1
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Roestel JA, Wiersema JH, Jansen RK, Borsch T, Gruenstaeudl M. On the importance of sequence alignment inspections in plastid phylogenomics - an example from revisiting the relationships of the water-lilies. Cladistics 2024. [PMID: 38761095 DOI: 10.1111/cla.12584] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2024] [Revised: 04/27/2024] [Accepted: 04/29/2024] [Indexed: 05/20/2024] Open
Abstract
The water-lily clade represents the second earliest-diverging branch of angiosperms. Most of its species belong to Nymphaeaceae, of which the "core Nymphaeaceae"-comprising the genera Euryale, Nymphaea and Victoria-is the most diverse clade. Despite previous molecular phylogenetic studies on the core Nymphaeaceae, various aspects of their evolutionary relationships have remained unresolved. The length-variable introns and intergenic spacers are known to contain most of the sequence variability within the water-lily plastomes. Despite the challenges with multiple sequence alignment, any new molecular phylogenetic investigation on the core Nymphaeaceae should focus on these noncoding plastome regions. For example, a new plastid phylogenomic study on the core Nymphaeaceae should generate DNA sequence alignments of all plastid introns and intergenic spacers based on the principle of conserved sequence motifs. In this investigation, we revisit the phylogenetic history of the core Nymphaeaceae by employing such an approach. Specifically, we use a plastid phylogenomic analysis strategy in which all coding and noncoding partitions are separated and then undergo software-driven DNA sequence alignment, followed by a motif-based alignment inspection and adjustment. This approach allows us to increase the reliability of the character base compared to the default practice of aligning complete plastomes through software algorithms alone. Our approach produces significantly different phylogenetic tree reconstructions for several of the plastome regions under study. The results of these reconstructions underscore that Nymphaea is paraphyletic in its current circumscription, that each of the five subgenera of Nymphaea is monophyletic, and that the subgenus Nymphaea is sister to all other subgenera of Nymphaea. Our results also clarify many evolutionary relationships within the Nymphaea subgenera Brachyceras, Hydrocallis and Nymphaea. In closing, we discuss whether the phylogenetic reconstructions obtained through our motif-based alignment adjustments are in line with morphological evidence on water-lily evolution.
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Affiliation(s)
- Jessica A Roestel
- Institut für Biologie, Systematische Botanik und Pflanzengeographie, Freie Universität Berlin, Berlin, 14195, Germany
| | - John H Wiersema
- Department of Botany, National Museum of Natural History - Smithsonian Institution, Washington, DC, 37012, USA
| | - Robert K Jansen
- Department of Integrative Biology, University of Texas at Austin, Austin, TX, 78712, USA
| | - Thomas Borsch
- Institut für Biologie, Systematische Botanik und Pflanzengeographie, Freie Universität Berlin, Berlin, 14195, Germany
- Botanischer Garten und Botanisches Museum Berlin, Freie Universität Berlin, 14195, Berlin, Germany
| | - Michael Gruenstaeudl
- Institut für Biologie, Systematische Botanik und Pflanzengeographie, Freie Universität Berlin, Berlin, 14195, Germany
- Department of Biological Sciences, Fort Hays State University, Hays, KS, 67601, USA
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2
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Simmons MP, Maurin O, Bailey P, Brewer GE, Roy S, Lombardi JA, Forest F, Baker WJ. Benefits of alignment quality-control processing steps and an Angiosperms353 phylogenomics pipeline applied to the Celastrales. Cladistics 2022; 38:595-611. [PMID: 35569142 DOI: 10.1111/cla.12507] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 04/24/2022] [Indexed: 01/31/2023] Open
Abstract
We examined the impact of successive alignment quality-control steps on downstream phylogenomic analyses. We applied a recently published phylogenomics pipeline that was developed for the Angiosperms353 target-sequence-capture probe set to the flowering plant order Celastrales. Our final dataset consists of 158 species, including at least one exemplar from all 109 currently recognized Celastrales genera. We performed nine quality-control steps and compared the inferred resolution, branch support, and topological congruence of the inferred gene and species trees with those generated after each of the first six steps. We describe and justify each of our quality-control steps, including manual masking, in detail so that they may be readily applied to other lineages. We found that highly supported clades could generally be relied upon even if stringent orthology and alignment quality-control measures had not been applied. But separate instances were identified, for both concatenation and coalescence, wherein a clade was highly supported before manual masking but then subsequently contradicted. These results are generally reassuring for broad-scale analyses that use phylogenomics pipelines, but also indicate that we cannot rely exclusively on these analyses to conclude how challenging phylogenetic problems are best resolved.
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Affiliation(s)
- Mark P Simmons
- Department of Biology, Colorado State University, Fort Collins, Colorado, 80523-1878, USA
| | - Olivier Maurin
- Royal Botanic Gardens, Kew, Richmond, Surrey, TW9 3AE, UK
| | - Paul Bailey
- Royal Botanic Gardens, Kew, Richmond, Surrey, TW9 3AE, UK
| | - Grace E Brewer
- Royal Botanic Gardens, Kew, Richmond, Surrey, TW9 3AE, UK
| | - Shyamali Roy
- Royal Botanic Gardens, Kew, Richmond, Surrey, TW9 3AE, UK
| | - Julio A Lombardi
- Departamento de Botânica, Instituto de Biociências de Rio Claro, Universidade Estadual Paulista - UNESP, Av. 24-A 1515 - Bela Vista, Caixa Postal 199, São Paulo, Brazil
| | - Félix Forest
- Royal Botanic Gardens, Kew, Richmond, Surrey, TW9 3AE, UK
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3
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McInerney TW, Fulton-Howard B, Patterson C, Paliwal D, Jermiin LS, Patel HR, Pa J, Swerdlow RH, Goate A, Easteal S, Andrews SJ. A globally diverse reference alignment and panel for imputation of mitochondrial DNA variants. BMC Bioinformatics 2021; 22:417. [PMID: 34470617 PMCID: PMC8409003 DOI: 10.1186/s12859-021-04337-8] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2021] [Accepted: 08/16/2021] [Indexed: 12/27/2022] Open
Abstract
BACKGROUND Variation in mitochondrial DNA (mtDNA) identified by genotyping microarrays or by sequencing only the hypervariable regions of the genome may be insufficient to reliably assign mitochondrial genomes to phylogenetic lineages or haplogroups. This lack of resolution can limit functional and clinical interpretation of a substantial body of existing mtDNA data. To address this limitation, we developed and evaluated a large, curated reference alignment of complete mtDNA sequences as part of a pipeline for imputing missing mtDNA single nucleotide variants (mtSNVs). We call our reference alignment and pipeline MitoImpute. RESULTS We aligned the sequences of 36,960 complete human mitochondrial genomes downloaded from GenBank, filtered and controlled for quality. These sequences were reformatted for use in imputation software, IMPUTE2. We assessed the imputation accuracy of MitoImpute by measuring haplogroup and genotype concordance in data from the 1000 Genomes Project and the Alzheimer's Disease Neuroimaging Initiative (ADNI). The mean improvement of haplogroup assignment in the 1000 Genomes samples was 42.7% (Matthew's correlation coefficient = 0.64). In the ADNI cohort, we imputed missing single nucleotide variants. CONCLUSION These results show that our reference alignment and panel can be used to impute missing mtSNVs in existing data obtained from using microarrays, thereby broadening the scope of functional and clinical investigation of mtDNA. This improvement may be particularly useful in studies where participants have been recruited over time and mtDNA data obtained using different methods, enabling better integration of early data collected using less accurate methods with more recent sequence data.
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Affiliation(s)
- Tim W McInerney
- John Curtin School of Medical Research, Australian National University, Australian Capital Territory, Canberra, Australia
| | - Brian Fulton-Howard
- Genetics and Genomic Sciences, Ronald M. Loeb Center for Alzheimer's Disease, Icahn School of Medicine at Mount Sinai, 1 Gustave L. Levy Place, New York, NY, 10029, USA
| | - Christopher Patterson
- Keck School of Medicine, Mark and Mary Stevens Neuroimaging and Informatics Institute, University of Southern California, Los Angeles, CA, USA
- Department of Neurology, Alzheimer's Disease Research Center, Keck School of Medicine, University of Southern California, Los Angeles, CA, USA
| | - Devashi Paliwal
- John Curtin School of Medical Research, Australian National University, Australian Capital Territory, Canberra, Australia
| | - Lars S Jermiin
- CSIRO Land and Water, Commonwealth Scientific Industrial and Research Organization, Acton, ACT, 2601, Australia
- Research School of Biology, Australian National University, Canberra, ACT, 2601, Australia
- School of Biology and Environmental Science, University College Dublin, Belfield, Dublin 4, Ireland
- Earth Institute, University College Dublin, Belfield, Dublin 4, Ireland
| | - Hardip R Patel
- John Curtin School of Medical Research, Australian National University, Australian Capital Territory, Canberra, Australia
| | - Judy Pa
- Keck School of Medicine, Mark and Mary Stevens Neuroimaging and Informatics Institute, University of Southern California, Los Angeles, CA, USA
- Department of Neurology, Alzheimer's Disease Research Center, Keck School of Medicine, University of Southern California, Los Angeles, CA, USA
| | - Russell H Swerdlow
- Department of Neurology, Alzheimer's Disease Center, University of Kansas, Fairway, KS, USA
| | - Alison Goate
- Genetics and Genomic Sciences, Ronald M. Loeb Center for Alzheimer's Disease, Icahn School of Medicine at Mount Sinai, 1 Gustave L. Levy Place, New York, NY, 10029, USA
| | - Simon Easteal
- John Curtin School of Medical Research, Australian National University, Australian Capital Territory, Canberra, Australia
| | - Shea J Andrews
- Genetics and Genomic Sciences, Ronald M. Loeb Center for Alzheimer's Disease, Icahn School of Medicine at Mount Sinai, 1 Gustave L. Levy Place, New York, NY, 10029, USA.
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4
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Nasir A, Mughal F, Caetano-Anollés G. The tree of life describes a tripartite cellular world. Bioessays 2021; 43:e2000343. [PMID: 33837594 DOI: 10.1002/bies.202000343] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/25/2020] [Revised: 03/11/2021] [Accepted: 03/15/2021] [Indexed: 12/28/2022]
Abstract
The canonical view of a 3-domain (3D) tree of life was recently challenged by the discovery of Asgardarchaeota encoding eukaryote signature proteins (ESPs), which were treated as missing links of a 2-domain (2D) tree. Here we revisit the debate. We discuss methodological limitations of building trees with alignment-dependent approaches, which often fail to satisfactorily address the problem of ''gaps.'' In addition, most phylogenies are reconstructed unrooted, neglecting the power of direct rooting methods. Alignment-free methodologies lift most difficulties but require employing realistic evolutionary models. We argue that the discoveries of Asgards and ESPs, by themselves, do not rule out the 3D tree, which is strongly supported by comparative and evolutionary genomic analyses and vast genomic and biochemical superkingdom distinctions. Given uncertainties of retrodiction and interpretation difficulties, we conclude that the 3D view has not been falsified but instead has been strengthened by genomic analyses. In turn, the objections to the 2D model have not been lifted. The debate remains open. Also see the video abstract here: https://youtu.be/-6TBN0bubI8.
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Affiliation(s)
- Arshan Nasir
- Theoretical Biology and Biophysics (T-6), Los Alamos National Laboratory, Los Alamos, New Mexico, USA
| | - Fizza Mughal
- Department of Crop Sciences, University of Illinois at Urbana-Champaign, Urbana, Illinois, USA
| | - Gustavo Caetano-Anollés
- Department of Crop Sciences, University of Illinois at Urbana-Champaign, Urbana, Illinois, USA
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5
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Jermiin LS, Catullo RA, Holland BR. A new phylogenetic protocol: dealing with model misspecification and confirmation bias in molecular phylogenetics. NAR Genom Bioinform 2020; 2:lqaa041. [PMID: 33575594 PMCID: PMC7671319 DOI: 10.1093/nargab/lqaa041] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2020] [Revised: 05/18/2020] [Accepted: 06/04/2020] [Indexed: 12/15/2022] Open
Abstract
Molecular phylogenetics plays a key role in comparative genomics and has increasingly significant impacts on science, industry, government, public health and society. In this paper, we posit that the current phylogenetic protocol is missing two critical steps, and that their absence allows model misspecification and confirmation bias to unduly influence phylogenetic estimates. Based on the potential offered by well-established but under-used procedures, such as assessment of phylogenetic assumptions and tests of goodness of fit, we introduce a new phylogenetic protocol that will reduce confirmation bias and increase the accuracy of phylogenetic estimates.
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Affiliation(s)
- Lars S Jermiin
- CSIRO Land & Water, Canberra, ACT 2601, Australia
- Research School of Biology, Australian National University, Canberra, ACT 2601, Australia
- School of Biology & Environment Science, University College Dublin, Belfield, Dublin 4, Ireland
- Earth Institute, University College Dublin, Belfield, Dublin 4, Ireland
| | - Renee A Catullo
- CSIRO Land & Water, Canberra, ACT 2601, Australia
- Research School of Biology, Australian National University, Canberra, ACT 2601, Australia
- School of Science and Health & Hawkesbury Institute of the Environment, Western Sydney University, Penrith, NSW 2751, Australia
| | - Barbara R Holland
- School of Natural Sciences, University of Tasmania, Hobart, TAS 7001, Australia
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6
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Wright ES. RNAconTest: comparing tools for noncoding RNA multiple sequence alignment based on structural consistency. RNA (NEW YORK, N.Y.) 2020; 26:531-540. [PMID: 32005745 PMCID: PMC7161358 DOI: 10.1261/rna.073015.119] [Citation(s) in RCA: 23] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/20/2019] [Accepted: 01/28/2020] [Indexed: 05/05/2023]
Abstract
The importance of noncoding RNA sequences has become increasingly clear over the past decade. New RNA families are often detected and analyzed using comparative methods based on multiple sequence alignments. Accordingly, a number of programs have been developed for aligning and deriving secondary structures from sets of RNA sequences. Yet, the best tools for these tasks remain unclear because existing benchmarks contain too few sequences belonging to only a small number of RNA families. RNAconTest (RNA consistency test) is a new benchmarking approach relying on the observation that secondary structure is often conserved across highly divergent RNA sequences from the same family. RNAconTest scores multiple sequence alignments based on the level of consistency among known secondary structures belonging to reference sequences in their output alignment. Similarly, consensus secondary structure predictions are scored according to their agreement with one or more known structures in a family. Comparing the performance of 10 popular alignment programs using RNAconTest revealed that DAFS, DECIPHER, LocARNA, and MAFFT created the most structurally consistent alignments. The best consensus secondary structure predictions were generated by DAFS and LocARNA (via RNAalifold). Many of the methods specific to noncoding RNAs exhibited poor scalability as the number or length of input sequences increased, and several programs displayed substantial declines in score as more sequences were aligned. Overall, RNAconTest provides a means of testing and improving tools for comparative RNA analysis, as well as highlighting the best available approaches. RNAconTest is available from the DECIPHER website (http://DECIPHER.codes/Downloads.html).
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Affiliation(s)
- Erik S Wright
- Department of Biomedical Informatics, University of Pittsburgh, Pittsburgh, Pennsylvania 15219, USA
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7
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Walker JF, Walker-Hale N, Vargas OM, Larson DA, Stull GW. Characterizing gene tree conflict in plastome-inferred phylogenies. PeerJ 2019; 7:e7747. [PMID: 31579615 PMCID: PMC6764362 DOI: 10.7717/peerj.7747] [Citation(s) in RCA: 56] [Impact Index Per Article: 11.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2019] [Accepted: 08/25/2019] [Indexed: 11/20/2022] Open
Abstract
Evolutionary relationships among plants have been inferred primarily using chloroplast data. To date, no study has comprehensively examined the plastome for gene tree conflict. Using a broad sampling of angiosperm plastomes, we characterize gene tree conflict among plastid genes at various time scales and explore correlates to conflict (e.g., evolutionary rate, gene length, molecule type). We uncover notable gene tree conflict against a backdrop of largely uninformative genes. We find alignment length and tree length are strong predictors of concordance, and that nucleotides outperform amino acids. Of the most commonly used markers, matK, greatly outperforms rbcL; however, the rarely used gene rpoC2 is the top-performing gene in every analysis. We find that rpoC2 reconstructs angiosperm phylogeny as well as the entire concatenated set of protein-coding chloroplast genes. Our results suggest that longer genes are superior for phylogeny reconstruction. The alleviation of some conflict through the use of nucleotides suggests that stochastic and systematic error is likely the root of most of the observed conflict, but further research on biological conflict within plastome is warranted given documented cases of heteroplasmic recombination. We suggest that researchers should filter genes for topological concordance when performing downstream comparative analyses on phylogenetic data, even when using chloroplast genomes.
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Affiliation(s)
- Joseph F. Walker
- Sainsbury Laboratory (SLCU), University of Cambridge, Cambridge, United Kingdom
| | - Nathanael Walker-Hale
- Department of Plant Sciences, University of Cambridge, Cambridge, Cambridgeshire, United Kingdom
| | - Oscar M. Vargas
- University of California, Santa Cruz, Santa Cruz, United States of America
| | - Drew A. Larson
- University of Michigan—Ann Arbor, Ann Arbor, MI, United States of America
| | - Gregory W. Stull
- Department of Botany, Smithsonian Institution, Washington, United States of America
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8
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Fuertes MA, Rodrigo JR, Alonso C. Conserved Critical Evolutionary Gene Structures in Orthologs. J Mol Evol 2019; 87:93-105. [PMID: 30815710 DOI: 10.1007/s00239-019-09889-1] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2018] [Accepted: 02/13/2019] [Indexed: 12/18/2022]
Abstract
Unravelling gene structure requires the identification and understanding of the constraints that are often associated with the evolutionary history and functional domains of genes. We speculated in this manuscript with the possibility of the existence in orthologs of an emergent highly conserved gene structure that might explain their coordinated evolution during speciation events and their parental function. Here, we will address the following issues: (1) is there any conserved hypothetical structure along ortholog gene sequences? (2) If any, are such conserved structures maintained and conserved during speciation events? The data presented show evidences supporting this hypothesis. We have found that, (1) most orthologs studied share highly conserved compositional structures not observed previously. (2) While the percent identity of nucleotide sequences of orthologs correlates with the percent identity of composon sequences, the number of emergent compositional structures conserved during speciation does not correlate with the percent identity. (3) A broad range of species conserves the emergent compositional stretches. We will also discuss the concept of critical gene structure.
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Affiliation(s)
- Miguel A Fuertes
- Centro de Biología Molecular "Severo Ochoa" (CSIC-UAM), Universidad Autónoma de Madrid, c/Nicolás Cabrera 1, 28049, Madrid, Spain.
| | | | - Carlos Alonso
- Centro de Biología Molecular "Severo Ochoa" (CSIC-UAM), Universidad Autónoma de Madrid, c/Nicolás Cabrera 1, 28049, Madrid, Spain
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9
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Catanach TA, Sweet AD, Nguyen NPD, Peery RM, Debevec AH, Thomer AK, Owings AC, Boyd BM, Katz AD, Soto-Adames FN, Allen JM. Fully automated sequence alignment methods are comparable to, and much faster than, traditional methods in large data sets: an example with hepatitis B virus. PeerJ 2019; 7:e6142. [PMID: 30627489 PMCID: PMC6321758 DOI: 10.7717/peerj.6142] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2018] [Accepted: 11/14/2018] [Indexed: 01/05/2023] Open
Abstract
Aligning sequences for phylogenetic analysis (multiple sequence alignment; MSA) is an important, but increasingly computationally expensive step with the recent surge in DNA sequence data. Much of this sequence data is publicly available, but can be extremely fragmentary (i.e., a combination of full genomes and genomic fragments), which can compound the computational issues related to MSA. Traditionally, alignments are produced with automated algorithms and then checked and/or corrected "by eye" prior to phylogenetic inference. However, this manual curation is inefficient at the data scales required of modern phylogenetics and results in alignments that are not reproducible. Recently, methods have been developed for fully automating alignments of large data sets, but it is unclear if these methods produce alignments that result in compatible phylogenies when compared to more traditional alignment approaches that combined automated and manual methods. Here we use approximately 33,000 publicly available sequences from the hepatitis B virus (HBV), a globally distributed and rapidly evolving virus, to compare different alignment approaches. Using one data set comprised exclusively of whole genomes and a second that also included sequence fragments, we compared three MSA methods: (1) a purely automated approach using traditional software, (2) an automated approach including by eye manual editing, and (3) more recent fully automated approaches. To understand how these methods affect phylogenetic results, we compared resulting tree topologies based on these different alignment methods using multiple metrics. We further determined if the monophyly of existing HBV genotypes was supported in phylogenies estimated from each alignment type and under different statistical support thresholds. Traditional and fully automated alignments produced similar HBV phylogenies. Although there was variability between branch support thresholds, allowing lower support thresholds tended to result in more differences among trees. Therefore, differences between the trees could be best explained by phylogenetic uncertainty unrelated to the MSA method used. Nevertheless, automated alignment approaches did not require human intervention and were therefore considerably less time-intensive than traditional approaches. Because of this, we conclude that fully automated algorithms for MSA are fully compatible with older methods even in extremely difficult to align data sets. Additionally, we found that most HBV diagnostic genotypes did not correspond to evolutionarily-sound groups, regardless of alignment type and support threshold. This suggests there may be errors in genotype classification in the database or that HBV genotypes may need a revision.
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Affiliation(s)
- Therese A. Catanach
- Ornithology Department, Academy of Natural Sciences of Drexel University, Philadelphia, PA, United States of America
- Illinois Natural History Survey, University of Illinois at Urbana-Champaign, Champaign, IL, United States of America
- Department of Wildlife and Fisheries Sciences, Texas A&M University, College Station, TX, United States of America
| | - Andrew D. Sweet
- Illinois Natural History Survey, University of Illinois at Urbana-Champaign, Champaign, IL, United States of America
- Department of Entomology, Purdue University, West Lafayette, IN, United States of America
| | - Nam-phuong D. Nguyen
- Computer Science and Engineering, University of San Diego, California, La Jolla, CA, United States of America
| | - Rhiannon M. Peery
- Department of Biology, University of Alberta, Edmonton, Alberta, Canada
- Department of Plant Biology, University of Illinois at Urbana-Champaign, Champaign, IL, United States of America
| | - Andrew H. Debevec
- School of Integrative Biology, University of Illinois at Urbana-Champaign, Champaign, IL, United States of America
| | - Andrea K. Thomer
- School of Information, University of Michigan—Ann Arbor, Ann Arbor, MI, United States of America
| | - Amanda C. Owings
- Program in Ecology, Evolution, and Conservation Biology, University of Illinois at Urbana-Champaign, Urbana, IL, United States of America
| | - Bret M. Boyd
- Illinois Natural History Survey, University of Illinois at Urbana-Champaign, Champaign, IL, United States of America
- Department of Entomology, University of Georga, Athens, GA, United States of America
| | - Aron D. Katz
- Illinois Natural History Survey, University of Illinois at Urbana-Champaign, Champaign, IL, United States of America
- Department of Entomology, University of Illinois at Urbana-Champaign, Champaign, IL, United States of America
| | - Felipe N. Soto-Adames
- Florida State Collection of Arthropods, Florida Department of Agriculture and Consumer Services, Gainesville, FL, United States of America
- Department of Entomology and Nematology, University of Florida, Gainesville, FL, United States of America
| | - Julie M. Allen
- Biology Department, University of Nevada, Reno, Reno, NV, United States of America
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10
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Walker JF, Walker-Hale N, Vargas OM, Larson DA, Stull GW. Characterizing gene tree conflict in plastome-inferred phylogenies. PeerJ 2019. [PMID: 31579615 DOI: 10.1101/512079] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/12/2023] Open
Abstract
Evolutionary relationships among plants have been inferred primarily using chloroplast data. To date, no study has comprehensively examined the plastome for gene tree conflict. Using a broad sampling of angiosperm plastomes, we characterize gene tree conflict among plastid genes at various time scales and explore correlates to conflict (e.g., evolutionary rate, gene length, molecule type). We uncover notable gene tree conflict against a backdrop of largely uninformative genes. We find alignment length and tree length are strong predictors of concordance, and that nucleotides outperform amino acids. Of the most commonly used markers, matK, greatly outperforms rbcL; however, the rarely used gene rpoC2 is the top-performing gene in every analysis. We find that rpoC2 reconstructs angiosperm phylogeny as well as the entire concatenated set of protein-coding chloroplast genes. Our results suggest that longer genes are superior for phylogeny reconstruction. The alleviation of some conflict through the use of nucleotides suggests that stochastic and systematic error is likely the root of most of the observed conflict, but further research on biological conflict within plastome is warranted given documented cases of heteroplasmic recombination. We suggest that researchers should filter genes for topological concordance when performing downstream comparative analyses on phylogenetic data, even when using chloroplast genomes.
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Affiliation(s)
- Joseph F Walker
- Sainsbury Laboratory (SLCU), University of Cambridge, Cambridge, United Kingdom
| | - Nathanael Walker-Hale
- Department of Plant Sciences, University of Cambridge, Cambridge, Cambridgeshire, United Kingdom
| | - Oscar M Vargas
- University of California, Santa Cruz, Santa Cruz, United States of America
| | - Drew A Larson
- University of Michigan-Ann Arbor, Ann Arbor, MI, United States of America
| | - Gregory W Stull
- Department of Botany, Smithsonian Institution, Washington, United States of America
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11
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Staley JT, Caetano-Anollés G. Archaea-First and the Co-Evolutionary Diversification of Domains of Life. Bioessays 2018; 40:e1800036. [PMID: 29944192 DOI: 10.1002/bies.201800036] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2018] [Revised: 05/12/2018] [Indexed: 12/13/2022]
Abstract
The origins and evolution of the Archaea, Bacteria, and Eukarya remain controversial. Phylogenomic-wide studies of molecular features that are evolutionarily conserved, such as protein structural domains, suggest Archaea is the first domain of life to diversify from a stem line of descent. This line embodies the last universal common ancestor of cellular life. Here, we propose that ancestors of Euryarchaeota co-evolved with those of Bacteria prior to the diversification of Eukarya. This co-evolutionary scenario is supported by comparative genomic and phylogenomic analyses of the distributions of fold families of domains in the proteomes of free-living organisms, which show horizontal gene recruitments and informational process homologies. It also benefits from the molecular study of cell physiologies responsible for membrane phospholipids, methanogenesis, methane oxidation, cell division, gas vesicles, and the cell wall. Our theory however challenges popular cell fusion and two-domain of life scenarios derived from sequence analysis, demanding phylogenetic reconciliation. Also see the video abstract here: https://youtu.be/9yVWn_Q9faY.
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Affiliation(s)
- James T Staley
- Department of Microbiology and Astrobiology Program, University of Washington, Seattle, WA, 98195, USA
| | - Gustavo Caetano-Anollés
- Department of Crop Sciences, C. R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, IL, 61801, USA
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12
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Bromham L, Duchêne S, Hua X, Ritchie AM, Duchêne DA, Ho SYW. Bayesian molecular dating: opening up the black box. Biol Rev Camb Philos Soc 2017; 93:1165-1191. [DOI: 10.1111/brv.12390] [Citation(s) in RCA: 104] [Impact Index Per Article: 14.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2017] [Revised: 11/13/2017] [Accepted: 11/17/2017] [Indexed: 12/27/2022]
Affiliation(s)
- Lindell Bromham
- Macroevolution & Macroecology, Division of Ecology & Evolution, Research School of Biology; Australian National University; Canberra ACT 2601 Australia
| | - Sebastián Duchêne
- Department of Biochemistry and Molecular Biology, Bio21 Molecular Science and Biotechnology Institute; The University of Melbourne; Melbourne VIC 3010 Australia
- School of Life and Environmental Sciences; University of Sydney; Sydney NSW 2006 Australia
| | - Xia Hua
- Macroevolution & Macroecology, Division of Ecology & Evolution, Research School of Biology; Australian National University; Canberra ACT 2601 Australia
| | - Andrew M. Ritchie
- School of Life and Environmental Sciences; University of Sydney; Sydney NSW 2006 Australia
| | - David A. Duchêne
- Macroevolution & Macroecology, Division of Ecology & Evolution, Research School of Biology; Australian National University; Canberra ACT 2601 Australia
- School of Life and Environmental Sciences; University of Sydney; Sydney NSW 2006 Australia
| | - Simon Y. W. Ho
- School of Life and Environmental Sciences; University of Sydney; Sydney NSW 2006 Australia
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Reply to Gatesy and Springer: Claims of homology errors and zombie lineages do not compromise the dating of placental diversification. Proc Natl Acad Sci U S A 2017; 114:E9433-E9434. [PMID: 29078408 DOI: 10.1073/pnas.1715371114] [Citation(s) in RCA: 37] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
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14
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Hallas JM, Chichvarkhin A, Gosliner TM. Aligning evidence: concerns regarding multiple sequence alignments in estimating the phylogeny of the Nudibranchia suborder Doridina. ROYAL SOCIETY OPEN SCIENCE 2017; 4:171095. [PMID: 29134101 PMCID: PMC5666284 DOI: 10.1098/rsos.171095] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/09/2017] [Accepted: 09/20/2017] [Indexed: 06/07/2023]
Abstract
Molecular estimates of phylogenetic relationships rely heavily on multiple sequence alignment construction. There has been little consensus, however, on how to properly address issues pertaining to the alignment of variable regions. Here, we construct alignments from four commonly sequenced molecular markers (16S, 18S, 28S and cytochrome c oxidase subunit I) for the Nudibranchia using three different methodologies: (i) strict mathematical algorithm; (ii) exclusion of variable or divergent regions and (iii) manually curated, and examine how different alignment construction methods can affect phylogenetic signal and phylogenetic estimates for the suborder Doridina. Phylogenetic informativeness (PI) profiles suggest that the molecular markers tested lack the power to resolve relationships at the base of the Doridina, while being more robust at family-level classifications. This supports the lack of consistent resolution between the 19 families within the Doridina across all three alignments. Most of the 19 families were recovered as monophyletic, and instances of non-monophyletic families were consistently recovered between analyses. We conclude that the alignment of variable regions has some effect on phylogenetic estimates of the Doridina, but these effects can vary depending on the size and scope of the phylogenetic query and PI of molecular markers.
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Affiliation(s)
- Joshua M. Hallas
- Department of Biology, University of Nevada, Reno. 1664 N. Virginia St, Reno, NV 89557, USA
- Department of Invertebrate Zoology and Geology, California Academy of Sciences, 55 Music Concourse Dr Golden Gate Park, San Francisco, CA 94118, USA
| | - Anton Chichvarkhin
- National Scientific Center of Marine Biology, Far East Branch of Russian Academy of Sciences, Palchevskogo 17, Vladivostok 690041, Russia
- Far Eastern Federal University, Sukhanova 8, Vladivostok 690950, Russia
| | - Terrence M. Gosliner
- Department of Invertebrate Zoology and Geology, California Academy of Sciences, 55 Music Concourse Dr Golden Gate Park, San Francisco, CA 94118, USA
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15
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Swain TD. Revisiting the phylogeny of Zoanthidea (Cnidaria: Anthozoa): Staggered alignment of hypervariable sequences improves species tree inference. Mol Phylogenet Evol 2017; 118:1-12. [PMID: 28919505 DOI: 10.1016/j.ympev.2017.09.008] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2016] [Revised: 09/11/2017] [Accepted: 09/13/2017] [Indexed: 10/18/2022]
Abstract
The recent rapid proliferation of novel taxon identification in the Zoanthidea has been accompanied by a parallel propagation of gene trees as a tool of species discovery, but not a corresponding increase in our understanding of phylogeny. This disparity is caused by the trade-off between the capabilities of automated DNA sequence alignment and data content of genes applied to phylogenetic inference in this group. Conserved genes or segments are easily aligned across the order, but produce poorly resolved trees; hypervariable genes or segments contain the evolutionary signal necessary for resolution and robust support, but sequence alignment is daunting. Staggered alignments are a form of phylogeny-informed sequence alignment composed of a mosaic of local and universal regions that allow phylogenetic inference to be applied to all nucleotides from both hypervariable and conserved gene segments. Comparisons between species tree phylogenies inferred from all data (staggered alignment) and hypervariable-excluded data (standard alignment) demonstrate improved confidence and greater topological agreement with other sources of data for the complete-data tree. This novel phylogeny is the most comprehensive to date (in terms of taxa and data) and can serve as an expandable tool for evolutionary hypothesis testing in the Zoanthidea. Spanish language abstract available in Text S1. Translation by L. O. Swain, DePaul University, Chicago, Illinois, 60604, USA.
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Affiliation(s)
- Timothy D Swain
- Integrative Research Center, Field Museum of Natural History, Chicago, IL 60605, USA; Department of Civil and Environmental Engineering, Northwestern University, Evanston, IL 60208, USA.
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16
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Lavoué S, Arnegard ME, Rabosky DL, McIntyre PB, Arcila D, Vari RP, Nishida M. Trophic evolution in African citharinoid fishes (Teleostei: Characiformes) and the origin of intraordinal pterygophagy. Mol Phylogenet Evol 2017; 113:23-32. [DOI: 10.1016/j.ympev.2017.05.001] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2016] [Revised: 04/29/2017] [Accepted: 05/01/2017] [Indexed: 11/25/2022]
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17
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Chatzou M, Magis C, Chang JM, Kemena C, Bussotti G, Erb I, Notredame C. Multiple sequence alignment modeling: methods and applications. Brief Bioinform 2015; 17:1009-1023. [PMID: 26615024 DOI: 10.1093/bib/bbv099] [Citation(s) in RCA: 84] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2015] [Revised: 10/16/2015] [Indexed: 12/20/2022] Open
Abstract
This review provides an overview on the development of Multiple sequence alignment (MSA) methods and their main applications. It is focused on progress made over the past decade. The three first sections review recent algorithmic developments for protein, RNA/DNA and genomic alignments. The fourth section deals with benchmarks and explores the relationship between empirical and simulated data, along with the impact on method developments. The last part of the review gives an overview on available MSA local reliability estimators and their dependence on various algorithmic properties of available methods.
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Tan G, Muffato M, Ledergerber C, Herrero J, Goldman N, Gil M, Dessimoz C. Current Methods for Automated Filtering of Multiple Sequence Alignments Frequently Worsen Single-Gene Phylogenetic Inference. Syst Biol 2015; 64:778-91. [PMID: 26031838 PMCID: PMC4538881 DOI: 10.1093/sysbio/syv033] [Citation(s) in RCA: 143] [Impact Index Per Article: 15.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2014] [Accepted: 05/26/2015] [Indexed: 01/09/2023] Open
Abstract
Phylogenetic inference is generally performed on the basis of multiple sequence alignments (MSA). Because errors in an alignment can lead to errors in tree estimation, there is a strong interest in identifying and removing unreliable parts of the alignment. In recent years several automated filtering approaches have been proposed, but despite their popularity, a systematic and comprehensive comparison of different alignment filtering methods on real data has been lacking. Here, we extend and apply recently introduced phylogenetic tests of alignment accuracy on a large number of gene families and contrast the performance of unfiltered versus filtered alignments in the context of single-gene phylogeny reconstruction. Based on multiple genome-wide empirical and simulated data sets, we show that the trees obtained from filtered MSAs are on average worse than those obtained from unfiltered MSAs. Furthermore, alignment filtering often leads to an increase in the proportion of well-supported branches that are actually wrong. We confirm that our findings hold for a wide range of parameters and methods. Although our results suggest that light filtering (up to 20% of alignment positions) has little impact on tree accuracy and may save some computation time, contrary to widespread practice, we do not generally recommend the use of current alignment filtering methods for phylogenetic inference. By providing a way to rigorously and systematically measure the impact of filtering on alignments, the methodology set forth here will guide the development of better filtering algorithms.
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Affiliation(s)
- Ge Tan
- Department of Computer Science, ETH Zurich, Universitätstr. 6, 8092 Zurich, Switzerland, Department of Molecular Sciences, Institute of Clinical Sciences, Faculty of Medicine, Imperial College London, London, UK; MRC Clinical Sciences Centre, London W12 0NN, UK
| | - Matthieu Muffato
- European Molecular Biology Laboratory, European Bioinformatics Institute, Hinxton, Cambridge, CB10 1SD, UK
| | - Christian Ledergerber
- Department of Computer Science, ETH Zurich, Universitätstr. 6, 8092 Zurich, Switzerland
| | - Javier Herrero
- European Molecular Biology Laboratory, European Bioinformatics Institute, Hinxton, Cambridge, CB10 1SD, UK; University College London, Gower St, London WC1E 6BT, UK; and
| | - Nick Goldman
- European Molecular Biology Laboratory, European Bioinformatics Institute, Hinxton, Cambridge, CB10 1SD, UK
| | - Manuel Gil
- Institute of Molecular Life Sciences, University of Zurich, Winterthurerstr. 190 , 8057 Zurich, Switzerland; and Swiss Institute of Bioinformatics, Universitätstr. 6, 8092 Zurich, Switzerland
| | - Christophe Dessimoz
- University College London, Gower St, London WC1E 6BT, UK; and European Molecular Biology Laboratory, European Bioinformatics Institute, Hinxton, Cambridge, CB10 1SD, UK;
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Affiliation(s)
- David A. Morrison
- Systematic Biology, Evolutionary Biology Centre, Norbyvägen 18D, 752 36 Uppsala, Sweden
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20
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Magee AF, May MR, Moore BR. The dawn of open access to phylogenetic data. PLoS One 2014; 9:e110268. [PMID: 25343725 PMCID: PMC4208793 DOI: 10.1371/journal.pone.0110268] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2014] [Accepted: 09/09/2014] [Indexed: 01/29/2023] Open
Abstract
The scientific enterprise depends critically on the preservation of and open access to published data. This basic tenet applies acutely to phylogenies (estimates of evolutionary relationships among species). Increasingly, phylogenies are estimated from increasingly large, genome-scale datasets using increasingly complex statistical methods that require increasing levels of expertise and computational investment. Moreover, the resulting phylogenetic data provide an explicit historical perspective that critically informs research in a vast and growing number of scientific disciplines. One such use is the study of changes in rates of lineage diversification (speciation--extinction) through time. As part of a meta-analysis in this area, we sought to collect phylogenetic data (comprising nucleotide sequence alignment and tree files) from 217 studies published in 46 journals over a 13-year period. We document our attempts to procure those data (from online archives and by direct request to corresponding authors), and report results of analyses (using Bayesian logistic regression) to assess the impact of various factors on the success of our efforts. Overall, complete phylogenetic data for [Formula: see text] of these studies are effectively lost to science. Our study indicates that phylogenetic data are more likely to be deposited in online archives and/or shared upon request when: (1) the publishing journal has a strong data-sharing policy; (2) the publishing journal has a higher impact factor, and; (3) the data are requested from faculty rather than students. Importantly, our survey spans recent policy initiatives and infrastructural changes; our analyses indicate that the positive impact of these community initiatives has been both dramatic and immediate. Although the results of our study indicate that the situation is dire, our findings also reveal tremendous recent progress in the sharing and preservation of phylogenetic data.
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Affiliation(s)
- Andrew F. Magee
- Department of Evolution and Ecology, University of California Davis, Davis, CA, United States of America
| | - Michael R. May
- Department of Evolution and Ecology, University of California Davis, Davis, CA, United States of America
| | - Brian R. Moore
- Department of Evolution and Ecology, University of California Davis, Davis, CA, United States of America
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Global patterns of protein domain gain and loss in superkingdoms. PLoS Comput Biol 2014; 10:e1003452. [PMID: 24499935 PMCID: PMC3907288 DOI: 10.1371/journal.pcbi.1003452] [Citation(s) in RCA: 51] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2013] [Accepted: 12/03/2013] [Indexed: 12/21/2022] Open
Abstract
Domains are modules within proteins that can fold and function independently and are evolutionarily conserved. Here we compared the usage and distribution of protein domain families in the free-living proteomes of Archaea, Bacteria and Eukarya and reconstructed species phylogenies while tracing the history of domain emergence and loss in proteomes. We show that both gains and losses of domains occurred frequently during proteome evolution. The rate of domain discovery increased approximately linearly in evolutionary time. Remarkably, gains generally outnumbered losses and the gain-to-loss ratios were much higher in akaryotes compared to eukaryotes. Functional annotations of domain families revealed that both Archaea and Bacteria gained and lost metabolic capabilities during the course of evolution while Eukarya acquired a number of diverse molecular functions including those involved in extracellular processes, immunological mechanisms, and cell regulation. Results also highlighted significant contemporary sharing of informational enzymes between Archaea and Eukarya and metabolic enzymes between Bacteria and Eukarya. Finally, the analysis provided useful insights into the evolution of species. The archaeal superkingdom appeared first in evolution by gradual loss of ancestral domains, bacterial lineages were the first to gain superkingdom-specific domains, and eukaryotes (likely) originated when an expanding proto-eukaryotic stem lineage gained organelles through endosymbiosis of already diversified bacterial lineages. The evolutionary dynamics of domain families in proteomes and the increasing number of domain gains is predicted to redefine the persistence strategies of organisms in superkingdoms, influence the make up of molecular functions, and enhance organismal complexity by the generation of new domain architectures. This dynamics highlights ongoing secondary evolutionary adaptations in akaryotic microbes, especially Archaea.
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22
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Who watches the watchmen? An appraisal of benchmarks for multiple sequence alignment. Methods Mol Biol 2014; 1079:59-73. [PMID: 24170395 DOI: 10.1007/978-1-62703-646-7_4] [Citation(s) in RCA: 36] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
Multiple sequence alignment (MSA) is a fundamental and ubiquitous technique in bioinformatics used to infer related residues among biological sequences. Thus alignment accuracy is crucial to a vast range of analyses, often in ways difficult to assess in those analyses. To compare the performance of different aligners and help detect systematic errors in alignments, a number of benchmarking strategies have been pursued. Here we present an overview of the main strategies-based on simulation, consistency, protein structure, and phylogeny-and discuss their different advantages and associated risks. We outline a set of desirable characteristics for effective benchmarking, and evaluate each strategy in light of them. We conclude that there is currently no universally applicable means of benchmarking MSA, and that developers and users of alignment tools should base their choice of benchmark depending on the context of application-with a keen awareness of the assumptions underlying each benchmarking strategy.
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Diversification in a biodiversity hotspot – The evolution of Southeast Asian rhacophorid tree frogs on Borneo (Amphibia: Anura: Rhacophoridae). Mol Phylogenet Evol 2013; 68:567-81. [DOI: 10.1016/j.ympev.2013.04.001] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2012] [Revised: 03/28/2013] [Accepted: 04/01/2013] [Indexed: 12/24/2022]
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25
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Klopfstein S, Vilhelmsen L, Heraty JM, Sharkey M, Ronquist F. The hymenopteran tree of life: evidence from protein-coding genes and objectively aligned ribosomal data. PLoS One 2013; 8:e69344. [PMID: 23936325 PMCID: PMC3732274 DOI: 10.1371/journal.pone.0069344] [Citation(s) in RCA: 98] [Impact Index Per Article: 8.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2013] [Accepted: 06/07/2013] [Indexed: 11/18/2022] Open
Abstract
Previous molecular analyses of higher hymenopteran relationships have largely been based on subjectively aligned ribosomal sequences (18S and 28S). Here, we reanalyze the 18S and 28S data (unaligned about 4.4 kb) using an objective and a semi-objective alignment approach, based on MAFFT and BAli-Phy, respectively. Furthermore, we present the first analyses of a substantial protein-coding data set (4.6 kb from one mitochondrial and four nuclear genes). Our results indicate that previous studies may have suffered from inflated support values due to subjective alignment of the ribosomal sequences, but apparently not from significant biases. The protein data provide independent confirmation of several earlier results, including the monophyly of non-xyelid hymenopterans, Pamphilioidea + Unicalcarida, Unicalcarida, Vespina, Apocrita, Proctotrupomorpha and core Proctotrupomorpha. The protein data confirm that Aculeata are nested within a paraphyletic Evaniomorpha, but cast doubt on the monophyly of Evanioidea. Combining the available morphological, ribosomal and protein-coding data, we examine the total-evidence signal as well as congruence and conflict among the three data sources. Despite an emerging consensus on many higher-level hymenopteran relationships, several problems remain unresolved or contentious, including rooting of the hymenopteran tree, relationships of the woodwasps, placement of Stephanoidea and Ceraphronoidea, and the sister group of Aculeata.
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Affiliation(s)
- Seraina Klopfstein
- Department of Biodiversity Informatics, Swedish Museum of Natural History, Stockholm, Sweden.
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26
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Truong C, Divakar PK, Yahr R, Crespo A, Clerc P. Testing the use of ITS rDNA and protein-coding genes in the generic and species delimitation of the lichen genus Usnea (Parmeliaceae, Ascomycota). Mol Phylogenet Evol 2013; 68:357-72. [DOI: 10.1016/j.ympev.2013.04.005] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2012] [Revised: 02/01/2013] [Accepted: 04/02/2013] [Indexed: 12/31/2022]
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Abstract
The traditional bacterial rooting of the three superkingdoms in sequence-based gene trees is inconsistent with new phylogenetic reconstructions based on genome content of compact protein domains. We find that protein domains at the level of the SCOP superfamily (SF) from sequenced genomes implement with maximum parsimony fully resolved rooted trees. Such genome content trees identify archaea and bacteria (akaryotes) as sister clades that diverge from an akaryote common ancestor, LACA. Several eukaryote sister clades diverge from a eukaryote common ancestor, LECA. LACA and LECA descend in parallel from the most recent universal common ancestor (MRUCA), which is not a bacterium. Rather, MRUCA presents 75% of the unique SFs encoded by extant genomes of the three superkingdoms, each encoding a proteome that partially overlaps all others. This alone implies that the common ancestor to the superkingdoms was very complex. Such ancestral complexity is confirmed by phylogenetic reconstructions. In addition, the divergence of proteomes from the complex ancestor in each superkingdom is both reductive in numbers of unique SFs as well as cumulative in the abundance of surviving SFs. These data suggest that the common ancestor was not the first cell lineage and that modern global phylogeny is the crown of a "recently" re-rooted tree. We suggest that a bottlenecked survivor of an environmental collapse, which preceded the flourishing of the modern crown, seeded the current phylogenetic tree.
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Yuri T, Kimball RT, Harshman J, Bowie RCK, Braun MJ, Chojnowski JL, Han KL, Hackett SJ, Huddleston CJ, Moore WS, Reddy S, Sheldon FH, Steadman DW, Witt CC, Braun EL. Parsimony and model-based analyses of indels in avian nuclear genes reveal congruent and incongruent phylogenetic signals. BIOLOGY 2013; 2:419-44. [PMID: 24832669 PMCID: PMC4009869 DOI: 10.3390/biology2010419] [Citation(s) in RCA: 76] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/28/2012] [Revised: 02/21/2013] [Accepted: 02/22/2013] [Indexed: 11/19/2022]
Abstract
Insertion/deletion (indel) mutations, which are represented by gaps in multiple sequence alignments, have been used to examine phylogenetic hypotheses for some time. However, most analyses combine gap data with the nucleotide sequences in which they are embedded, probably because most phylogenetic datasets include few gap characters. Here, we report analyses of 12,030 gap characters from an alignment of avian nuclear genes using maximum parsimony (MP) and a simple maximum likelihood (ML) framework. Both trees were similar, and they exhibited almost all of the strongly supported relationships in the nucleotide tree, although neither gap tree supported many relationships that have proven difficult to recover in previous studies. Moreover, independent lines of evidence typically corroborated the nucleotide topology instead of the gap topology when they disagreed, although the number of conflicting nodes with high bootstrap support was limited. Filtering to remove short indels did not substantially reduce homoplasy or reduce conflict. Combined analyses of nucleotides and gaps resulted in the nucleotide topology, but with increased support, suggesting that gap data may prove most useful when analyzed in combination with nucleotide substitutions.
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Affiliation(s)
- Tamaki Yuri
- Department of Biology, University of Florida, Gainesville, FL 32611, USA; E-Mails: (T.Y.); (R.T.K.); (J.L.C.); (K.-L.H.)
- Sam Noble Oklahoma Museum of Natural History, University of Oklahoma, Norman, OK 73072, USA
| | - Rebecca T. Kimball
- Department of Biology, University of Florida, Gainesville, FL 32611, USA; E-Mails: (T.Y.); (R.T.K.); (J.L.C.); (K.-L.H.)
| | - John Harshman
- 4869 Pepperwood Way, San Jose, CA 95124, USA; E-Mail:
| | - Rauri C. K. Bowie
- Museum of Vertebrate Zoology and Department of Integrative Biology, University of California, Berkeley, CA 94720, USA; E-Mail:
| | - Michael J. Braun
- Department of Vertebrate Zoology, National Museum of Natural History, Smithsonian Institution, 4210 Silver Hill Road, Suitland, MD 20746, USA; E-Mails: (M.J.B.); (C.J.H.)
- Behavior, Ecology, Evolution and Systematics Program, University of Maryland, College Park, MD 20742, USA
| | - Jena L. Chojnowski
- Department of Biology, University of Florida, Gainesville, FL 32611, USA; E-Mails: (T.Y.); (R.T.K.); (J.L.C.); (K.-L.H.)
| | - Kin-Lan Han
- Department of Biology, University of Florida, Gainesville, FL 32611, USA; E-Mails: (T.Y.); (R.T.K.); (J.L.C.); (K.-L.H.)
| | - Shannon J. Hackett
- Zoology Department, Field Museum of Natural History, 1400 South Lakeshore Drive, Chicago, IL 60605, USA; E-Mail:
| | - Christopher J. Huddleston
- Department of Vertebrate Zoology, National Museum of Natural History, Smithsonian Institution, 4210 Silver Hill Road, Suitland, MD 20746, USA; E-Mails: (M.J.B.); (C.J.H.)
| | - William S. Moore
- Department of Biological Sciences, Wayne State University, 5047 Gullen Mall, Detroit, MI 48202, USA; E-Mail:
| | - Sushma Reddy
- Biology Department, Loyola University Chicago, Chicago, IL 60660, USA; E-Mail:
| | - Frederick H. Sheldon
- Museum of Natural Science, 119 Foster Hall, Louisiana State University, Baton Rouge, LA 70803, USA; E-Mail:
| | - David W. Steadman
- Florida Museum of Natural History, University of Florida, Gainesville, FL 32611, USA; E-Mail:
| | - Christopher C. Witt
- Department of Biology and Museum of Southwestern Biology, University of New Mexico, Albuquerque, NM 87131, USA; E-Mail:
| | - Edward L. Braun
- Department of Biology, University of Florida, Gainesville, FL 32611, USA; E-Mails: (T.Y.); (R.T.K.); (J.L.C.); (K.-L.H.)
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Tóth A, Hausknecht A, Krisai-Greilhuber I, Papp T, Vágvölgyi C, Nagy LG. Iteratively refined guide trees help improving alignment and phylogenetic inference in the mushroom family Bolbitiaceae. PLoS One 2013; 8:e56143. [PMID: 23418526 PMCID: PMC3572013 DOI: 10.1371/journal.pone.0056143] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2012] [Accepted: 01/07/2013] [Indexed: 11/19/2022] Open
Abstract
Reconciling traditional classifications, morphology, and the phylogenetic relationships of brown-spored agaric mushrooms has proven difficult in many groups, due to extensive convergence in morphological features. Here, we address the monophyly of the Bolbitiaceae, a family with over 700 described species and examine the higher-level relationships within the family using a newly constructed multilocus dataset (ITS, nrLSU rDNA and EF1-alpha). We tested whether the fast-evolving Internal Transcribed Spacer (ITS) sequences can be accurately aligned across the family, by comparing the outcome of two iterative alignment refining approaches (an automated and a manual) and various indel-treatment strategies. We used PRANK to align sequences in both cases. Our results suggest that--although PRANK successfully evades overmatching of gapped sites, referred previously to as alignment overmatching--it infers an unrealistically high number of indel events with natively generated guide-trees. This 'alignment undermatching' could be avoided by using more rigorous (e.g. ML) guide trees. The trees inferred in this study support the monophyly of the core Bolbitiaceae, with the exclusion of Panaeolus, Agrocybe, and some of the genera formerly placed in the family. Bolbitius and Conocybe were found monophyletic, however, Pholiotina and Galerella require redefinition. The phylogeny revealed that stipe coverage type is a poor predictor of phylogenetic relationships, indicating the need for a revision of the intrageneric relationships within Conocybe.
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Affiliation(s)
- Annamária Tóth
- Department of Microbiology, Faculty of Science and Informatics, University of Szeged, Szeged, Hungary
| | - Anton Hausknecht
- Department of Systematic and Evolutionary Botany, Faculty Centre of Biodiversity, University of Vienna, Wien, Austria
| | - Irmgard Krisai-Greilhuber
- Department of Systematic and Evolutionary Botany, Faculty Centre of Biodiversity, University of Vienna, Wien, Austria
| | - Tamás Papp
- Department of Microbiology, Faculty of Science and Informatics, University of Szeged, Szeged, Hungary
| | - Csaba Vágvölgyi
- Department of Microbiology, Faculty of Science and Informatics, University of Szeged, Szeged, Hungary
| | - László G. Nagy
- Department of Microbiology, Faculty of Science and Informatics, University of Szeged, Szeged, Hungary
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30
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Warnow T. Large-Scale Multiple Sequence Alignment and Phylogeny Estimation. MODELS AND ALGORITHMS FOR GENOME EVOLUTION 2013. [DOI: 10.1007/978-1-4471-5298-9_6] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
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31
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Caetano-Anollés G, Nasir A. Benefits of using molecular structure and abundance in phylogenomic analysis. Front Genet 2012; 3:172. [PMID: 22973296 PMCID: PMC3434437 DOI: 10.3389/fgene.2012.00172] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2012] [Accepted: 08/18/2012] [Indexed: 12/25/2022] Open
Affiliation(s)
- Gustavo Caetano-Anollés
- Evolutionary Bioinformatics Laboratory, Department of Crop Sciences, University of Illinois Urbana-Champaign, IL, USA
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32
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Saurabh K, Holland BR, Gibb GC, Penny D. Gaps: an elusive source of phylogenetic information. Syst Biol 2012; 61:1075-82. [PMID: 22438330 DOI: 10.1093/sysbio/sys043] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023] Open
Affiliation(s)
- Kumar Saurabh
- IMBS/IFS/INR, Massey University, Palmerston North 4442, New Zealand
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Abstract
The standard approach to phylogeny estimation uses two phases, in which the first phase produces an alignment on a set of homologous sequences, and the second phase estimates a tree on the multiple sequence alignment. POY, a method which seeks a tree/alignment pair minimizing the total treelength, is the most widely used alternative to this two-phase approach. The topological accuracy of trees computed under treelength optimization is, however, controversial. In particular, one study showed that treelength optimization using simple gap penalties produced poor trees and alignments, and suggested the possibility that if POY were used with an affine gap penalty, it might be able to be competitive with the best two-phase methods. In this paper we report on a study addressing this possibility. We present a new heuristic for treelength, called BeeTLe (Better Treelength), that is guaranteed to produce trees at least as short as POY. We then use this heuristic to analyze a large number of simulated and biological datasets, and compare the resultant trees and alignments to those produced using POY and also maximum likelihood (ML) and maximum parsimony (MP) trees computed on a number of alignments. In general, we find that trees produced by BeeTLe are shorter and more topologically accurate than POY trees, but that neither POY nor BeeTLe produces trees as topologically accurate as ML trees produced on standard alignments. These findings, taken as a whole, suggest that treelength optimization is not as good an approach to phylogenetic tree estimation as maximum likelihood based upon good alignment methods.
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Affiliation(s)
| | - Tandy Warnow
- Department of Computer Science, University of Texas at Austin, Austin, Texas, United States of America
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Löytynoja A. Alignment methods: strategies, challenges, benchmarking, and comparative overview. Methods Mol Biol 2012; 855:203-35. [PMID: 22407710 DOI: 10.1007/978-1-61779-582-4_7] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023]
Abstract
Comparative evolutionary analyses of molecular sequences are solely based on the identities and differences detected between homologous characters. Errors in this homology statement, that is errors in the alignment of the sequences, are likely to lead to errors in the downstream analyses. Sequence alignment and phylogenetic inference are tightly connected and many popular alignment programs use the phylogeny to divide the alignment problem into smaller tasks. They then neglect the phylogenetic tree, however, and produce alignments that are not evolutionarily meaningful. The use of phylogeny-aware methods reduces the error but the resulting alignments, with evolutionarily correct representation of homology, can challenge the existing practices and methods for viewing and visualising the sequences. The inter-dependency of alignment and phylogeny can be resolved by joint estimation of the two; methods based on statistical models allow for inferring the alignment parameters from the data and correctly take into account the uncertainty of the solution but remain computationally challenging. Widely used alignment methods are based on heuristic algorithms and unlikely to find globally optimal solutions. The whole concept of one correct alignment for the sequences is questionable, however, as there typically exist vast numbers of alternative, roughly equally good alignments that should also be considered. This uncertainty is hidden by many popular alignment programs and is rarely correctly taken into account in the downstream analyses. The quest for finding and improving the alignment solution is complicated by the lack of suitable measures of alignment goodness. The difficulty of comparing alternative solutions also affects benchmarks of alignment methods and the results strongly depend on the measure used. As the effects of alignment error cannot be predicted, comparing the alignments' performance in downstream analyses is recommended.
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Affiliation(s)
- Ari Löytynoja
- European Bioinformatics Institute (EMBL), Hinxton, UK.
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Hertwig ST, Das I, Schweizer M, Brown R, Haas A. Phylogenetic relationships of the Rhacophorus everetti-group and implications for the evolution of reproductive modes in Philautus (Amphibia: Anura: Rhacophoridae). ZOOL SCR 2011. [DOI: 10.1111/j.1463-6409.2011.00499.x] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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Molecular phylogenetics of Hypoxidaceae – Evidence from plastid DNA data and inferences on morphology and biogeography. Mol Phylogenet Evol 2011; 60:122-36. [DOI: 10.1016/j.ympev.2011.02.021] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2010] [Revised: 02/02/2011] [Accepted: 02/14/2011] [Indexed: 11/20/2022]
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Kim KM, Caetano-Anollés G. The proteomic complexity and rise of the primordial ancestor of diversified life. BMC Evol Biol 2011; 11:140. [PMID: 21612591 PMCID: PMC3123224 DOI: 10.1186/1471-2148-11-140] [Citation(s) in RCA: 77] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2011] [Accepted: 05/25/2011] [Indexed: 01/07/2023] Open
Abstract
BACKGROUND The last universal common ancestor represents the primordial cellular organism from which diversified life was derived. This urancestor accumulated genetic information before the rise of organismal lineages and is considered to be either a simple 'progenote' organism with a rudimentary translational apparatus or a more complex 'cenancestor' with almost all essential biological processes. Recent comparative genomic studies support the latter model and propose that the urancestor was similar to modern organisms in terms of gene content. However, most of these studies were based on molecular sequences, which are fast evolving and of limited value for deep evolutionary explorations. RESULTS Here we engage in a phylogenomic study of protein domain structure in the proteomes of 420 free-living fully sequenced organisms. Domains were defined at the highly conserved fold superfamily (FSF) level of structural classification and an iterative phylogenomic approach was used to reconstruct max_set and min_set FSF repertoires as upper and lower bounds of the urancestral proteome. While the functional make up of the urancestral sets was complex, they represent only 5-11% of the 1,420 FSFs of extant proteomes and their make up and reuse was at least 5 and 3 times smaller than proteomes of free-living organisms, repectively. Trees of proteomes reconstructed directly from FSFs or from molecular functions, which included the max_set and min_set as articial taxa, showed that urancestors were always placed at their base and rooted the tree of life in Archaea. Finally, a molecular clock of FSFs suggests the min_set reflects urancestral genetic make up more reliably and confirms diversified life emerged about 2.9 billion years ago during the start of planet oxygenation. CONCLUSIONS The minimum urancestral FSF set reveals the urancestor had advanced metabolic capabilities, was especially rich in nucleotide metabolism enzymes, had pathways for the biosynthesis of membrane sn1,2 glycerol ester and ether lipids, and had crucial elements of translation, including a primordial ribosome with protein synthesis capabilities. It lacked however fundamental functions, including transcription, processes for extracellular communication, and enzymes for deoxyribonucleotide synthesis. Proteomic history reveals the urancestor is closer to a simple progenote organism but harbors a rather complex set of modern molecular functions.
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Affiliation(s)
- Kyung Mo Kim
- Evolutionary Bioinformatics Laboratory, Department of Crop Science, University of Illinois, Urbana, IL 61801, USA
- Korean Bioinformation Center, Korea Research Institute of Bioscience and Biotechnology, 111 Gwahangno, Yuseong-gu, Daejeon 305-806, Korea
| | - Gustavo Caetano-Anollés
- Evolutionary Bioinformatics Laboratory, Department of Crop Science, University of Illinois, Urbana, IL 61801, USA
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Anderson CL, Strope CL, Moriyama EN. SuiteMSA: visual tools for multiple sequence alignment comparison and molecular sequence simulation. BMC Bioinformatics 2011; 12:184. [PMID: 21600033 PMCID: PMC3133551 DOI: 10.1186/1471-2105-12-184] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2011] [Accepted: 05/21/2011] [Indexed: 11/12/2022] Open
Abstract
Background Multiple sequence alignment (MSA) plays a central role in nearly all bioinformatics and molecular evolutionary applications. MSA reconstruction is thus one of the most heavily scrutinized bioinformatics fields. Evaluating the quality of MSA reconstruction is often hindered by the lack of good reference MSAs. The use of sequence evolution simulation can provide such reference MSAs. Furthermore, none of the MSA viewing/editing programs currently available allows the user to make direct comparisons between two or more MSAs. Considering the importance of MSA quality in a wide range of research, it is desirable if MSA assessment can be performed more easily. Results We have developed SuiteMSA, a java-based application that provides unique MSA viewers. Users can directly compare multiple MSAs and evaluate where the MSAs agree (are consistent) or disagree (are inconsistent). Several alignment statistics are provided to assist such comparisons. SuiteMSA also includes a graphical phylogeny editor/viewer as well as a graphical user interface for a sequence evolution simulator that can be used to construct reference MSAs. Conclusions SuiteMSA provides researchers easy access to a sequence evolution simulator, reference alignments generated by the simulator, and a series of tools to evaluate the performance of the MSA reconstruction programs. It will help us improve the quality of MSAs, often the most important first steps of bioinformatics and other biological research.
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Affiliation(s)
- Catherine L Anderson
- Department of Computer Science and Engineering, University of Nebraska, Lincoln, Nebraska 68588, USA
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Ekman S, Blaalid R. The Devil in the Details: Interactions between the Branch-Length Prior and Likelihood Model Affect Node Support and Branch Lengths in the Phylogeny of the Psoraceae. Syst Biol 2011; 60:541-61. [DOI: 10.1093/sysbio/syr022] [Citation(s) in RCA: 36] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Affiliation(s)
- Stefan Ekman
- Museum of Evolution, Uppsala University, Norbyvägen 16, SE-752 36 Uppsala, Sweden
- Department of Biology, University of Bergen, PO Box 7800, N-5020 Bergen, Norway
| | - Rakel Blaalid
- Department of Biology, University of Bergen, PO Box 7800, N-5020 Bergen, Norway
- Department of Biology, University of Oslo, PO Box 1066 Blindern, N-0316 Oslo, Norway
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Markova-Raina P, Petrov D. High sensitivity to aligner and high rate of false positives in the estimates of positive selection in the 12 Drosophila genomes. Genome Res 2011; 21:863-74. [PMID: 21393387 DOI: 10.1101/gr.115949.110] [Citation(s) in RCA: 108] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Abstract
We investigate the effect of aligner choice on inferences of positive selection using site-specific models of molecular evolution. We find that independently of the choice of aligner, the rate of false positives is unacceptably high. Our study is a whole-genome analysis of all protein-coding genes in 12 Drosophila genomes annotated in either all 12 species (~6690 genes) or in the six melanogaster group species. We compare six popular aligners: PRANK, T-Coffee, ClustalW, ProbCons, AMAP, and MUSCLE, and find that the aligner choice strongly influences the estimates of positive selection. Differences persist when we use (1) different stringency cutoffs, (2) different selection inference models, (3) alignments with or without gaps, and/or additional masking, (4) per-site versus per-gene statistics, (5) closely related melanogaster group species versus more distant 12 Drosophila genomes. Furthermore, we find that these differences are consequential for downstream analyses such as determination of over/under-represented GO terms associated with positive selection. Visual analysis indicates that most sites inferred as positively selected are, in fact, misaligned at the codon level, resulting in false positive rates of 48%-82%. PRANK, which has been reported to outperform other aligners in simulations, performed best in our empirical study as well. Unfortunately, PRANK still had a high, and unacceptable for most applications, false positives rate of 50%-55%. We identify misannotations and indels, many of which appear to be located in disordered protein regions, as primary culprits for the high misalignment-related error levels and discuss possible workaround approaches to this apparently pervasive problem in genome-wide evolutionary analyses.
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Affiliation(s)
- Penka Markova-Raina
- Department of Biology, Stanford University, Stanford, California 94305, USA.
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Gotzek D, Robertson HM, Wurm Y, Shoemaker D. Odorant binding proteins of the red imported fire ant, Solenopsis invicta: an example of the problems facing the analysis of widely divergent proteins. PLoS One 2011; 6:e16289. [PMID: 21305009 PMCID: PMC3031547 DOI: 10.1371/journal.pone.0016289] [Citation(s) in RCA: 37] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2010] [Accepted: 12/10/2010] [Indexed: 11/18/2022] Open
Abstract
We describe the odorant binding proteins (OBPs) of the red imported fire ant, Solenopsis invicta, obtained from analyses of an EST library and separate 454 sequencing runs of two normalized cDNA libraries. We identified a total of 18 putative functional OBPs in this ant. A third of the fire ant OBPs are orthologs to honey bee OBPs. Another third of the OBPs belong to a lineage-specific expansion, which is a common feature of insect OBP evolution. Like other OBPs, the different fire ant OBPs share little sequence similarity (∼ 20%), rendering evolutionary analyses difficult. We discuss the resulting problems with sequence alignment, phylogenetic analysis, and tests of selection. As previously suggested, our results underscore the importance for careful exploration of the sensitivity to the effects of alignment methods for data comprising widely divergent sequences.
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Affiliation(s)
- Dietrich Gotzek
- Department of Ecology and Evolution, University of Lausanne, Lausanne, Switzerland.
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Kornobis E, Pálsson S, Sidorov DA, Holsinger JR, Kristjánsson BK. Molecular taxonomy and phylogenetic affinities of two groundwater amphipods, Crangonyx islandicus and Crymostygius thingvallensis, endemic to Iceland. Mol Phylogenet Evol 2010; 58:527-39. [PMID: 21195201 DOI: 10.1016/j.ympev.2010.12.010] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2010] [Revised: 12/17/2010] [Accepted: 12/20/2010] [Indexed: 11/16/2022]
Abstract
The amphipod superfamily Crangonyctoidea is distributed exclusively in freshwater habitats worldwide and is characteristic of subterranean habitats. Two members of the family, Crangonyx islandicus and Crymostygius thingvallensis, are endemic to Iceland and were recently discovered in groundwater underneath lava fields. Crangonyx islandicus belongs to a well-known genus with representatives both in North America and in Eurasia. Crymostygius thingvallensis defines a new family, Crymostygidae. Considering the incongruences observed recently between molecular and morphological taxonomy within subterranean species, we aim to assess the taxonomical status of the two species using molecular data. Additionally, the study contributes to the phylogenetic relationships among several crangonyctoidean species and specifically among species from four genera of the family Crangonyctidae. Given the available data we consider how the two Icelandic species could have colonized Iceland, by comparing geographical origin of the species with the phylogeny. Regions of two nuclear (18S and 28S rRNA) and two mitochondrial genes (16S rRNA and COI) for 20 different species of three families of the Crangonyctoidea were sequenced. Four different methods were used to align the RNA gene sequences and phylogenetic trees were constructed using bayesian and maximum likelihood analysis. The Crangonyctidae monophyly is supported. Crangonyx islandicus appeared more closely related to species from the Nearctic region. Crymostygius thingvallensis is clearly divergent from the other species of Crangonyctoidea. Crangonyx and Synurella genera are clearly polyphyletic and showed a geographical association, being split into a Nearctic and a Palearctic group. This research confirms that the studied species of Crangonyctidae share a common ancestor, which was probably widespread in the Northern hemisphere well before the break up of Laurasia. The Icelandic species are of particular interest since Iceland emerged after the separation of Eurasia and North America, is geographically isolated and has repeatedly been covered by glaciers during the Ice Age. The close relation between Crangonyx islandicus and North American species supports the hypothesis of the Trans-Atlantic land bridge between Greenland and Iceland which might have persisted until 6 million years ago. The status of the family Crymostygidae is supported, whereas Crangonyx islandicus might represent a new genus. As commonly observed in subterranean animals, molecular and morphological taxonomy led to different conclusions, probably due to convergent evolution of morphological traits. Our molecular analysis suggests that the family Crangonyctidae needs taxonomic revisions.
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Affiliation(s)
- Etienne Kornobis
- Department of Biology, University of Iceland, Reykjavik, Iceland.
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Pettengill JB, Neel MC. An evaluation of candidate plant DNA barcodes and assignment methods in diagnosing 29 species in the genus Agalinis (Orobanchaceae). AMERICAN JOURNAL OF BOTANY 2010; 97:1391-406. [PMID: 21616891 DOI: 10.3732/ajb.0900176] [Citation(s) in RCA: 37] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/16/2023]
Abstract
PREMISE OF THE STUDY DNA barcoding has been proposed as a useful technique within many disciplines (e.g., conservation biology and forensics) for determining the taxonomic identity of a sample based on nucleotide similarity to samples of known taxonomy. Application of DNA barcoding to plants has primarily focused on evaluating the success of candidate barcodes across a broad spectrum of evolutionary divergence. Less attention has been paid to evaluating performance when distinguishing congeners or to differential success of analytical techniques despite the fact that the practical application and utility of barcoding hinges on the ability to distinguish closely related species. • METHODS We tested the ability to distinguish among 92 samples representing 29 putative species in the genus Agalinis (Orobanchaceae) using 13 candidate barcodes and three analytical methods (i.e., threshold genetic distances, hierarchical tree-based, and diagnostic character differences). Due to questions regarding evolutionary distinctiveness of some taxa, we evaluated success under two taxonomic hypotheses. • KEY RESULTS The psbA-trnH and trnT-trnL barcodes in conjunction with the "best close match" distance-based method best met the objectives of DNA barcoding. Success was also a function of the taxonomy used. • CONCLUSIONS In addition to accurately identifying query sequences, our results showed that DNA barcoding is useful for detecting taxonomic uncertainty; determining whether erroneous taxonomy or incomplete lineage sorting is the cause requires additional information provided by traditional taxonomic approaches. The magnitude of differentiation within and among the Agalinis species sampled suggests that our results inform how DNA barcoding will perform among closely related species in other genera.
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Affiliation(s)
- James B Pettengill
- Behavior, Ecology, Evolution, and Systematics Graduate Program, 2174 Plant Sciences Building, University of Maryland College Park, College Park, Maryland 20742
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Molecular systematics: A synthesis of the common methods and the state of knowledge. Cell Mol Biol Lett 2010; 15:311-41. [PMID: 20213503 PMCID: PMC6275913 DOI: 10.2478/s11658-010-0010-8] [Citation(s) in RCA: 41] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2009] [Accepted: 03/01/2010] [Indexed: 11/21/2022] Open
Abstract
The comparative and evolutionary analysis of molecular data has allowed researchers to tackle biological questions that have long remained unresolved. The evolution of DNA and amino acid sequences can now be modeled accurately enough that the information conveyed can be used to reconstruct the past. The methods to infer phylogeny (the pattern of historical relationships among lineages of organisms and/or sequences) range from the simplest, based on parsimony, to more sophisticated and highly parametric ones based on likelihood and Bayesian approaches. In general, molecular systematics provides a powerful statistical framework for hypothesis testing and the estimation of evolutionary processes, including the estimation of divergence times among taxa. The field of molecular systematics has experienced a revolution in recent years, and, although there are still methodological problems and pitfalls, it has become an essential tool for the study of evolutionary patterns and processes at different levels of biological organization. This review aims to present a brief synthesis of the approaches and methodologies that are most widely used in the field of molecular systematics today, as well as indications of future trends and state-of-the-art approaches.
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Affiliation(s)
- David A. Morrison
- Section for Parasitology (SWEPAR), Swedish University of Agricultural Sciences, 751 89 Uppsala, Sweden
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