses. BMC PLANT BIOLOGY 2023; 23:564. [PMID: 37964203 PMCID: PMC10647099 DOI: 10.1186/s12870-023-04532-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/30/2023] [Accepted: 10/17/2023] [Indexed: 11/16/2023]
Abstract
BACKGROUND Justicia L. is the largest genus in Acanthaceae Juss. and widely distributed in tropical and subtropical regions of the world. Previous phylogenetic studies have proposed a general phylogenetic framework for Justicia based on several molecular markers. However, their studies were mainly focused on resolution of phylogenetic issues of Justicia in Africa, Australia and South America due to limited sampling from Asia. Additionally, although Justicia plants are of high medical and ornamental values, little research on its genetics was reported. Therefore, to improve the understanding of its genomic structure and relationships among Asian Justicia plants, we sequenced complete chloroplast (cp.) genomes of 12 Asian plants and combined with the previously published cp. genome of Justicia leptostachya Hemsl. for further comparative genomics and phylogenetic analyses. RESULTS All the cp. genomes exhibit a typical quadripartite structure without genomic rearrangement and gene loss. Their sizes range from 148,374 to 151,739 bp, including a large single copy (LSC, 81,434-83,676 bp), a small single copy (SSC, 16,833-17,507 bp) and two inverted repeats (IR, 24,947-25,549 bp). GC contents range from 38.1 to 38.4%. All the plastomes contain 114 genes, including 80 protein-coding genes, 30 tRNAs and 4 rRNAs. IR variation and repetitive sequences analyses both indicated that Justicia grossa C. B. Clarke is different from other Justicia species because its lengths of ndhF and ycf1 in IRs are shorter than others and it is richest in SSRs and dispersed repeats. The ycf1 gene was identified as the candidate DNA barcode for the genus Justicia. Our phylogenetic results showed that Justicia is a polyphyletic group, which is consistent with previous studies. Among them, J. grossa belongs to subtribe Tetramerinae of tribe Justicieae while the other Justicia members belong to subtribe Justiciinae. Therefore, based on morphological and molecular evidence, J. grossa should be undoubtedly recognized as a new genus. Interestingly, the evolutionary history of Justicia was discovered to be congruent with the morphology evolution. CONCLUSION Our study not only elucidates basic features of Justicia whole plastomes, but also sheds light on interspecific relationships of Asian Justicia plants for the first time.
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Affiliation(s)
- Zhengyang Niu
- Key Laboratory of Plant Resources Conservation and Sustainable Utilization, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou, 510650, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Zheli Lin
- Key Laboratory of Plant Resources Conservation and Sustainable Utilization, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou, 510650, China
- School of Biology and Agriculture, Shaoguan University, Shaoguan, Guangdong, 512005, China
| | - Yi Tong
- School of Chinese Materia Medica Medical, Guangzhou University of Chinese Medicine, Guangzhou, 510006, China
| | - Xin Chen
- Co-Innovation Center for Sustainable Forestry in Southern China, College of Life Sciences, Nanjing Forestry University, Nanjing, Jiangsu, 210037, China
| | - Yunfei Deng
- Key Laboratory of Plant Resources Conservation and Sustainable Utilization, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou, 510650, China.
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Vecchi M, Tsvetkova A, Stec D, Ferrari C, Calhim S, Tumanov D. Expanding Acutuncus: Phylogenetics and morphological analyses reveal a considerably wider distribution for this tardigrade genus. Mol Phylogenet Evol 2023; 180:107707. [PMID: 36681365 DOI: 10.1016/j.ympev.2023.107707] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2022] [Revised: 01/11/2023] [Accepted: 01/12/2023] [Indexed: 01/20/2023]
Abstract
The tardigrade genus Acutuncus has been long thought to be an Antarctic endemism, well adapted to this harsh environment. The Antarctic endemicity of Acutuncus was recently dispelled with the description of Acutuncus mariae Zawierucha, 2020 found in the Svalbard archipelago. The integrated analyses on two newly found Acutuncus populations from UK and Italy, and a population of Acutuncus antarcticus found close to its type locality allowed us to expand the climatic and geographic range of the genus Acutuncus. These findings also allowed us to re-evaluate the morphological diagnoses of Acutuncus and accommodate it in the newly proposed monotypic family Acutuncidae fam. nov. Two new Acutuncus species morpho-groups are instituted based on eggs morphology: one (Acutuncus antarcticus morphogroup) including the Antarctic Acutuncus taxa characterized by eggs with long pillars within the chorion and eggs laid freely to the environment, the other (Acutuncus mariae morphogroup) including the European species, characterized by eggs with short pillars within the chorion and eggs laid in the exuvium. Finally, we describe two new Acutuncus species from Europe: Acutuncus mecnuffisp. nov. and Acutuncus giovanniniaesp. nov.
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Affiliation(s)
- Matteo Vecchi
- Department of Biological and Environmental Science, University of Jyvaskyla, PO Box 35, FI-40014 Jyvaskyla, Finland.
| | - Alexandra Tsvetkova
- Department of Invertebrate Zoology, Faculty of Biology, Saint Petersburg State University, 199034, Universitetskaya nab. 7/9, Saint Petersburg, Russia
| | - Daniel Stec
- Institute of Systematics and Evolution of Animals, Polish Academy of Sciences, Sławkowska 17, 31-016 Kraków, Poland
| | - Claudio Ferrari
- Department of Chemistry, Life Sciences and Environmental Sustainability, University of Parma, Parco Area delle Scienze 33/A, 43124 Parma, Italy
| | - Sara Calhim
- Department of Biological and Environmental Science, University of Jyvaskyla, PO Box 35, FI-40014 Jyvaskyla, Finland
| | - Denis Tumanov
- Department of Invertebrate Zoology, Faculty of Biology, Saint Petersburg State University, 199034, Universitetskaya nab. 7/9, Saint Petersburg, Russia; Zoological Institute of the Russian Academy of Sciences, 199034, Universitetskaja nab. 1, Saint Petersburg, Russia.
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Rodríguez-Aguilar ED, Martínez-Barnetche J, Rodríguez MH. Three highly variable genome regions of the four dengue virus serotypes can accurately recapitulate the CDS phylogeny. MethodsX 2022; 9:101859. [PMID: 36187156 PMCID: PMC9516459 DOI: 10.1016/j.mex.2022.101859] [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] [Received: 07/12/2022] [Accepted: 09/10/2022] [Indexed: 11/18/2022] Open
Abstract
The circulation of the four-dengue virus (DENV) serotypes has significantly increased in recent years, accompanied by an increase in viral genetic diversity. In order to conduct disease surveillance and understand DENV evolution and its effects on virus transmission and disease, efficient and accurate methods for phylogenetic classification are required. Phylogenetic analysis of different viral genes sequences is the most used method, the envelope gene (E) being the most frequently selected target. We explored the genetic variability of the four DENV serotypes throughout their complete coding sequence (CDS) of sequences available in GenBank and used genomic regions of different variability rate to recapitulate the phylogeny obtained with the DENV CDS. Our results indicate that the use of high or low variable regions accurately recapitulate the phylogeny obtained with CDS of sequences from different DENV genotypes. However, when analyzing the phylogeny of a single genotype, highly variable regions performed better in recapitulating the distance branch length, topology, and support of the CDS phylogeny. The use of three concatenated highly variable regions was not statistically different in distance branch length and support to that obtained in CDS phylogeny.•This study demonstrated the ability of highly variable regions of the DENV genome to recapitulate the phylogeny obtained with the full coding sequence (CDS).•The use of genomic regions of high or low variability did not affect the performance in recapitulating the phylogeny obtained with CDS from different genotypes. However, when phylogeny was analyzed for sequences from a single genotype, highly variable regions performed better in recapitulating the distance branch length, topology, and support of the CDS phylogeny.•The use of concatenated highly variable genome regions represent a useful option for recapitulating genome-wide phylogenies in analyses of sequences belonging to the same DENV genotype.
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Piñeros VJ, Del R Pedraza-Marrón C, Betancourt-Resendes I, Calderón-Cortés N, Betancur-R R, Domínguez-Domínguez O. Genome-wide species delimitation analyses of a silverside fish species complex in central Mexico indicate taxonomic over-splitting. BMC Ecol Evol 2022; 22:108. [PMID: 36104671 PMCID: PMC9472351 DOI: 10.1186/s12862-022-02063-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2022] [Accepted: 09/06/2022] [Indexed: 11/29/2022] Open
Abstract
BACKGROUND Delimiting species across a speciation continuum is a complex task, as the process of species origin is not generally instantaneous. The use of genome-wide data provides unprecedented resolution to address convoluted species delimitation cases, often unraveling cryptic diversity. However, because genome-wide approaches based on the multispecies coalescent model are known to confound population structure with species boundaries, often resulting in taxonomic over-splitting, it has become increasingly evident that species delimitation research must consider multiple lines of evidence. In this study, we used phylogenomic, population genomic, and coalescent-based species delimitation approaches, and examined those in light of morphological and ecological information, to investigate species numbers and boundaries comprising the Chirostoma "humboltianum group" (family Atherinidae). The humboltianum group is a taxonomically controversial species complex where previous morphological and mitochondrial studies produced conflicting species delimitation outcomes. We generated ddRADseq data for 77 individuals representing the nine nominal species in the group, spanning their distribution range in the central Mexican plateau. RESULTS Our results conflict with the morphospecies and ecological delimitation hypotheses, identifying four independently evolving lineages organized in three geographically cohesive clades: (i) chapalae and sphyraena groups in Lake Chapala, (ii) estor group in Lakes Pátzcuaro and Zirahuén, and (iii) humboltianum sensu stricto group in Lake Zacapu and Lerma river system. CONCLUSIONS Overall, our study provides an atypical example where genome-wide analyses delineate fewer species than previously recognized on the basis of morphology. It also highlights the influence of the geological history of the Chapala-Lerma hydrological system in driving allopatric speciation in the humboltianum group.
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Affiliation(s)
- Victor Julio Piñeros
- Laboratorio de Ecología Molecular, Escuela Nacional de Estudios Superiores Unidad Morelia, Universidad Nacional Autónoma de México, Antigua Carretera a Pátzcuaro 8701, Ex-Hacienda de San José de La Huerta, 58190, Morelia, Michoacán, Mexico
| | | | - Isaí Betancourt-Resendes
- Facultad de Ciencias Naturales, Universidad Autónoma de Querétaro, Avenida de Las Ciencias S/N Juriquilla, Delegación Santa Rosa Jáuregui, 76230, Querétaro, Mexico
| | - Nancy Calderón-Cortés
- Laboratorio de Ecología Molecular, Escuela Nacional de Estudios Superiores Unidad Morelia, Universidad Nacional Autónoma de México, Antigua Carretera a Pátzcuaro 8701, Ex-Hacienda de San José de La Huerta, 58190, Morelia, Michoacán, Mexico.
| | - Ricardo Betancur-R
- Department of Biology, The University of Oklahoma, 730 Van Vleet Oval, Norman, OK, 73019, USA
| | - Omar Domínguez-Domínguez
- Laboratorio de Biología Acuática, Facultad de Biología, Universidad Michoacana de San Nicolás de Hidalgo, Edificio "R" Planta Baja, Ciudad Universitaria, 58030, Morelia, Michoacán, Mexico.
- Laboratorio Nacional de Análisis y Síntesis Ecológica Para la Conservación de Recursos Genéticos de México, Escuela Nacional de Estudios Superiores, Unidad Morelia, Universidad Nacional Autónoma de México, Apartado Postal 27-3 (Xangari), 58089, Michoacán, Morelia, Mexico.
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Lozano-Fernandez J. A Practical Guide to Design and Assess a Phylogenomic Study. Genome Biol Evol 2022; 14:evac129. [PMID: 35946263 PMCID: PMC9452790 DOI: 10.1093/gbe/evac129] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 08/03/2022] [Indexed: 11/13/2022] Open
Abstract
Over the last decade, molecular systematics has undergone a change of paradigm as high-throughput sequencing now makes it possible to reconstruct evolutionary relationships using genome-scale datasets. The advent of "big data" molecular phylogenetics provided a battery of new tools for biologists but simultaneously brought new methodological challenges. The increase in analytical complexity comes at the price of highly specific training in computational biology and molecular phylogenetics, resulting very often in a polarized accumulation of knowledge (technical on one side and biological on the other). Interpreting the robustness of genome-scale phylogenetic studies is not straightforward, particularly as new methodological developments have consistently shown that the general belief of "more genes, more robustness" often does not apply, and because there is a range of systematic errors that plague phylogenomic investigations. This is particularly problematic because phylogenomic studies are highly heterogeneous in their methodology, and best practices are often not clearly defined. The main aim of this article is to present what I consider as the ten most important points to take into consideration when planning a well-thought-out phylogenomic study and while evaluating the quality of published papers. The goal is to provide a practical step-by-step guide that can be easily followed by nonexperts and phylogenomic novices in order to assess the technical robustness of phylogenomic studies or improve the experimental design of a project.
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Affiliation(s)
- Jesus Lozano-Fernandez
- Department of Genetics, Microbiology and Statistics, Biodiversity Research Institute (IRBio), University of Barcelona, Avd. Diagonal 643, 08028 Barcelona, Spain
- Institute of Evolutionary Biology (CSIC – Universitat Pompeu Fabra), Passeig marítim de la Barcelona 37-49, 08003 Barcelona, Spain
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8
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Rodríguez-Aguilar ED, Martínez-Barnetche J, Juárez-Palma L, Alvarado-Delgado A, González-Bonilla CR, Rodríguez MH. Genetic diversity and spatiotemporal dynamics of DENV-1 and DENV-2 infections during the 2012-2013 outbreak in Mexico. Virology 2022; 573:141-150. [PMID: 35779336 DOI: 10.1016/j.virol.2022.06.011] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2022] [Revised: 06/15/2022] [Accepted: 06/16/2022] [Indexed: 10/18/2022]
Abstract
Dengue fever is caused by four related dengue virus serotypes, DENV-1 to DENV-4, where each serotype comprises distinct genotypes and lineages. The last major outbreak in Mexico occurred during 2012 and 2013, when 112,698 confirmed cases were reported (DENV-1 and DENV-2 were predominant). Following partial E, NS2A and NS5 gene sequencing, based on the virus genome variability, we analyzed 396 DENV-1 and 248 DENV-2 gene sequences from serum samples from dengue acute clinical cases from 13 Mexican states, Mutations were identified, and their genetic variability estimated, along with their evolutionary relationship with DENV sequences sampled globally. DENV-1 genotype V and DENV-2 Asian-American genotype V were the only genotypes circulating during the outbreak. Mutations in NS2A and NS5 proteins were widely disseminated and suggested local emergence of new lineages. Phylogeographic analysis suggested viral spread occurred from coastal regions, and tourist destinations, such as Yucatan and Quintana Roo, which played important roles in disseminating these lineages.
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Affiliation(s)
- Eduardo D Rodríguez-Aguilar
- Centro de Investigación Sobre Enfermedades Infecciosas, Instituto Nacional de Salud Pública, Av. Universidad 655, Cuernavaca, 62100, Mexico.
| | - Jesús Martínez-Barnetche
- Centro de Investigación Sobre Enfermedades Infecciosas, Instituto Nacional de Salud Pública, Av. Universidad 655, Cuernavaca, 62100, Mexico.
| | - Lilia Juárez-Palma
- Centro de Investigación Sobre Enfermedades Infecciosas, Instituto Nacional de Salud Pública, Av. Universidad 655, Cuernavaca, 62100, Mexico.
| | - Alejandro Alvarado-Delgado
- Centro de Investigación Sobre Enfermedades Infecciosas, Instituto Nacional de Salud Pública, Av. Universidad 655, Cuernavaca, 62100, Mexico.
| | - Cesar R González-Bonilla
- Universidad Nacional Autónoma de México and Instituto Mexicano del Seguro Social, Mexico City, 04510, Mexico.
| | - Mario H Rodríguez
- Centro de Investigación Sobre Enfermedades Infecciosas, Instituto Nacional de Salud Pública, Av. Universidad 655, Cuernavaca, 62100, Mexico.
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Owen CL, Marshall DC, Wade EJ, Meister R, Goemans G, Kunte K, Moulds M, Hill K, Villet M, Pham TH, Kortyna M, Lemmon EM, Lemmon AR, Simon C. Detecting and removing sample contamination in phylogenomic data: an example and its implications for Cicadidae phylogeny (Insecta: Hemiptera). Syst Biol 2022; 71:1504-1523. [PMID: 35708660 DOI: 10.1093/sysbio/syac043] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2021] [Revised: 05/23/2022] [Accepted: 06/07/2022] [Indexed: 11/13/2022] Open
Abstract
Contamination of a genetic sample with DNA from one or more non-target species is a continuing concern of molecular phylogenetic studies, both Sanger sequencing studies and Next-Generation Sequencing (NGS) studies. We developed an automated pipeline for identifying and excluding likely cross-contaminated loci based on detection of bimodal distributions of patristic distances across gene trees. When the contamination occurs between samples within a dataset, comparisons between a contaminated sample and its contaminant taxon will yield bimodal distributions with one peak close to zero patristic distance. This new method does not rely on a priori knowledge of taxon relatedness nor does it determine the causes(s) of the contamination. Exclusion of putatively contaminated loci from a dataset generated for the insect family Cicadidae showed that these sequences were affecting some topological patterns and branch supports, although the effects were sometimes subtle, with some contamination-influenced relationships exhibiting strong bootstrap support. Long tip branches and outlier values for one anchored phylogenomic pipeline statistic (AvgNHomologs) were correlated with the presence of contamination. While the AHE markers used here, which target hemipteroid taxa, proved effective in resolving deep and shallow level Cicadidae relationships in aggregate, individual markers contained inadequate phylogenetic signal, in part probably due to short length. The cleaned dataset, consisting of 429 loci, from 90 genera representing 44 of 56 current Cicadidae tribes, supported three of the four sampled Cicadidae subfamilies in concatenated-matrix maximum likelihood (ML) and multispecies coalescent-based species tree analyses, with the fourth subfamily weakly supported in the ML trees. No well-supported patterns from previous family-level Sanger sequencing studies of Cicadidae phylogeny were contradicted. One taxon (Aragualna plenalinea) did not fall with its current subfamily in the genetic tree, and this genus and its tribe Aragualnini is reclassified to Tibicininae following morphological re-examination. Only subtle differences were observed in trees after removal of loci for which divergent base frequencies were detected. Greater success may be achieved by increased taxon sampling and developing a probe set targeting a more recent common ancestor and longer loci. Searches for contamination are an essential step in phylogenomic analyses of all kinds and our pipeline is an effective solution.
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Affiliation(s)
- Christopher L Owen
- Systematic Entomology Laboratory, USDA-ARS, c/o National Museum of Natural History, Smithsonian Institution, Washington, DC, USA
| | - David C Marshall
- Dept. of Ecology and Evolutionary Biology, University of Connecticut, Storrs, CT 06269, USA
| | - Elizabeth J Wade
- Dept. of Natural Science and Mathematics, Curry College, Milton, MA 02186, USA
| | - Russ Meister
- Dept. of Ecology and Evolutionary Biology, University of Connecticut, Storrs, CT 06269, USA
| | - Geert Goemans
- Dept. of Ecology and Evolutionary Biology, University of Connecticut, Storrs, CT 06269, USA
| | - Krushnamegh Kunte
- National Centre for Biological Sciences, Tata Institute of Fundamental Research, GKVK Campus, Bellary Road, Bangalore 560 065, India
| | - Max Moulds
- Australian Museum Research Institute, 1 William Street, Sydney N.S.W, Australia. 2010
| | - Kathy Hill
- Dept. of Ecology and Evolutionary Biology, University of Connecticut, Storrs, CT 06269, USA
| | - M Villet
- Dept. of Biology, Rhodes University, Grahamstown 6140, South Africa
| | - Thai-Hong Pham
- Mientrung Institute for Scientific Research, Vietnam Academy of Science and Technology, Hue, Vietnam.,Vietnam National Museum of Nature and Graduate School of Science and Technology, Vietnam Academy of Science and Technology, Hanoi, Vietnam
| | - Michelle Kortyna
- Department of Biological Science, Florida State University, 319 Stadium Drive, Tallahassee, USA
| | - Emily Moriarty Lemmon
- Department of Biological Science, Florida State University, 319 Stadium Drive, Tallahassee, FL 32306, USA
| | - Alan R Lemmon
- Department of Scientific Computing, Florida State University 400 Dirac Science Library, Tallahassee, FL 32306, USA
| | - Chris Simon
- Dept. of Ecology and Evolutionary Biology, University of Connecticut, Storrs, CT 06269, USA
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10
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Tumanov DV. End of a mystery: Integrative approach reveals the phylogenetic position of an enigmatic Antarctic tardigrade genus
Ramajendas
(Tardigrada, Eutardigrada). ZOOL SCR 2021. [DOI: 10.1111/zsc.12521] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Denis V. Tumanov
- Department of Invertebrate Zoology Faculty of Biology Saint Petersburg State University Saint Petersburg Russia
- Marine Research Laboratory Zoological Institute of the Russian Academy of Sciences Saint Petersburg Russia
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11
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Forthman M, Braun EL, Kimball RT. Gene tree quality affects empirical coalescent branch length estimation. ZOOL SCR 2021. [DOI: 10.1111/zsc.12512] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Affiliation(s)
- Michael Forthman
- Department of Entomology & Nematology University of Florida Gainesville FL USA
- California State Collection of Arthropods Plant Pest Diagnostics Branch California Department of Food & Agriculture Sacramento CA USA
| | - Edward L. Braun
- Department of Biology University of Florida Gainesville FL USA
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Abstract
Phylogenomic subsampling is a procedure by which small sets of loci are selected from large genome-scale data sets and used for phylogenetic inference. This step is often motivated by either computational limitations associated with the use of complex inference methods or as a means of testing the robustness of phylogenetic results by discarding loci that are deemed potentially misleading. Although many alternative methods of phylogenomic subsampling have been proposed, little effort has gone into comparing their behavior across different data sets. Here, I calculate multiple gene properties for a range of phylogenomic data sets spanning animal, fungal, and plant clades, uncovering a remarkable predictability in their patterns of covariance. I also show how these patterns provide a means for ordering loci by both their rate of evolution and their relative phylogenetic usefulness. This method of retrieving phylogenetically useful loci is found to be among the top performing when compared with alternative subsampling protocols. Relatively common approaches such as minimizing potential sources of systematic bias or increasing the clock-likeness of the data are found to fare worse than selecting loci at random. Likewise, the general utility of rate-based subsampling is found to be limited: loci evolving at both low and high rates are among the least effective, and even those evolving at optimal rates can still widely differ in usefulness. This study shows that many common subsampling approaches introduce unintended effects in off-target gene properties and proposes an alternative multivariate method that simultaneously optimizes phylogenetic signal while controlling for known sources of bias.
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13
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Chen S, Yan H, Sha L, Chen N, Zhang H, Zhou Y, Fan X. Chloroplast Phylogenomic Analyses Resolve Multiple Origins of the Kengyilia Species (Poaceae: Triticeae) via Independent Polyploidization Events. FRONTIERS IN PLANT SCIENCE 2021; 12:682040. [PMID: 34421940 PMCID: PMC8377392 DOI: 10.3389/fpls.2021.682040] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 03/17/2021] [Accepted: 07/01/2021] [Indexed: 06/13/2023]
Abstract
Kengyilia is a group of allohexaploid species that arose from two hybridization events followed by genome doubling of three ancestral diploid species with different genomes St, Y, and P in the Triticeae. Estimating the phylogenetic relationship in resolution of the maternal lineages has been difficult, owing to the extremely low rate of sequence divergence. Here, phylogenetic reconstructions based on the plastome sequences were used to explore the role of maternal progenitors in the establishment of Kengyilia polyploid species. The plastome sequences of 11 Kengyilia species were analyzed together with 12 tetraploid species (PP, StP, and StY) and 33 diploid taxa representing 20 basic genomes in the Triticeae. Phylogenomic analysis and genetic divergence patterns suggested that (1) Kengyilia is closely related to Roegneria, Pseudoroegneria, Agropyron, Lophopyrum, Thinopyrum, and Dasypyrum; (2) both the StY genome Roegneria tetraploids and the PP genome Agropyron tetraploids served as the maternal donors during the speciation of Kengyilia species; (3) the different Kengyilia species derived their StY genome from different Roegneria species. Multiple origins of species via independent polyploidization events have occurred in the genus Kengyilia, resulting in a maternal haplotype polymorphism. This helps explain the rich diversity and wide adaptation of polyploid species in the genus Kengyilia.
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Affiliation(s)
- Shiyong Chen
- College of Animal and Veterinary Sciences, Southwest Minzu University, Chengdu, China
- Triticeae Research Institute, Sichuan Agricultural University, Chengdu, China
| | - Hao Yan
- Triticeae Research Institute, Sichuan Agricultural University, Chengdu, China
| | - Lina Sha
- Triticeae Research Institute, Sichuan Agricultural University, Chengdu, China
- Key Laboratory of Crop Genetic Resources and Improvement, Ministry of Education, Sichuan Agricultural University, Ya’an, China
| | - Ning Chen
- Triticeae Research Institute, Sichuan Agricultural University, Chengdu, China
| | - Haiqin Zhang
- Triticeae Research Institute, Sichuan Agricultural University, Chengdu, China
- Key Laboratory of Crop Genetic Resources and Improvement, Ministry of Education, Sichuan Agricultural University, Ya’an, China
| | - Yonghong Zhou
- Triticeae Research Institute, Sichuan Agricultural University, Chengdu, China
- Key Laboratory of Crop Genetic Resources and Improvement, Ministry of Education, Sichuan Agricultural University, Ya’an, China
| | - Xing Fan
- Triticeae Research Institute, Sichuan Agricultural University, Chengdu, China
- Key Laboratory of Crop Genetic Resources and Improvement, Ministry of Education, Sichuan Agricultural University, Ya’an, China
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14
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Walker JF, Smith SA, Hodel RGJ, Moyroud E. Concordance-based approaches for the inference of relationships and molecular rates with phylogenomic datasets. Syst Biol 2021; 71:943-958. [PMID: 34240209 DOI: 10.1093/sysbio/syab052] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2020] [Revised: 06/23/2021] [Accepted: 07/01/2021] [Indexed: 11/12/2022] Open
Abstract
Gene tree conflict is common and finding methods to analyze and alleviate the negative effects that conflict has on species tree analysis is a crucial part of phylogenomics. This study aims to expand the discussion of inferring species trees and molecular branch lengths when conflict is present. Conflict is typically examined in two ways: inferring its prevalence, and inferring the influence of the individual genes (how strongly one gene supports any given topology compared to an alternative topology). Here, we examine a procedure for incorporating both conflict and the influence of genes in order to infer evolutionary relationships. All supported relationships in the gene trees are analyzed and the likelihood of the genes constrained to these relationships is summed to provide a likelihood for the relationship. Consensus tree assembly is conducted based on the sum of likelihoods for a given relationship and choosing relationships based on the most likely relationship assuming it does not conflict with a relationship that has a higher likelihood score. If it is not possible for all most likely relationships to be combined into a single bifurcating tree then multiple trees are produced and a consensus tree with a polytomy is created. This procedure allows for more influential genes to have greater influence on an inferred relationship, does not assume conflict has arisen from any one source, and does not force the dataset to produce a single bifurcating tree. Using this approach on three empirical datasets, we examine and discuss the relationship between influence and prevalence of gene tree conflict. We find that in one of the datasets, assembling a bifurcating consensus tree solely composed of the most likely relationships is impossible. To account for conflict in molecular rate analysis we also introduce a concordance-based approach to the summary and estimation of branch lengths suitable for downstream comparative analyses. We demonstrate through simulation that even under high levels of stochastic conflict, the mean and median of the concordant rates recapitulate the true molecular rate better than using a supermatrix approach. Using a large phylogenomic dataset, we examine rate heterogeneity across concordant genes with a focus on the branch subtending crown angiosperms. Notably, we find highly variable rates of evolution along the branch subtending crown angiosperms. The approaches outlined here have several limitations, but they also represent some alternative methods for harnessing the complexity of phylogenomic datasets and enrich our inferences of both species' relationships and evolutionary processes.
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Affiliation(s)
- Joseph F Walker
- The Sainsbury Laboratory, University of Cambridge, 47 Bateman Street, Cambridge CB2 1LR, UK.,Department of Biological Sciences, University of Illinois at Chicago, Chicago, IL, 60607 U.S.A
| | - Stephen A Smith
- Department of Ecology and Evolutionary Biology, University of Michigan, Ann Arbor, MI, USA
| | - Richard G J Hodel
- Department of Botany, National Museum of Natural History, MRC 166, Smithsonian Institution, Washington, DC, 20013-7012, USA
| | - Edwige Moyroud
- The Sainsbury Laboratory, University of Cambridge, 47 Bateman Street, Cambridge CB2 1LR, UK.,Department of Genetics, University of Cambridge, Downing Street, Cambridge CB2 3EH, UK
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15
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Uengwetwanit T, Pootakham W, Nookaew I, Sonthirod C, Angthong P, Sittikankaew K, Rungrassamee W, Arayamethakorn S, Wongsurawat T, Jenjaroenpun P, Sangsrakru D, Leelatanawit R, Khudet J, Koehorst JJ, Schaap PJ, Martins dos Santos V, Tangy F, Karoonuthaisiri N. A chromosome-level assembly of the black tiger shrimp (Penaeus monodon) genome facilitates the identification of growth-associated genes. Mol Ecol Resour 2021; 21:1620-1640. [PMID: 33586292 PMCID: PMC8197738 DOI: 10.1111/1755-0998.13357] [Citation(s) in RCA: 27] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2020] [Revised: 01/31/2021] [Accepted: 02/10/2021] [Indexed: 12/13/2022]
Abstract
To salvage marine ecosystems from fishery overexploitation, sustainable and efficient aquaculture must be emphasized. The knowledge obtained from available genome sequence of marine organisms has accelerated marine aquaculture in many cases. The black tiger shrimp (Penaeus monodon) is one of the most prominent cultured penaeid shrimps (Crustacean) with an average annual global production of half a million tons in the last decade. However, its currently available genome assemblies lack the contiguity and completeness required for accurate genome annotation due to the highly repetitive nature of the genome and technical difficulty in extracting high-quality, high-molecular weight DNA. Here, we report the first chromosome-level whole-genome assembly of P. monodon. The combination of long-read Pacific Biosciences (PacBio) and long-range Chicago and Hi-C technologies enabled a successful assembly of this first high-quality genome sequence. The final assembly covered 2.39 Gb (92.3% of the estimated genome size) and contained 44 pseudomolecules, corresponding to the haploid chromosome number. Repetitive elements occupied a substantial portion of the assembly (62.5%), the highest of the figures reported among crustacean species. The availability of this high-quality genome assembly enabled the identification of genes associated with rapid growth in the black tiger shrimp through the comparison of hepatopancreas transcriptome of slow-growing and fast-growing shrimps. The results highlighted several growth-associated genes. Our high-quality genome assembly provides an invaluable resource for genetic improvement and breeding penaeid shrimp in aquaculture. The availability of P. monodon genome enables analyses of ecological impact, environment adaptation and evolution, as well as the role of the genome to protect the ecological resources by promoting sustainable shrimp farming.
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Affiliation(s)
- Tanaporn Uengwetwanit
- National Center for Genetic Engineering and Biotechnology (BIOTEC)National Science and Technology Development Agency (NSTDA)Pathum Thani12120Thailand
| | - Wirulda Pootakham
- National Omics CenterNational Science and Technology Development AgencyPathum ThaniThailand
| | - Intawat Nookaew
- Department of Biomedical Informatics, College of MedicineUniversity of Arkansas for Medical SciencesLittle RockArkansasUSA
| | - Chutima Sonthirod
- National Omics CenterNational Science and Technology Development AgencyPathum ThaniThailand
| | - Pacharaporn Angthong
- National Center for Genetic Engineering and Biotechnology (BIOTEC)National Science and Technology Development Agency (NSTDA)Pathum Thani12120Thailand
| | - Kanchana Sittikankaew
- National Center for Genetic Engineering and Biotechnology (BIOTEC)National Science and Technology Development Agency (NSTDA)Pathum Thani12120Thailand
| | - Wanilada Rungrassamee
- National Center for Genetic Engineering and Biotechnology (BIOTEC)National Science and Technology Development Agency (NSTDA)Pathum Thani12120Thailand
| | - Sopacha Arayamethakorn
- National Center for Genetic Engineering and Biotechnology (BIOTEC)National Science and Technology Development Agency (NSTDA)Pathum Thani12120Thailand
| | - Thidathip Wongsurawat
- Department of Biomedical Informatics, College of MedicineUniversity of Arkansas for Medical SciencesLittle RockArkansasUSA
- Division of Bioinformatics and Data Management for ResearchDepartment of Research and DevelopmentFaculty of MedicineSiriraj HospitalMahidol UniversityBangkokThailand
| | - Piroon Jenjaroenpun
- Department of Biomedical Informatics, College of MedicineUniversity of Arkansas for Medical SciencesLittle RockArkansasUSA
- Division of Bioinformatics and Data Management for ResearchDepartment of Research and DevelopmentFaculty of MedicineSiriraj HospitalMahidol UniversityBangkokThailand
| | - Duangjai Sangsrakru
- National Omics CenterNational Science and Technology Development AgencyPathum ThaniThailand
| | - Rungnapa Leelatanawit
- National Center for Genetic Engineering and Biotechnology (BIOTEC)National Science and Technology Development Agency (NSTDA)Pathum Thani12120Thailand
| | - Jutatip Khudet
- Shrimp Genetic Improvement CenterIntegrative Aquaculture Biotechnology Research GroupSurat ThaniThailand
| | - Jasper J. Koehorst
- Laboratory of Systems and Synthetic BiologyDepartment of Agrotechnology and Food SciencesWageningen University and ResearchWageningenThe Netherlands
| | - Peter J. Schaap
- Laboratory of Systems and Synthetic BiologyDepartment of Agrotechnology and Food SciencesWageningen University and ResearchWageningenThe Netherlands
| | - Vitor Martins dos Santos
- Laboratory of Systems and Synthetic BiologyDepartment of Agrotechnology and Food SciencesWageningen University and ResearchWageningenThe Netherlands
| | - Frédéric Tangy
- Viral Genomics and Vaccination UnitUMR3569 CNRSVirology DepartmentInstitut PasteurParisFrance
| | - Nitsara Karoonuthaisiri
- National Center for Genetic Engineering and Biotechnology (BIOTEC)National Science and Technology Development Agency (NSTDA)Pathum Thani12120Thailand
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16
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Takezaki N. Resolving the Early Divergence Pattern of Teleost Fish Using Genome-Scale Data. Genome Biol Evol 2021; 13:6178791. [PMID: 33739405 PMCID: PMC8103497 DOI: 10.1093/gbe/evab052] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 03/10/2021] [Indexed: 12/13/2022] Open
Abstract
Regarding the phylogenetic relationship of the three primary groups of teleost fishes, Osteoglossomorpha (bonytongues and others), Elopomorpha (eels and relatives), Clupeocephala (the remaining teleost fish), early morphological studies hypothesized the first divergence of Osteoglossomorpha, whereas the recent prevailing view is the first divergence of Elopomorpha. Molecular studies supported all the possible relationships of the three primary groups. This study analyzed genome-scale data from four previous studies: 1) 412 genes from 12 species, 2) 772 genes from 15 species, 3) 1,062 genes from 30 species, and 4) 491 UCE loci from 27 species. The effects of the species, loci, and models used on the constructed tree topologies were investigated. In the analyses of the data sets (1)–(3), although the first divergence of Clupeocephala that left the other two groups in a sister relationship was supported by concatenated sequences and gene trees of all the species and genes, the first divergence of Elopomorpha among the three groups was supported using species and/or genes with low divergence of sequence and amino-acid frequencies. This result corresponded to that of the UCE data set (4), whose sequence divergence was low, which supported the first divergence of Elopomorpha with high statistical significance. The increase in accuracy of the phylogenetic construction by using species and genes with low sequence divergence was predicted by a phylogenetic informativeness approach and confirmed by computer simulation. These results supported that Elopomorpha was the first basal group of teleost fish to have diverged, consistent with the prevailing view of recent morphological studies.
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Affiliation(s)
- Naoko Takezaki
- Life Science Research Center, Kagawa University, Mikicho, Kitagun, Kagawa, Japan
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17
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Karin BR, Gamble T, Jackman TR. Optimizing Phylogenomics with Rapidly Evolving Long Exons: Comparison with Anchored Hybrid Enrichment and Ultraconserved Elements. Mol Biol Evol 2020; 37:904-922. [PMID: 31710677 PMCID: PMC7038749 DOI: 10.1093/molbev/msz263] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022] Open
Abstract
Marker selection has emerged as an important component of phylogenomic study design due to rising concerns of the effects of gene tree estimation error, model misspecification, and data-type differences. Researchers must balance various trade-offs associated with locus length and evolutionary rate among other factors. The most commonly used reduced representation data sets for phylogenomics are ultraconserved elements (UCEs) and Anchored Hybrid Enrichment (AHE). Here, we introduce Rapidly Evolving Long Exon Capture (RELEC), a new set of loci that targets single exons that are both rapidly evolving (evolutionary rate faster than RAG1) and relatively long in length (>1,500 bp), while at the same time avoiding paralogy issues across amniotes. We compare the RELEC data set to UCEs and AHE in squamate reptiles by aligning and analyzing orthologous sequences from 17 squamate genomes, composed of 10 snakes and 7 lizards. The RELEC data set (179 loci) outperforms AHE and UCEs by maximizing per-locus genetic variation while maintaining presence and orthology across a range of evolutionary scales. RELEC markers show higher phylogenetic informativeness than UCE and AHE loci, and RELEC gene trees show greater similarity to the species tree than AHE or UCE gene trees. Furthermore, with fewer loci, RELEC remains computationally tractable for full Bayesian coalescent species tree analyses. We contrast RELEC to and discuss important aspects of comparable methods, and demonstrate how RELEC may be the most effective set of loci for resolving difficult nodes and rapid radiations. We provide several resources for capturing or extracting RELEC loci from other amniote groups.
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Affiliation(s)
- Benjamin R Karin
- Department of Biology, Villanova University, Villanova, PA
- Museum of Vertebrate Zoology and Department of Integrative Biology, University of California, Berkeley, CA
| | - Tony Gamble
- Department of Biological Sciences, Marquette University, Milwaukee, WI
- Milwaukee Public Museum, Milwaukee, WI
- Bell Museum of Natural History, University of Minnesota, St. Paul, MN
| | - Todd R Jackman
- Department of Biology, Villanova University, Villanova, PA
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18
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Laumer CE. Inferring Ancient Relationships with Genomic Data: A Commentary on Current Practices. Integr Comp Biol 2019; 58:623-639. [PMID: 29982611 DOI: 10.1093/icb/icy075] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023] Open
Abstract
Contemporary phylogeneticists enjoy an embarrassment of riches, not only in the volumes of data now available, but also in the diversity of bioinformatic tools for handling these data. Here, I discuss a subset of these tools I consider well-suited to the task of inferring ancient relationships with coding sequence data in particular, encompassing data generation, orthology assignment, alignment and gene tree inference, supermatrix construction, and analysis under the best-fitting models applicable to large-scale datasets. Throughout, I compare and critique methods, considering both their theoretical principles and the details of their implementation, and offering practical tips on usage where appropriate. I also entertain different motivations for analyzing what are almost always originally DNA sequence data as codons, amino acids, and higher-order recodings. Although presented in a linear order, I see value in using the diversity of tools available to us to assess the sensitivity of clades of biological interest to different gene and taxon sets and analytical modes, which can be an indication of the presence of systematic error, of which a few forms remain poorly controlled by even the best available inference methods.
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Affiliation(s)
- Christopher E Laumer
- EMBL-European Bioinformatics Institute, Wellcome Trust Genome Campus, EBML-EBI South Building, Hinxton CB10 1SD, UK
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19
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Wang Y, Zhou X, Wang L, Liu X, Yang D, Rokas A. Gene Selection and Evolutionary Modeling Affect Phylogenomic Inference of Neuropterida Based on Transcriptome Data. Int J Mol Sci 2019; 20:E1072. [PMID: 30832228 PMCID: PMC6429444 DOI: 10.3390/ijms20051072] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/24/2018] [Revised: 02/18/2019] [Accepted: 02/26/2019] [Indexed: 11/30/2022] Open
Abstract
Neuropterida is a super order of Holometabola that consists of the orders Megaloptera (dobsonflies, fishflies, and alderflies), Neuroptera (lacewings) and Raphidioptera (snakeflies). Several proposed higher-level relationships within Neuropterida, such as the relationships between the orders or between the families, have been extensively debated. To further understand the evolutionary history of Neuropterida, we conducted phylogenomic analyses of all 13 published transcriptomes of the neuropterid species, as well as of a new transcriptome of the fishfly species Ctenochauliodes similis of Liu and Yang, 2006 (Megaloptera: Corydalidae: Chauliodinae) that we sequenced. Our phylogenomic data matrix contained 1392 ortholog genes from 22 holometabolan species representing six families from Neuroptera, two families from Raphidioptera, and two families from Megaloptera as the ingroup taxa, and nine orders of Holometabola as outgroups. Phylogenetic reconstruction was performed using both concatenation and coalescent-based approaches under a site-homogeneous model as well as under a site-heterogeneous model. Surprisingly, analyses using the site-homogeneous model strongly supported a paraphyletic Neuroptera, with Coniopterygidae assigned as the sister group of all other Neuropterida. In contrast, analyses using the site-heterogeneous model recovered Neuroptera as monophyletic. The monophyly of Neuroptera was also recovered in concatenation and coalescent-based analyses using genes with stronger phylogenetic signals [i.e., higher average bootstrap support (ABS) values and higher relative tree certainty including all conflicting bipartitions (RTCA) values] under the site-homogeneous model. The present study illustrated how both data selection and model selection influence phylogenomic analyses of large-scale data matrices comprehensively.
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Affiliation(s)
- Yuyu Wang
- College of Plant Protection, Hebei Agricultural University, Baoding 071001, China.
- Department of Entomology, China Agricultural University, Beijing 100193, China.
- Department of Biological Sciences, Vanderbilt University, Nashville, TN 37235, USA.
| | - Xiaofan Zhou
- Department of Biological Sciences, Vanderbilt University, Nashville, TN 37235, USA.
- Guangdong Province Key Laboratory of Microbial Signals and Disease Control, Integrative Microbiology Research Centre, South China Agricultural University, Guangzhou 510642, China.
| | - Liming Wang
- College of Plant Protection, Hebei Agricultural University, Baoding 071001, China.
| | - Xingyue Liu
- Department of Entomology, China Agricultural University, Beijing 100193, China.
| | - Ding Yang
- Department of Entomology, China Agricultural University, Beijing 100193, China.
| | - Antonis Rokas
- Department of Biological Sciences, Vanderbilt University, Nashville, TN 37235, USA.
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20
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Bravo GA, Antonelli A, Bacon CD, Bartoszek K, Blom MPK, Huynh S, Jones G, Knowles LL, Lamichhaney S, Marcussen T, Morlon H, Nakhleh LK, Oxelman B, Pfeil B, Schliep A, Wahlberg N, Werneck FP, Wiedenhoeft J, Willows-Munro S, Edwards SV. Embracing heterogeneity: coalescing the Tree of Life and the future of phylogenomics. PeerJ 2019; 7:e6399. [PMID: 30783571 PMCID: PMC6378093 DOI: 10.7717/peerj.6399] [Citation(s) in RCA: 67] [Impact Index Per Article: 13.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2018] [Accepted: 01/07/2019] [Indexed: 12/23/2022] Open
Abstract
Building the Tree of Life (ToL) is a major challenge of modern biology, requiring advances in cyberinfrastructure, data collection, theory, and more. Here, we argue that phylogenomics stands to benefit by embracing the many heterogeneous genomic signals emerging from the first decade of large-scale phylogenetic analysis spawned by high-throughput sequencing (HTS). Such signals include those most commonly encountered in phylogenomic datasets, such as incomplete lineage sorting, but also those reticulate processes emerging with greater frequency, such as recombination and introgression. Here we focus specifically on how phylogenetic methods can accommodate the heterogeneity incurred by such population genetic processes; we do not discuss phylogenetic methods that ignore such processes, such as concatenation or supermatrix approaches or supertrees. We suggest that methods of data acquisition and the types of markers used in phylogenomics will remain restricted until a posteriori methods of marker choice are made possible with routine whole-genome sequencing of taxa of interest. We discuss limitations and potential extensions of a model supporting innovation in phylogenomics today, the multispecies coalescent model (MSC). Macroevolutionary models that use phylogenies, such as character mapping, often ignore the heterogeneity on which building phylogenies increasingly rely and suggest that assimilating such heterogeneity is an important goal moving forward. Finally, we argue that an integrative cyberinfrastructure linking all steps of the process of building the ToL, from specimen acquisition in the field to publication and tracking of phylogenomic data, as well as a culture that values contributors at each step, are essential for progress.
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Affiliation(s)
- Gustavo A. Bravo
- Department of Organismic and Evolutionary Biology, Museum of Comparative Zoology, Harvard University, Cambridge, MA, USA
| | - Alexandre Antonelli
- Department of Organismic and Evolutionary Biology, Museum of Comparative Zoology, Harvard University, Cambridge, MA, USA
- Gothenburg Global Biodiversity Centre, Göteborg, Sweden
- Department of Biological and Environmental Sciences, University of Gothenburg, Göteborg, Sweden
- Gothenburg Botanical Garden, Göteborg, Sweden
| | - Christine D. Bacon
- Gothenburg Global Biodiversity Centre, Göteborg, Sweden
- Department of Biological and Environmental Sciences, University of Gothenburg, Göteborg, Sweden
| | - Krzysztof Bartoszek
- Department of Computer and Information Science, Linköping University, Linköping, Sweden
| | - Mozes P. K. Blom
- Department of Bioinformatics and Genetics, Swedish Museum of Natural History, Stockholm, Sweden
| | - Stella Huynh
- Institut de Biologie, Université de Neuchâtel, Neuchâtel, Switzerland
| | - Graham Jones
- Department of Biological and Environmental Sciences, University of Gothenburg, Göteborg, Sweden
| | - L. Lacey Knowles
- Department of Ecology and Evolutionary Biology, University of Michigan, Ann Arbor, MI, USA
| | - Sangeet Lamichhaney
- Department of Organismic and Evolutionary Biology, Museum of Comparative Zoology, Harvard University, Cambridge, MA, USA
| | - Thomas Marcussen
- Centre for Ecological and Evolutionary Synthesis, University of Oslo, Oslo, Norway
| | - Hélène Morlon
- Institut de Biologie, Ecole Normale Supérieure de Paris, Paris, France
| | - Luay K. Nakhleh
- Department of Computer Science, Rice University, Houston, TX, USA
| | - Bengt Oxelman
- Gothenburg Global Biodiversity Centre, Göteborg, Sweden
- Department of Biological and Environmental Sciences, University of Gothenburg, Göteborg, Sweden
| | - Bernard Pfeil
- Department of Biological and Environmental Sciences, University of Gothenburg, Göteborg, Sweden
| | - Alexander Schliep
- Department of Computer Science and Engineering, Chalmers University of Technology and University of Gothenburg, Göteborg, Sweden
| | | | - Fernanda P. Werneck
- Coordenação de Biodiversidade, Programa de Coleções Científicas Biológicas, Instituto Nacional de Pesquisa da Amazônia, Manaus, AM, Brazil
| | - John Wiedenhoeft
- Department of Computer Science and Engineering, Chalmers University of Technology and University of Gothenburg, Göteborg, Sweden
- Department of Computer Science, Rutgers University, Piscataway, NJ, USA
| | - Sandi Willows-Munro
- School of Life Sciences, University of Kwazulu-Natal, Pietermaritzburg, South Africa
| | - Scott V. Edwards
- Department of Organismic and Evolutionary Biology, Museum of Comparative Zoology, Harvard University, Cambridge, MA, USA
- Gothenburg Centre for Advanced Studies in Science and Technology, Chalmers University of Technology and University of Gothenburg, Göteborg, Sweden
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21
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Simmons MP, Sloan DB, Springer MS, Gatesy J. Gene-wise resampling outperforms site-wise resampling in phylogenetic coalescence analyses. Mol Phylogenet Evol 2019; 131:80-92. [DOI: 10.1016/j.ympev.2018.10.001] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2018] [Accepted: 10/01/2018] [Indexed: 01/15/2023]
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22
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Borowiec ML. Convergent Evolution of the Army Ant Syndrome and Congruence in Big-Data Phylogenetics. Syst Biol 2019; 68:642-656. [DOI: 10.1093/sysbio/syy088] [Citation(s) in RCA: 35] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2018] [Revised: 11/09/2018] [Accepted: 12/15/2018] [Indexed: 11/12/2022] Open
Affiliation(s)
- Marek L Borowiec
- Department of Entomology, Plant Pathology and Nematology, 875 Perimeter Drive, University of Idaho, Moscow, ID 83844, USA
- School of Life Sciences, Social Insect Research Group, Arizona State University, Tempe, AZ 85287, USA
- Department of Entomology and Nematology, One Shields Avenue, University of California at Davis, Davis, CA 95616, USA
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23
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Betancur-R R, Arcila D, Vari RP, Hughes LC, Oliveira C, Sabaj MH, Ortí G. Phylogenomic incongruence, hypothesis testing, and taxonomic sampling: The monophyly of characiform fishes. Evolution 2018; 73:329-345. [PMID: 30426469 DOI: 10.1111/evo.13649] [Citation(s) in RCA: 58] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2018] [Revised: 10/23/2018] [Accepted: 11/05/2018] [Indexed: 11/30/2022]
Abstract
Phylogenomic studies using genome-wide datasets are quickly becoming the state of the art for systematics and comparative studies, but in many cases, they result in strongly supported incongruent results. The extent to which this conflict is real depends on different sources of error potentially affecting big datasets (assembly, stochastic, and systematic error). Here, we apply a recently developed methodology (GGI or gene genealogy interrogation) and data curation to new and published datasets with more than 1000 exons, 500 ultraconserved element (UCE) loci, and transcriptomic sequences that support incongruent hypotheses. The contentious non-monophyly of the order Characiformes proposed by two studies is shown to be a spurious outcome induced by sample contamination in the transcriptomic dataset and an ambiguous result due to poor taxonomic sampling in the UCE dataset. By exploring the effects of number of taxa and loci used for analysis, we show that the power of GGI to discriminate among competing hypotheses is diminished by limited taxonomic sampling, but not equally sensitive to gene sampling. Taken together, our results reinforce the notion that merely increasing the number of genetic loci for a few representative taxa is not a robust strategy to advance phylogenetic knowledge of recalcitrant groups. We leverage the expanded exon capture dataset generated here for Characiformes (206 species in 23 out of 24 families) to produce a comprehensive phylogeny and a revised classification of the order.
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Affiliation(s)
- Ricardo Betancur-R
- Department of Biology, University of Puerto Rico, Río Piedras Campus, San Juan, Puerto Rico, 00931.,Department of Biology, University of Oklahoma, Norman, Oklahoma, 73019.,Department of Vertebrate Zoology, National Museum of Natural History Smithsonian Institution, Washington, DC, 20013
| | - Dahiana Arcila
- Department of Biology, University of Oklahoma, Norman, Oklahoma, 73019.,Department of Vertebrate Zoology, National Museum of Natural History Smithsonian Institution, Washington, DC, 20013.,Sam Noble Oklahoma Museum of Natural History, University of Oklahoma, Norman, Oklahoma, 73019
| | - Richard P Vari
- Sam Noble Oklahoma Museum of Natural History, University of Oklahoma, Norman, Oklahoma, 73019
| | - Lily C Hughes
- Department of Vertebrate Zoology, National Museum of Natural History Smithsonian Institution, Washington, DC, 20013.,Department of Biological Sciences, The George Washington University, Washington, DC, 20052
| | - Claudio Oliveira
- Departamento de Morfologia, Instituto de Biociências, Universidade Estadual Paulista, Botucatu, Brazil
| | - Mark H Sabaj
- Department of Ichthyology, The Academy of Natural Sciences of Drexel University, Philadelphia, Pennsylvania, 19103
| | - Guillermo Ortí
- Department of Vertebrate Zoology, National Museum of Natural History Smithsonian Institution, Washington, DC, 20013.,Department of Biological Sciences, The George Washington University, Washington, DC, 20052
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24
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Mclean BS, Bell KC, Allen JM, Helgen KM, Cook JA. Impacts of Inference Method and Data set Filtering on Phylogenomic Resolution in a Rapid Radiation of Ground Squirrels (Xerinae: Marmotini). Syst Biol 2018; 68:298-316. [DOI: 10.1093/sysbio/syy064] [Citation(s) in RCA: 26] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2017] [Accepted: 09/12/2018] [Indexed: 12/20/2022] Open
Affiliation(s)
- Bryan S Mclean
- Department of Biology and Museum of Southwestern Biology, 1 University of New Mexico, MSC03-2020, Albuquerque, NM 87131, USA
- Florida Museum of Natural History, University of Florida, 1659 Museum Road, Gainesville, FL 32611, USA
| | - Kayce C Bell
- Department of Biology and Museum of Southwestern Biology, 1 University of New Mexico, MSC03-2020, Albuquerque, NM 87131, USA
- Department of Invertebrate Zoology, Smithsonian Institution National Museum of Natural History, P.O. Box 37012, MRC 163, Washington, DC 20013-7012, USA
| | - Julie M Allen
- Department of Biology, University of Nevada, 1664 N. Virginia Street, Reno, NV 89557, USA
| | - Kristofer M Helgen
- Department of Ecology and Evolutionary Biology, School of Biological Sciences, University of Adelaide, North Terrace, Adelaide SA 5005, Australia
| | - Joseph A Cook
- Department of Biology and Museum of Southwestern Biology, 1 University of New Mexico, MSC03-2020, Albuquerque, NM 87131, USA
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25
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Dong W, Xu C, Wu P, Cheng T, Yu J, Zhou S, Hong DY. Resolving the systematic positions of enigmatic taxa: Manipulating the chloroplast genome data of Saxifragales. Mol Phylogenet Evol 2018; 126:321-330. [PMID: 29702217 DOI: 10.1016/j.ympev.2018.04.033] [Citation(s) in RCA: 49] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/26/2017] [Revised: 04/20/2018] [Accepted: 04/20/2018] [Indexed: 01/30/2023]
Abstract
Accurately resolving the phylogeny of enigmatic taxa is always a challenge in phylogenetic inference. Such uncertainties could be due to systematic errors or model violations. Here, we provide an example demonstrating how these factors affect the positioning of Paeoniaceae within Saxifragales based on chloroplast genome data. We newly assembled 14 chloroplast genomes from Saxifragales, and by combining these genomes with those of 63 other angiosperms, three datasets were assembled to test different hypotheses proposed by recent studies. These datasets were subjected to maximum parsimony, maximum likelihood and Bayesian analyses with site-homogeneous/heterogeneous models, different data partitioning strategies, and the inclusion/exclusion of weak phylogenetic signals. Three datasets exhibited remarkable heterogeneity among sites and among taxa of Saxifragales. Phylogenetic analyses under homogeneous models or maximum parsimony showed a closer relationship of Paeoniaceae with herbaceous families in the order. Data partitioning strategies did not change the general tree topology. However, PhyloBayes analysis under the CAT+GTR model resulted in a relationship closer to woody families. We conclude that although genomic data significantly increase the phylogenetic resolution of enigmatic taxa with high support, the phylogenetic results inferred from such data might be analysis or signal dependent. The analytical pipeline outlined here combines phylogenomic inference methods with evaluation of lineage-specific rates of substitution, model selection, and assessment of systematic error. These methods would be applicable to resolve similar difficult questions in the tree of life.
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Affiliation(s)
- Wenpan Dong
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, Beijing 100093, China; Peking-Tsinghua Center for Life Sciences, Academy for Advanced Interdisciplinary Studies, Peking University, Beijing 100871, China
| | - Chao Xu
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, Beijing 100093, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Ping Wu
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, Beijing 100093, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Tao Cheng
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, Beijing 100093, China
| | - Jing Yu
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, Beijing 100093, China
| | - Shiliang Zhou
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, Beijing 100093, China; University of Chinese Academy of Sciences, Beijing 100049, China.
| | - De-Yuan Hong
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, Beijing 100093, China.
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26
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Streicher JW, Miller EC, Guerrero PC, Correa C, Ortiz JC, Crawford AJ, Pie MR, Wiens JJ. Evaluating methods for phylogenomic analyses, and a new phylogeny for a major frog clade (Hyloidea) based on 2214 loci. Mol Phylogenet Evol 2018; 119:128-143. [DOI: 10.1016/j.ympev.2017.10.013] [Citation(s) in RCA: 44] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2017] [Revised: 10/21/2017] [Accepted: 10/22/2017] [Indexed: 01/28/2023]
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27
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Klopfstein S, Massingham T, Goldman N. More on the Best Evolutionary Rate for Phylogenetic Analysis. Syst Biol 2018; 66:769-785. [PMID: 28595363 PMCID: PMC5790136 DOI: 10.1093/sysbio/syx051] [Citation(s) in RCA: 41] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2016] [Accepted: 05/24/2017] [Indexed: 11/13/2022] Open
Abstract
The accumulation of genome-scale molecular data sets for nonmodel taxa brings us ever closer to resolving the tree of life of all living organisms. However, despite the depth of data available, a number of studies that each used thousands of genes have reported conflicting results. The focus of phylogenomic projects must thus shift to more careful experimental design. Even though we still have a limited understanding of what are the best predictors of the phylogenetic informativeness of a gene, there is wide agreement that one key factor is its evolutionary rate; but there is no consensus as to whether the rates derived as optimal in various analytical, empirical, and simulation approaches have any general applicability. We here use simulations to infer optimal rates in a set of realistic phylogenetic scenarios with varying tree sizes, numbers of terminals, and tree shapes. Furthermore, we study the relationship between the optimal rate and rate variation among sites and among lineages. Finally, we examine how well the predictions made by a range of experimental design methods correlate with the observed performance in our simulations.We find that the optimal level of divergence is surprisingly robust to differences in taxon sampling and even to among-site and among-lineage rate variation as often encountered in empirical data sets. This finding encourages the use of methods that rely on a single optimal rate to predict a gene's utility. Focusing on correct recovery either of the most basal node in the phylogeny or of the entire topology, the optimal rate is about 0.45 substitutions from root to tip in average Yule trees and about 0.2 in difficult trees with short basal and long-apical branches, but all rates leading to divergence levels between about 0.1 and 0.5 perform reasonably well.Testing the performance of six methods that can be used to predict a gene's utility against our simulation results, we find that the probability of resolution, signal-noise analysis, and Fisher information are good predictors of phylogenetic informativeness, but they require specification of at least part of a model tree. Likelihood quartet mapping also shows very good performance but only requires sequence alignments and is thus applicable without making assumptions about the phylogeny. Despite them being the most commonly used methods for experimental design, geometric quartet mapping and the integration of phylogenetic informativeness curves perform rather poorly in our comparison. Instead of derived predictors of phylogenetic informativeness, we suggest that the number of sites in a gene that evolve at near-optimal rates (as inferred here) could be used directly to prioritize genes for phylogenetic inference. In combination with measures of model fit, especially with respect to compositional biases and among-site and among-lineage rate variation, such an approach has the potential to greatly improve marker choice and should be tested on empirical data.
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Affiliation(s)
- Seraina Klopfstein
- Naturhistorisches Museum der Burgergemeinde Bern, Bernastr. 15, CH-3005 Bern, Switzerland.,University of Bern, Institute of Ecology and Evolution, Baltzerstr. 6, CH-3012 Bern, Switzerland
| | - Tim Massingham
- European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus, Hinxton CB10 1SD, UK
| | - Nick Goldman
- European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus, Hinxton CB10 1SD, UK
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28
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Zhang SQ, Che LH, Li Y, Dan Liang, Pang H, Ślipiński A, Zhang P. Evolutionary history of Coleoptera revealed by extensive sampling of genes and species. Nat Commun 2018; 9:205. [PMID: 29335414 PMCID: PMC5768713 DOI: 10.1038/s41467-017-02644-4] [Citation(s) in RCA: 182] [Impact Index Per Article: 30.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2017] [Accepted: 12/15/2017] [Indexed: 01/04/2023] Open
Abstract
Beetles (Coleoptera) are the most diverse and species-rich group of insects, and a robust, time-calibrated phylogeny is fundamental to understanding macroevolutionary processes that underlie their diversity. Here we infer the phylogeny and divergence times of all major lineages of Coleoptera by analyzing 95 protein-coding genes in 373 beetle species, including ~67% of the currently recognized families. The subordinal relationships are strongly supported as Polyphaga (Adephaga (Archostemata, Myxophaga)). The series and superfamilies of Polyphaga are mostly monophyletic. The species-poor Nosodendridae is robustly recovered in a novel position sister to Staphyliniformia, Bostrichiformia, and Cucujiformia. Our divergence time analyses suggest that the crown group of extant beetles occurred ~297 million years ago (Mya) and that ~64% of families originated in the Cretaceous. Most of the herbivorous families experienced a significant increase in diversification rate during the Cretaceous, thus suggesting that the rise of angiosperms in the Cretaceous may have been an 'evolutionary impetus' driving the hyperdiversity of herbivorous beetles.
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Affiliation(s)
- Shao-Qian Zhang
- State Key Laboratory of Biocontrol, College of Ecology and Evolution, School of Life Sciences, Sun Yat-Sen University, Guangzhou, 510006, China
| | - Li-Heng Che
- State Key Laboratory of Biocontrol, College of Ecology and Evolution, School of Life Sciences, Sun Yat-Sen University, Guangzhou, 510006, China
| | - Yun Li
- State Key Laboratory of Biocontrol, College of Ecology and Evolution, School of Life Sciences, Sun Yat-Sen University, Guangzhou, 510006, China
| | - Dan Liang
- State Key Laboratory of Biocontrol, College of Ecology and Evolution, School of Life Sciences, Sun Yat-Sen University, Guangzhou, 510006, China
| | - Hong Pang
- State Key Laboratory of Biocontrol, College of Ecology and Evolution, School of Life Sciences, Sun Yat-Sen University, Guangzhou, 510006, China
| | - Adam Ślipiński
- Australian National Insect Collection, CSIRO, GPO Box 1700, Canberra, ACT 2601, Australia.
| | - Peng Zhang
- State Key Laboratory of Biocontrol, College of Ecology and Evolution, School of Life Sciences, Sun Yat-Sen University, Guangzhou, 510006, China.
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29
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Wang YH, Wu HY, Rédei D, Xie Q, Chen Y, Chen PP, Dong ZE, Dang K, Damgaard J, Štys P, Wu YZ, Luo JY, Sun XY, Hartung V, Kuechler SM, Liu Y, Liu HX, Bu WJ. When did the ancestor of true bugs become stinky? Disentangling the phylogenomics of Hemiptera-Heteroptera. Cladistics 2017; 35:42-66. [DOI: 10.1111/cla.12232] [Citation(s) in RCA: 38] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 11/07/2017] [Indexed: 01/27/2023] Open
Affiliation(s)
- Yan-Hui Wang
- Department of Ecology and Evolution; College of Life Sciences; Sun Yat-sen University; 135 Xingangxi Road Guangzhou 510275 Guangdong China
- State Key Laboratory of Biocontrol; Sun Yat-sen University; 135 Xingangxi Road Guangzhou 510275 Guangdong China
- Institute of Entomology; College of Life Sciences; Nankai University; 94 Weijin Road 300071 Tianjin China
| | - Hao-Yang Wu
- Department of Ecology and Evolution; College of Life Sciences; Sun Yat-sen University; 135 Xingangxi Road Guangzhou 510275 Guangdong China
- State Key Laboratory of Biocontrol; Sun Yat-sen University; 135 Xingangxi Road Guangzhou 510275 Guangdong China
- Institute of Entomology; College of Life Sciences; Nankai University; 94 Weijin Road 300071 Tianjin China
| | - Dávid Rédei
- Institute of Entomology; College of Life Sciences; Nankai University; 94 Weijin Road 300071 Tianjin China
| | - Qiang Xie
- Department of Ecology and Evolution; College of Life Sciences; Sun Yat-sen University; 135 Xingangxi Road Guangzhou 510275 Guangdong China
- State Key Laboratory of Biocontrol; Sun Yat-sen University; 135 Xingangxi Road Guangzhou 510275 Guangdong China
- Institute of Entomology; College of Life Sciences; Nankai University; 94 Weijin Road 300071 Tianjin China
| | - Yan Chen
- Chinese Academy of Inspection and Quarantine; No. A3, Gaobeidian Bei Lu Chaoyang District Beijing 100123 China
| | - Ping-Ping Chen
- Netherlands Centre of Biodiversity Naturalis; 2300 RA Leiden Netherlands
| | - Zhuo-Er Dong
- Institute of Entomology; College of Life Sciences; Nankai University; 94 Weijin Road 300071 Tianjin China
| | - Kai Dang
- Institute of Entomology; College of Life Sciences; Nankai University; 94 Weijin Road 300071 Tianjin China
| | - Jakob Damgaard
- Natural History Museum of Denmark; Universitetsparken 15 2100 Copenhagen Ø Denmark
| | - Pavel Štys
- Department of Zoology; Faculty of Science; Charles University in Prague; Viničná 7 CZ-128 44 Praha 2 Czech Republic
| | - Yan-Zhuo Wu
- Institute of Entomology; College of Life Sciences; Nankai University; 94 Weijin Road 300071 Tianjin China
| | - Jiu-Yang Luo
- Institute of Entomology; College of Life Sciences; Nankai University; 94 Weijin Road 300071 Tianjin China
| | - Xiao-Ya Sun
- Institute of Entomology; College of Life Sciences; Nankai University; 94 Weijin Road 300071 Tianjin China
| | - Viktor Hartung
- Staatliches Museum für Naturkunde Karslruhe; Erbprinzenstrasse 13 76133 Karlsruhe Germany
- Museum für Naturkunde - Leibniz-Institute for Research on Evolution and Biodiversity; Invalidenstrasse 43 10115 Berlin Germany
| | - Stefan M. Kuechler
- Department of Animal Ecology II; University of Bayreuth; Universitaetsstrasse 30 95440 Bayreuth Germany
| | - Yang Liu
- Institute of Entomology; College of Life Sciences; Nankai University; 94 Weijin Road 300071 Tianjin China
| | - Hua-Xi Liu
- Institute of Entomology; College of Life Sciences; Nankai University; 94 Weijin Road 300071 Tianjin China
| | - Wen-Jun Bu
- Institute of Entomology; College of Life Sciences; Nankai University; 94 Weijin Road 300071 Tianjin China
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30
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Zhong B, Betancur-R R. Expanded Taxonomic Sampling Coupled with Gene Genealogy Interrogation Provides Unambiguous Resolution for the Evolutionary Root of Angiosperms. Genome Biol Evol 2017. [PMCID: PMC5710718 DOI: 10.1093/gbe/evx233] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
The branching order of major angiosperm lineages is a challenging phylogenetic question that has received substantial attention in recent years. Two main competing hypotheses place the New Caledonian Amborella as either sister to all other extant angiosperms (Amborella-sister) or to the water lilies (Amborella + Nymphaeales). Here, we revisit this question by expanding a transcriptomic data set of 310 genes previously assembled to include data from seven species comprising two major lineages of flowering plants that were poorly represented or missing from the original study. We also applied gene genealogy interrogation, a recent approach based on constrained tree searches in combination with topology tests, to account for gene tree estimation error and its downstream effects in coalescent analyses. In addition to gene genealogy interrogation, we conducted a large number of multilocus analyses, including concatenation and coalescent approaches (using both unconstrained and constrained gene trees), and based on different data sets (original and expanded) and data types (nucleotide and amino acid sequences). We show that the majority of gene trees favor Amborella-sister topology, and all multilocus analyses conducted (concatenation and coalescent) provide overwhelming support for this hypothesis regardless of data type. Beyond resolving the evolutionary root of angiosperms with confidence, our results highlight the importance of both broadening taxonomic sampling in phylogenomics and addressing the effects of gene tree error in summary coalescent inferences.
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Affiliation(s)
- Bojian Zhong
- College of Life Sciences, Nanjing Normal University, China
- Corresponding authors: E-mails: ;
| | - Ricardo Betancur-R
- Department of Biology, University of Puerto Rico – Río Piedras, San Juan, Puerto Rico
- Corresponding authors: E-mails: ;
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31
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Molloy EK, Warnow T. To Include or Not to Include: The Impact of Gene Filtering on Species Tree Estimation Methods. Syst Biol 2017; 67:285-303. [DOI: 10.1093/sysbio/syx077] [Citation(s) in RCA: 138] [Impact Index Per Article: 19.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2016] [Accepted: 09/13/2017] [Indexed: 01/27/2023] Open
Affiliation(s)
- Erin K Molloy
- Department of Computer Science, University of Illinois at Urbana-Champaign, Urbana, IL, USA
| | - Tandy Warnow
- Department of Computer Science, University of Illinois at Urbana-Champaign, Urbana, IL, USA
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32
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Owen CL, Marshall DC, Hill KBR, Simon C. How the Aridification of Australia Structured the Biogeography and Influenced the Diversification of a Large Lineage of Australian Cicadas. Syst Biol 2017; 66:569-589. [PMID: 28123112 DOI: 10.1093/sysbio/syw078] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2014] [Accepted: 08/24/2016] [Indexed: 11/14/2022] Open
Abstract
Over the last 30 million years, Australia's landscape has undergone dramatic cooling and drying due to the establishment of the Antarctic Circumpolar Current and change in global CO$_{2}$ levels. Studies have shown that many Australian organisms went extinct during these major cooling events, while others experienced adaptive radiations and increases in diversification rates as a result of exploiting new niches in the arid zone. Despite the many studies on diversification and biogeography in Australia, few have been continent-wide and none have focused on a group of organisms adapted to feeding on plants. We studied 162 species of cicadas in the Australian Pauropsalta complex, a large generic lineage within the tribe Cicadettini. We asked whether there were changes in the diversification rate of Pauropsalta over time and if so: 1) which clades were associated with the rate change? 2) did timing of rate shifts correspond to known periods of dramatic historical climate change, 3) did increases in diversification rate along select lineages correspond to adaptive radiations with movement into the arid zone? To address these questions, we estimated a molecular phylogeny of the Pauropsalta complex using ${\sim}$5300 bp of nucleotide sequence data distributed among five loci (one mtDNA locus and four nDNA loci). We found that this large group of cicadas did not diversify at a constant rate as they spread through Australia; instead the signature of decreasing diversification rate changed roughly around the time of the expansion of the east Antarctic ice sheets ${\sim}$16 Ma and the glaciation of the northern hemisphere ${\sim}$3 Ma. Unlike other Australian taxa, the Pauropsalta complex did not explosively radiate in response to an early invasion of the arid zone. Instead multiple groups invaded the arid zone and experienced rates of diversification similar to mesic-distributed taxa. We found evidence for relictual groups, located in pre-Mesozoic habitat, that have not diversified and continue to reside on mesic hosts in isolated "habitat islands". Future work should focus on groups of similar ages with similar distribution patterns to determine whether this tempo and pattern of diversification and biogeography is consistent with evidence from other phytophagous insects.
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Affiliation(s)
- Christopher L Owen
- Department of Ecology and Evolutionary Biology, University of Connecticut, 75 N. Eagleville Road, Unit 3043, Storrs, CT 06269-3043, USA.,Computational Biology Institute, George Washington University, Innovation Hall, Suite 305, 45085 University Drive, Ashburn, VA 20147-2766, USA
| | - David C Marshall
- Department of Ecology and Evolutionary Biology, University of Connecticut, 75 N. Eagleville Road, Unit 3043, Storrs, CT 06269-3043, USA
| | - Kathy B R Hill
- Department of Ecology and Evolutionary Biology, University of Connecticut, 75 N. Eagleville Road, Unit 3043, Storrs, CT 06269-3043, USA
| | - Chris Simon
- Department of Ecology and Evolutionary Biology, University of Connecticut, 75 N. Eagleville Road, Unit 3043, Storrs, CT 06269-3043, USA
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33
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Sha LN, Fan X, Li J, Liao JQ, Zeng J, Wang Y, Kang HY, Zhang HQ, Zheng YL, Zhou YH. Contrasting evolutionary patterns of multiple loci uncover new aspects in the genome origin and evolutionary history of Leymus (Triticeae; Poaceae). Mol Phylogenet Evol 2017; 114:175-188. [PMID: 28533082 DOI: 10.1016/j.ympev.2017.05.015] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2016] [Revised: 05/14/2017] [Accepted: 05/16/2017] [Indexed: 12/28/2022]
Abstract
Leymus Hochst. (Triticeae: Poaceae), a group of allopolyploid species with the NsXm genomes, is a perennial genus with diversity in morphology, cytology, ecology, and distribution in the Triticeae. To investigate the genome origin and evolutionary history of Leymus, three unlinked low-copy nuclear genes (Acc1, Pgk1, and GBSSI) and three chloroplast regions (trnL-F, matK, and rbcL) of 32 Leymus species were analyzed with those of 36 diploid species representing 18 basic genomes in the Triticeae. The phylogenetic relationships were reconstructed using Bayesian inference, Maximum parsimony, and NeighborNet methods. A time-calibrated phylogeny was generated to estimate the evolutionary history of Leymus. The results suggest that reticulate evolution has occurred in Leymus species, with several distinct progenitors contributing to the Leymus. The molecular data in resolution of the Xm-genome lineage resulted in two apparently contradictory results, with one placing the Xm-genome lineage as closely related to the P/F genome and the other splitting the Xm-genome lineage as sister to the Ns-genome donor. Our results suggested that (1) the Ns genome of Leymus was donated by Psathyrostachys, and additional Ns-containing alleles may be introgressed into some Leymus polyploids by recurrent hybridization; (2) The phylogenetic incongruence regarding the resolution of the Xm-genome lineage suggested that the Xm genome of Leymus was closely related to the P genome of Agropyron; (3) Both Ns- and Xm-genome lineages served as the maternal donor during the speciation of Leymus species; (4) The Pseudoroegneria, Lophopyrum and Australopyrum genomes contributed to some Leymus species.
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Affiliation(s)
- Li-Na Sha
- Triticeae Research Institute, Sichuan Agricultural University, Wenjiang 611130, Sichuan, China; Key Laboratory of Crop Genetic Resources and Improvement, Ministry of Education, Sichuan Agricultural University, Yaan 625014, Sichuan, China
| | - Xing Fan
- Triticeae Research Institute, Sichuan Agricultural University, Wenjiang 611130, Sichuan, China
| | - Jun Li
- Crop Research Institute, Sichuan Academy of Agricultural Science, Chengdu 610066, Sichuan, China
| | - Jin-Qiu Liao
- College of Life Science, Sichuan Agricultural University, Yaan 625014, Sichuan, China
| | - Jian Zeng
- College of Resources, Sichuan Agricultural University, Wenjiang 611130, Sichuan, China
| | - Yi Wang
- Triticeae Research Institute, Sichuan Agricultural University, Wenjiang 611130, Sichuan, China
| | - Hou-Yang Kang
- Triticeae Research Institute, Sichuan Agricultural University, Wenjiang 611130, Sichuan, China
| | - Hai-Qin Zhang
- Triticeae Research Institute, Sichuan Agricultural University, Wenjiang 611130, Sichuan, China
| | - You-Liang Zheng
- Triticeae Research Institute, Sichuan Agricultural University, Wenjiang 611130, Sichuan, China; Key Laboratory of Crop Genetic Resources and Improvement, Ministry of Education, Sichuan Agricultural University, Yaan 625014, Sichuan, China
| | - Yong-Hong Zhou
- Triticeae Research Institute, Sichuan Agricultural University, Wenjiang 611130, Sichuan, China; Key Laboratory of Crop Genetic Resources and Improvement, Ministry of Education, Sichuan Agricultural University, Yaan 625014, Sichuan, China.
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34
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Léveillé-Bourret É, Starr JR, Ford BA, Moriarty Lemmon E, Lemmon AR. Resolving Rapid Radiations within Angiosperm Families Using Anchored Phylogenomics. Syst Biol 2017; 67:94-112. [DOI: 10.1093/sysbio/syx050] [Citation(s) in RCA: 70] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2016] [Accepted: 04/28/2017] [Indexed: 11/13/2022] Open
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35
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Arcila D, Ortí G, Vari R, Armbruster JW, Stiassny MLJ, Ko KD, Sabaj MH, Lundberg J, Revell LJ, Betancur-R R. Genome-wide interrogation advances resolution of recalcitrant groups in the tree of life. Nat Ecol Evol 2017; 1:20. [PMID: 28812610 DOI: 10.1038/s41559-016-0020] [Citation(s) in RCA: 150] [Impact Index Per Article: 21.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2016] [Accepted: 10/25/2016] [Indexed: 12/21/2022]
Abstract
Much progress has been achieved in disentangling evolutionary relationships among species in the tree of life, but some taxonomic groups remain difficult to resolve despite increasing availability of genome-scale data sets. Here we present a practical approach to studying ancient divergences in the face of high levels of conflict, based on explicit gene genealogy interrogation (GGI). We show its efficacy in resolving the controversial relationships within the largest freshwater fish radiation (Otophysi) based on newly generated DNA sequences for 1,051 loci from 225 species. Initial results using a suite of standard methodologies revealed conflicting phylogenetic signal, which supports ten alternative evolutionary histories among early otophysan lineages. By contrast, GGI revealed that the vast majority of gene genealogies supports a single tree topology grounded on morphology that was not obtained by previous molecular studies. We also reanalysed published data sets for exemplary groups with recalcitrant resolution to assess the power of this approach. GGI supports the notion that ctenophores are the earliest-branching animal lineage, and adds insight into relationships within clades of yeasts, birds and mammals. GGI opens up a promising avenue to account for incompatible signals in large data sets and to discern between estimation error and actual biological conflict explaining gene tree discordance.
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Affiliation(s)
- Dahiana Arcila
- Department of Biological Sciences, The George Washington University, 2023 G Street NW, Washington DC 20052, USA.,Department of Vertebrate Zoology, National Museum of Natural History Smithsonian Institution, PO Box 37012, MRC 159, Washington DC 20013, USA
| | - Guillermo Ortí
- Department of Biological Sciences, The George Washington University, 2023 G Street NW, Washington DC 20052, USA
| | - Richard Vari
- Department of Vertebrate Zoology, National Museum of Natural History Smithsonian Institution, PO Box 37012, MRC 159, Washington DC 20013, USA
| | | | - Melanie L J Stiassny
- Department of Ichthyology, Division of Vertebrate Zoology, American Museum of Natural History, New York, New York 10024, USA
| | - Kyung D Ko
- Department of Biological Sciences, The George Washington University, 2023 G Street NW, Washington DC 20052, USA
| | - Mark H Sabaj
- Department of Ichthyology, The Academy of Natural Sciences, 1900 Benjamin Franklin Parkway, Philadelphia, Pennsylvania 19103, USA
| | - John Lundberg
- Department of Ichthyology, The Academy of Natural Sciences, 1900 Benjamin Franklin Parkway, Philadelphia, Pennsylvania 19103, USA
| | - Liam J Revell
- Department of Biology, University of Massachusetts Boston, Boston, Massachusetts 02125, USA
| | - Ricardo Betancur-R
- Department of Vertebrate Zoology, National Museum of Natural History Smithsonian Institution, PO Box 37012, MRC 159, Washington DC 20013, USA.,Department of Biology, University of Puerto Rico - Río Piedras, PO Box 23360, San Juan, Puerto Rico
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36
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Simmons MP. Mutually exclusive phylogenomic inferences at the root of the angiosperms: Amborella
is supported as sister and Observed Variability is biased. Cladistics 2016; 33:488-512. [DOI: 10.1111/cla.12177] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 09/17/2016] [Indexed: 01/16/2023] Open
Affiliation(s)
- Mark P. Simmons
- Department of Biology; Colorado State University; Fort Collins CO 80523-1878 USA
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37
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Shen XX, Salichos L, Rokas A. A Genome-Scale Investigation of How Sequence, Function, and Tree-Based Gene Properties Influence Phylogenetic Inference. Genome Biol Evol 2016; 8:2565-80. [PMID: 27492233 PMCID: PMC5010910 DOI: 10.1093/gbe/evw179] [Citation(s) in RCA: 47] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 07/25/2016] [Indexed: 12/13/2022] Open
Abstract
Molecular phylogenetic inference is inherently dependent on choices in both methodology and data. Many insightful studies have shown how choices in methodology, such as the model of sequence evolution or optimality criterion used, can strongly influence inference. In contrast, much less is known about the impact of choices in the properties of the data, typically genes, on phylogenetic inference. We investigated the relationships between 52 gene properties (24 sequence-based, 19 function-based, and 9 tree-based) with each other and with three measures of phylogenetic signal in two assembled data sets of 2,832 yeast and 2,002 mammalian genes. We found that most gene properties, such as evolutionary rate (measured through the percent average of pairwise identity across taxa) and total tree length, were highly correlated with each other. Similarly, several gene properties, such as gene alignment length, Guanine-Cytosine content, and the proportion of tree distance on internal branches divided by relative composition variability (treeness/RCV), were strongly correlated with phylogenetic signal. Analysis of partial correlations between gene properties and phylogenetic signal in which gene evolutionary rate and alignment length were simultaneously controlled, showed similar patterns of correlations, albeit weaker in strength. Examination of the relative importance of each gene property on phylogenetic signal identified gene alignment length, alongside with number of parsimony-informative sites and variable sites, as the most important predictors. Interestingly, the subsets of gene properties that optimally predicted phylogenetic signal differed considerably across our three phylogenetic measures and two data sets; however, gene alignment length and RCV were consistently included as predictors of all three phylogenetic measures in both yeasts and mammals. These results suggest that a handful of sequence-based gene properties are reliable predictors of phylogenetic signal and could be useful in guiding the choice of phylogenetic markers.
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Affiliation(s)
- Xing-Xing Shen
- Department of Biological Sciences, Vanderbilt University
| | - Leonidas Salichos
- Department of Biological Sciences, Vanderbilt University Department of Molecular Biophysics and Biochemistry, Yale University
| | - Antonis Rokas
- Department of Biological Sciences, Vanderbilt University
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38
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Lachance MA, Hurtado E, Hsiang T. A stable phylogeny of the large-sporedMetschnikowiaclade. Yeast 2016; 33:261-75. [DOI: 10.1002/yea.3163] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2015] [Revised: 03/14/2016] [Accepted: 03/19/2016] [Indexed: 11/12/2022] Open
Affiliation(s)
- Marc-André Lachance
- Department of Biology; University of Western Ontario; London Ontario Canada N6A 5B7
| | - Emilia Hurtado
- Department of Biology; University of Western Ontario; London Ontario Canada N6A 5B7
| | - Tom Hsiang
- School of Environmental Sciences; University of Guelph; Guelph Ontario Canada N1G 2W1
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39
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Linkem CW, Minin VN, Leaché AD. Detecting the Anomaly Zone in Species Trees and Evidence for a Misleading Signal in Higher-Level Skink Phylogeny (Squamata: Scincidae). Syst Biol 2016; 65:465-77. [PMID: 26738927 PMCID: PMC6383586 DOI: 10.1093/sysbio/syw001] [Citation(s) in RCA: 62] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2014] [Accepted: 12/29/2015] [Indexed: 01/28/2023] Open
Abstract
The anomaly zone, defined by the presence of gene tree topologies that are more probable than the true species tree, presents a major challenge to the accurate resolution of many parts of the Tree of Life. This discrepancy can result from consecutive rapid speciation events in the species tree. Similar to the problem of long-branch attraction, including more data via loci concatenation will only reinforce the support for the incorrect species tree. Empirical phylogenetic studies often employ coalescent-based species tree methods to avoid the anomaly zone, but to this point these studies have not had a method for providing any direct evidence that the species tree is actually in the anomaly zone. In this study, we use 16 species of lizards in the family Scincidae to investigate whether nodes that are difficult to resolve place the species tree within the anomaly zone. We analyze new phylogenomic data (429 loci), using both concatenation and coalescent-based species tree estimation, to locate conflicting topological signal. We then use the unifying principle of the anomaly zone, together with estimates of ancestral population sizes and species persistence times, to determine whether the observed phylogenetic conflict is a result of the anomaly zone. We identify at least three regions of the Scincidae phylogeny that provide demographic signatures consistent with the anomaly zone, and this new information helps reconcile the phylogenetic conflict in previously published studies on these lizards. The anomaly zone presents a real problem in phylogenetics, and our new framework for identifying anomalous relationships will help empiricists leverage their resources appropriately for investigating and overcoming this challenge.
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Affiliation(s)
| | - Vladimir N Minin
- Department of Biology, University of Washington, Seattle WA; Department of Statistics, University of Washington, Seattle WA
| | - Adam D Leaché
- Department of Biology, University of Washington, Seattle WA; Burke Museum of Natural History and Culture, University of Washington, Seattle, WA, 98195, USA
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40
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Meiklejohn KA, Faircloth BC, Glenn TC, Kimball RT, Braun EL. Analysis of a Rapid Evolutionary Radiation Using Ultraconserved Elements: Evidence for a Bias in Some Multispecies Coalescent Methods. Syst Biol 2016; 65:612-27. [DOI: 10.1093/sysbio/syw014] [Citation(s) in RCA: 114] [Impact Index Per Article: 14.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2015] [Accepted: 01/25/2016] [Indexed: 01/30/2023] Open
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41
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Rivers DM, Darwell CT, Althoff DM. Phylogenetic analysis of RAD-seq data: examining the influence of gene genealogy conflict on analysis of concatenated data. Cladistics 2016; 32:672-681. [DOI: 10.1111/cla.12149] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 11/19/2015] [Indexed: 01/15/2023] Open
Affiliation(s)
- David M. Rivers
- Department of Biology; Syracuse University; 107 College Place Syracuse NY 13244 USA
| | - Clive T. Darwell
- Department of Biology; Syracuse University; 107 College Place Syracuse NY 13244 USA
| | - David M. Althoff
- Department of Biology; Syracuse University; 107 College Place Syracuse NY 13244 USA
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42
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Simmons MP, Sloan DB, Gatesy J. The effects of subsampling gene trees on coalescent methods applied to ancient divergences. Mol Phylogenet Evol 2016; 97:76-89. [PMID: 26768112 DOI: 10.1016/j.ympev.2015.12.013] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2015] [Revised: 12/03/2015] [Accepted: 12/20/2015] [Indexed: 10/22/2022]
Abstract
Gene-tree-estimation error is a major concern for coalescent methods of phylogenetic inference. We sampled eight empirical studies of ancient lineages with diverse numbers of taxa and genes for which the original authors applied one or more coalescent methods. We found that the average pairwise congruence among gene trees varied greatly both between studies and also often within a study. We recommend that presenting plots of pairwise congruence among gene trees in a dataset be treated as a standard practice for empirical coalescent studies so that readers can readily assess the extent and distribution of incongruence among gene trees. ASTRAL-based coalescent analyses generally outperformed MP-EST and STAR with respect to both internal consistency (congruence between analyses of subsamples of genes with the complete dataset of all genes) and congruence with the concatenation-based topology. We evaluated the approach of subsampling gene trees that are, on average, more congruent with other gene trees as a method to reduce artifacts caused by gene-tree-estimation errors on coalescent analyses. We suggest that this method is well suited to testing whether gene-tree-estimation error is a primary cause of incongruence between concatenation- and coalescent-based results, to reconciling conflicting phylogenetic results based on different coalescent methods, and to identifying genes affected by artifacts that may then be targeted for reciprocal illumination. We provide scripts that automate the process of calculating pairwise gene-tree incongruence and subsampling trees while accounting for differential taxon sampling among genes. Finally, we assert that multiple tree-search replicates should be implemented as a standard practice for empirical coalescent studies that apply MP-EST.
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Affiliation(s)
- Mark P Simmons
- Department of Biology, Colorado State University, Fort Collins, CO 80523, USA.
| | - Daniel B Sloan
- Department of Biology, Colorado State University, Fort Collins, CO 80523, USA
| | - John Gatesy
- Department of Biology, University of California, Riverside, CA 92521, USA
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43
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Hosner PA, Faircloth BC, Glenn TC, Braun EL, Kimball RT. Avoiding Missing Data Biases in Phylogenomic Inference: An Empirical Study in the Landfowl (Aves: Galliformes). Mol Biol Evol 2015; 33:1110-25. [PMID: 26715628 DOI: 10.1093/molbev/msv347] [Citation(s) in RCA: 124] [Impact Index Per Article: 13.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022] Open
Abstract
Production of massive DNA sequence data sets is transforming phylogenetic inference, but best practices for analyzing such data sets are not well established. One uncertainty is robustness to missing data, particularly in coalescent frameworks. To understand the effects of increasing matrix size and loci at the cost of increasing missing data, we produced a 90 taxon, 2.2 megabase, 4,800 locus sequence matrix of landfowl using target capture of ultraconserved elements. We then compared phylogenies estimated with concatenated maximum likelihood, quartet-based methods executed on concatenated matrices and gene tree reconciliation methods, across five thresholds of missing data. Results of maximum likelihood and quartet analyses were similar, well resolved, and demonstrated increasing support with increasing matrix size and sparseness. Conversely, gene tree reconciliation produced unexpected relationships when we included all informative loci, with certain taxa placed toward the root compared with other approaches. Inspection of these taxa identified a prevalence of short average contigs, which potentially biased gene tree inference and caused erroneous results in gene tree reconciliation. This suggests that the more problematic missing data in gene tree-based analyses are partial sequences rather than entire missing sequences from locus alignments. Limiting gene tree reconciliation to the most informative loci solved this problem, producing well-supported topologies congruent with concatenation and quartet methods. Collectively, our analyses provide a well-resolved phylogeny of landfowl, including strong support for previously problematic relationships such as those among junglefowl (Gallus), and clarify the position of two enigmatic galliform genera (Lerwa, Melanoperdix) not sampled in previous molecular phylogenetic studies.
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Affiliation(s)
| | - Brant C Faircloth
- Department of Biological Sciences and Museum of Natural Science, Louisiana State University, Baton Rouge
| | - Travis C Glenn
- Department of Environmental Health Science, University of Georgia
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44
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Richart CH, Hayashi CY, Hedin M. Phylogenomic analyses resolve an ancient trichotomy at the base of Ischyropsalidoidea (Arachnida, Opiliones) despite high levels of gene tree conflict and unequal minority resolution frequencies. Mol Phylogenet Evol 2015; 95:171-82. [PMID: 26691642 DOI: 10.1016/j.ympev.2015.11.010] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2015] [Revised: 09/16/2015] [Accepted: 11/13/2015] [Indexed: 11/19/2022]
Abstract
Phylogenetic resolution of ancient rapid radiations has remained problematic despite major advances in statistical approaches and DNA sequencing technologies. Here we report on a combined phylogenetic approach utilizing transcriptome data in conjunction with Sanger sequence data to investigate a tandem of ancient divergences in the harvestmen superfamily Ischyropsalidoidea (Arachnida, Opiliones, Dyspnoi). We rely on Sanger sequences to resolve nodes within and between closely related genera, and use RNA-seq data from a subset of taxa to resolve a short and ancient internal branch. We use several analytical approaches to explore this succession of ancient diversification events, including concatenated and coalescent-based analyses and maximum likelihood gene trees for each locus. We evaluate the robustness of phylogenetic inferences using a randomized locus sub-sampling approach, and find congruence across these methods despite considerable incongruence across gene trees. Incongruent gene trees are not recovered in frequencies expected from a simple multispecies coalescent model, and we reject incomplete lineage sorting as the sole contributor to gene tree conflict. Using these approaches we attain robust support for higher-level phylogenetic relationships within Ischyropsalidoidea.
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Affiliation(s)
- Casey H Richart
- Department of Biology, San Diego State University, 5500 Campanile Drive, San Diego, CA 92182, USA; Department of Biology, University of California, Riverside, CA 92521, USA.
| | - Cheryl Y Hayashi
- Department of Biology, University of California, Riverside, CA 92521, USA
| | - Marshal Hedin
- Department of Biology, San Diego State University, 5500 Campanile Drive, San Diego, CA 92182, USA
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45
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Wang Y, Zhou X, Yang D, Rokas A. A Genome-Scale Investigation of Incongruence in Culicidae Mosquitoes. Genome Biol Evol 2015; 7:3463-71. [PMID: 26608059 PMCID: PMC4700963 DOI: 10.1093/gbe/evv235] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022] Open
Abstract
Comparison of individual gene trees in several recent phylogenomic studies from diverse lineages has revealed a surprising amount of topological conflict or incongruence, but we still know relatively little about its distribution across the tree of life. To further our understanding of incongruence, the factors that contribute to it and how it can be ameliorated, we examined its distribution in a clade of 20 Culicidae mosquito species through the reconstruction and analysis of the phylogenetic histories of 2,007 groups of orthologous genes. Levels of incongruence were generally low, the three exceptions being the internodes concerned with the branching of Anopheles christyi, with the branching of the subgenus Anopheles as well as the already reported incongruence within the Anopheles gambiae species complex. Two of these incongruence events (A. gambiae species complex and A. christyi) are likely due to biological factors, whereas the third (subgenus Anopheles) is likely due to analytical factors. Similar to previous studies, the use of genes or internodes with high bootstrap support or internode certainty values, both of which were positively correlated with gene alignment length, substantially reduced the observed incongruence. However, the clade support values of the internodes concerned with the branching of the subgenus Anopheles as well as within the A. gambiae species complex remained very low. Based on these results, we infer that the prevalence of incongruence in Culicidae mosquitoes is generally low, that it likely stems from both analytical and biological factors, and that it can be ameliorated through the selection of genes with strong phylogenetic signal. More generally, selection of genes with strong phylogenetic signal may be a general empirical solution for reducing incongruence and increasing the robustness of inference in phylogenomic studies.
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Affiliation(s)
- Yuyu Wang
- Department of Entomology, China Agricultural University, Beijing, China Department of Biological Sciences, Vanderbilt University
| | - Xiaofan Zhou
- Department of Biological Sciences, Vanderbilt University
| | - Ding Yang
- Department of Entomology, China Agricultural University, Beijing, China
| | - Antonis Rokas
- Department of Biological Sciences, Vanderbilt University
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46
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Murray GGR, Weinert LA, Rhule EL, Welch JJ. The Phylogeny of Rickettsia Using Different Evolutionary Signatures: How Tree-Like is Bacterial Evolution? Syst Biol 2015; 65:265-79. [PMID: 26559010 PMCID: PMC4748751 DOI: 10.1093/sysbio/syv084] [Citation(s) in RCA: 56] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2015] [Accepted: 11/04/2015] [Indexed: 11/14/2022] Open
Abstract
Rickettsia is a genus of intracellular bacteria whose hosts and transmission strategies are both impressively diverse, and this is reflected in a highly dynamic genome. Some previous studies have described the evolutionary history of Rickettsia as non-tree-like, due to incongruity between phylogenetic reconstructions using different portions of the genome. Here, we reconstruct the Rickettsia phylogeny using whole-genome data, including two new genomes from previously unsampled host groups. We find that a single topology, which is supported by multiple sources of phylogenetic signal, well describes the evolutionary history of the core genome. We do observe extensive incongruence between individual gene trees, but analyses of simulations over a single topology and interspersed partitions of sites show that this is more plausibly attributed to systematic error than to horizontal gene transfer. Some conflicting placements also result from phylogenetic analyses of accessory genome content (i.e., gene presence/absence), but we argue that these are also due to systematic error, stemming from convergent genome reduction, which cannot be accommodated by existing phylogenetic methods. Our results show that, even within a single genus, tests for gene exchange based on phylogenetic incongruence may be susceptible to false positives.
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Affiliation(s)
- Gemma G R Murray
- Department of Genetics, University of Cambridge, Downing Street, Cambridge CB2 3EH, UK; and
| | - Lucy A Weinert
- Department of Veterinary Medicine, University of Cambridge, Madingley Road, Cambridge CB3 0ES, UK
| | - Emma L Rhule
- Department of Genetics, University of Cambridge, Downing Street, Cambridge CB2 3EH, UK; and
| | - John J Welch
- Department of Genetics, University of Cambridge, Downing Street, Cambridge CB2 3EH, UK; and
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47
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Austin CM, Tan MH, Croft LJ, Hammer MP, Gan HM. Whole Genome Sequencing of the Asian Arowana (Scleropages formosus) Provides Insights into the Evolution of Ray-Finned Fishes. Genome Biol Evol 2015; 7:2885-95. [PMID: 26446539 PMCID: PMC4684697 DOI: 10.1093/gbe/evv186] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023] Open
Abstract
The Asian arowana (Scleropages formosus) is of commercial importance, conservation concern, and is a representative of one of the oldest lineages of ray-finned fish, the Osteoglossomorpha. To add to genomic knowledge of this species and the evolution of teleosts, the genome of a Malaysian specimen of arowana was sequenced. A draft genome is presented consisting of 42,110 scaffolds with a total size of 708 Mb (2.85% gaps) representing 93.95% of core eukaryotic genes. Using a k-mer-based method, a genome size of 900 Mb was also estimated. We present an update on the phylogenomics of fishes based on a total of 27 species (23 fish species and 4 tetrapods) using 177 orthologous proteins (71,360 amino acid sites), which supports established relationships except that arowana is placed as the sister lineage to all teleost clades (Bayesian posterior probability 1.00, bootstrap replicate 93%), that evolved after the teleost genome duplication event rather than the eels (Elopomorpha). Evolutionary rates are highly heterogeneous across the tree with fishes represented by both slowly and rapidly evolving lineages. A total of 94 putative pigment genes were identified, providing the impetus for development of molecular markers associated with the spectacular colored phenotypes found within this species.
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Affiliation(s)
- Christopher M Austin
- School of Science, Monash University Malaysia, Petaling Jaya, Selangor, Malaysia Monash University Malaysia Genomics Facility, Monash University Malaysia, Petaling Jaya, Selangor, Malaysia
| | - Mun Hua Tan
- School of Science, Monash University Malaysia, Petaling Jaya, Selangor, Malaysia Monash University Malaysia Genomics Facility, Monash University Malaysia, Petaling Jaya, Selangor, Malaysia
| | - Larry J Croft
- School of Science, Monash University Malaysia, Petaling Jaya, Selangor, Malaysia Monash University Malaysia Genomics Facility, Monash University Malaysia, Petaling Jaya, Selangor, Malaysia Malaysian Genomics Resource Centre Berhad, Boulevard Signature Office, Kuala Lumpur, Malaysia
| | - Michael P Hammer
- Museum and Art Gallery of the Northern Territory, Darwin, NT, Australia
| | - Han Ming Gan
- School of Science, Monash University Malaysia, Petaling Jaya, Selangor, Malaysia Monash University Malaysia Genomics Facility, Monash University Malaysia, Petaling Jaya, Selangor, Malaysia
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48
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Goodheart JA, Bazinet AL, Collins AG, Cummings MP. Relationships within Cladobranchia (Gastropoda: Nudibranchia) based on RNA-Seq data: an initial investigation. ROYAL SOCIETY OPEN SCIENCE 2015; 2:150196. [PMID: 26473045 PMCID: PMC4593679 DOI: 10.1098/rsos.150196] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/07/2015] [Accepted: 08/26/2015] [Indexed: 05/28/2023]
Abstract
Cladobranchia (Gastropoda: Nudibranchia) is a diverse (approx. 1000 species) but understudied group of sea slug molluscs. In order to fully comprehend the diversity of nudibranchs and the evolution of character traits within Cladobranchia, a solid understanding of evolutionary relationships is necessary. To date, only two direct attempts have been made to understand the evolutionary relationships within Cladobranchia, neither of which resulted in well-supported phylogenetic hypotheses. In addition to these studies, several others have addressed some of the relationships within this clade while investigating the evolutionary history of more inclusive groups (Nudibranchia and Euthyneura). However, all of the resulting phylogenetic hypotheses contain conflicting topologies within Cladobranchia. In this study, we address some of these long-standing issues regarding the evolutionary history of Cladobranchia using RNA-Seq data (transcriptomes). We sequenced 16 transcriptomes and combined these with four transcriptomes from the NCBI Sequence Read Archive. Transcript assembly using Trinity and orthology determination using HaMStR yielded 839 orthologous groups for analysis. These data provide a well-supported and almost fully resolved phylogenetic hypothesis for Cladobranchia. Our results support the monophyly of Cladobranchia and the sub-clade Aeolidida, but reject the monophyly of Dendronotida.
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Affiliation(s)
- Jessica A. Goodheart
- Laboratory of Molecular Evolution, Center for Bioinformatics and Computational Biology, University of Maryland, College Park, MD 20742, USA
- NMFS, National Systematics Laboratory, National Museum of Natural History, Smithsonian Institution, MRC-153, PO Box 37012, Washington, DC 20013, USA
| | - Adam L. Bazinet
- Laboratory of Molecular Evolution, Center for Bioinformatics and Computational Biology, University of Maryland, College Park, MD 20742, USA
| | - Allen G. Collins
- NMFS, National Systematics Laboratory, National Museum of Natural History, Smithsonian Institution, MRC-153, PO Box 37012, Washington, DC 20013, USA
| | - Michael P. Cummings
- Laboratory of Molecular Evolution, Center for Bioinformatics and Computational Biology, University of Maryland, College Park, MD 20742, USA
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49
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Chen MY, Liang D, Zhang P. Selecting Question-Specific Genes to Reduce Incongruence in Phylogenomics: A Case Study of Jawed Vertebrate Backbone Phylogeny. Syst Biol 2015; 64:1104-20. [PMID: 26276158 DOI: 10.1093/sysbio/syv059] [Citation(s) in RCA: 89] [Impact Index Per Article: 9.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2015] [Accepted: 08/10/2015] [Indexed: 11/13/2022] Open
Abstract
Incongruence between different phylogenomic analyses is the main challenge faced by phylogeneticists in the genomic era. To reduce incongruence, phylogenomic studies normally adopt some data filtering approaches, such as reducing missing data or using slowly evolving genes, to improve the signal quality of data. Here, we assembled a phylogenomic data set of 58 jawed vertebrate taxa and 4682 genes to investigate the backbone phylogeny of jawed vertebrates under both concatenation and coalescent-based frameworks. To evaluate the efficiency of extracting phylogenetic signals among different data filtering methods, we chose six highly intractable internodes within the backbone phylogeny of jawed vertebrates as our test questions. We found that our phylogenomic data set exhibits substantial conflicting signal among genes for these questions. Our analyses showed that non-specific data sets that are generated without bias toward specific questions are not sufficient to produce consistent results when there are several difficult nodes within a phylogeny. Moreover, phylogenetic accuracy based on non-specific data is considerably influenced by the size of data and the choice of tree inference methods. To address such incongruences, we selected genes that resolve a given internode but not the entire phylogeny. Notably, not only can this strategy yield correct relationships for the question, but it also reduces inconsistency associated with data sizes and inference methods. Our study highlights the importance of gene selection in phylogenomic analyses, suggesting that simply using a large amount of data cannot guarantee correct results. Constructing question-specific data sets may be more powerful for resolving problematic nodes.
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Affiliation(s)
- Meng-Yun Chen
- State Key Laboratory of Biocontrol, College of Ecology and Evolution, School of Life Sciences, Sun Yat-Sen University, Guangzhou 510006, China
| | - Dan Liang
- State Key Laboratory of Biocontrol, College of Ecology and Evolution, School of Life Sciences, Sun Yat-Sen University, Guangzhou 510006, China
| | - Peng Zhang
- State Key Laboratory of Biocontrol, College of Ecology and Evolution, School of Life Sciences, Sun Yat-Sen University, Guangzhou 510006, China
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50
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Doyle VP, Young RE, Naylor GJP, Brown JM. Can We Identify Genes with Increased Phylogenetic Reliability? Syst Biol 2015; 64:824-37. [DOI: 10.1093/sysbio/syv041] [Citation(s) in RCA: 68] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2014] [Accepted: 06/09/2015] [Indexed: 12/19/2022] Open
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