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Spirin S, Sigorskikh A, Efremov A, Penzar D, Karyagina A. PhyloBench: A Benchmark for Evaluating Phylogenetic Programs. Mol Biol Evol 2024; 41:msae084. [PMID: 38860506 PMCID: PMC11231946 DOI: 10.1093/molbev/msae084] [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: 11/17/2023] [Revised: 04/05/2024] [Accepted: 04/22/2024] [Indexed: 06/12/2024] Open
Abstract
Phylogenetic inference based on protein sequence alignment is a widely used procedure. Numerous phylogenetic algorithms have been developed, most of which have many parameters and options. Choosing a program, options, and parameters can be a nontrivial task. No benchmark for comparison of phylogenetic programs on real protein sequences was publicly available. We have developed PhyloBench, a benchmark for evaluating the quality of phylogenetic inference, and used it to test a number of popular phylogenetic programs. PhyloBench is based on natural, not simulated, protein sequences of orthologous evolutionary domains. The measure of accuracy of an inferred tree is its distance to the corresponding species tree. A number of tree-to-tree distance measures were tested. The most reliable results were obtained using the Robinson-Foulds distance. Our results confirmed recent findings that distance methods are more accurate than maximum likelihood (ML) and maximum parsimony. We tested the bayesian program MrBayes on natural protein sequences and found that, on our datasets, it performs better than ML, but worse than distance methods. Of the methods we tested, the Balanced Minimum Evolution method implemented in FastME yielded the best results on our material. Alignments and reference species trees are available at https://mouse.belozersky.msu.ru/tools/phylobench/ together with a web-interface that allows for a semi-automatic comparison of a user's method with a number of popular programs.
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Affiliation(s)
- Sergey Spirin
- Belozersky Institute, Lomonosov Moscow State University, Moscow, Russia
- Higher School of Economics, Moscow, Russia
| | - Andrey Sigorskikh
- Faculty of Bioengineering and Bioinformatics, Lomonosov Moscow State University, Moscow, Russia
| | - Aleksei Efremov
- Faculty of Bioengineering and Bioinformatics, Lomonosov Moscow State University, Moscow, Russia
| | - Dmitry Penzar
- Faculty of Bioengineering and Bioinformatics, Lomonosov Moscow State University, Moscow, Russia
- Artificial Intelligence Research Institute, Moscow, Russia
| | - Anna Karyagina
- Belozersky Institute, Lomonosov Moscow State University, Moscow, Russia
- Gamaleya Center of Epidemiology and Microbiology, Moscow, Russia
- Institute of Agricultural Biotechnology, Moscow, Russia
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2
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Kan S, Liao X, Lan L, Kong J, Wang J, Nie L, Zou J, An H, Wu Z. Cytonuclear Interactions and Subgenome Dominance Shape the Evolution of Organelle-Targeted Genes in the Brassica Triangle of U. Mol Biol Evol 2024; 41:msae043. [PMID: 38391484 PMCID: PMC10919925 DOI: 10.1093/molbev/msae043] [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: 10/24/2023] [Revised: 01/24/2024] [Accepted: 02/16/2024] [Indexed: 02/24/2024] Open
Abstract
The interaction and coevolution between nuclear and cytoplasmic genomes are one of the fundamental hallmarks of eukaryotic genome evolution and, 2 billion yr later, are still major contributors to the formation of new species. Although many studies have investigated the role of cytonuclear interactions following allopolyploidization, the relative magnitude of the effect of subgenome dominance versus cytonuclear interaction on genome evolution remains unclear. The Brassica triangle of U features 3 diploid species that together have formed 3 separate allotetraploid species on similar evolutionary timescales, providing an ideal system for understanding the contribution of the cytoplasmic donor to hybrid polyploid. Here, we investigated the evolutionary pattern of organelle-targeted genes in Brassica carinata (BBCC) and 2 varieties of Brassica juncea (AABB) at the whole-genome level, with particular focus on cytonuclear enzyme complexes. We found partial evidence that plastid-targeted genes experience selection to match plastid genomes, but no obvious corresponding signal in mitochondria-targeted genes from these 2 separately formed allopolyploids. Interestingly, selection acting on plastid genomes always reduced the retention rate of plastid-targeted genes encoded by the B subgenome, regardless of whether the Brassica nigra (BB) subgenome was contributed by the paternal or maternal progenitor. More broadly, this study illustrates the distinct selective pressures experienced by plastid- and mitochondria-targeted genes, despite a shared pattern of inheritance and natural history. Our study also highlights an important role for subgenome dominance in allopolyploid genome evolution, even in genes whose function depends on separately inherited molecules.
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Affiliation(s)
- Shenglong Kan
- Marine College, Shandong University, Weihai 264209, China
- Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Key Laboratory of Synthetic Biology, Laboratory of the Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen 518120, China
| | - Xuezhu Liao
- Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Key Laboratory of Synthetic Biology, Laboratory of the Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen 518120, China
| | - Lan Lan
- Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Key Laboratory of Synthetic Biology, Laboratory of the Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen 518120, China
- College of Science, Health, Engineering and Education, Murdoch University, Murdoch, 6150 Western Australia, Australia
| | - Jiali Kong
- Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Key Laboratory of Synthetic Biology, Laboratory of the Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen 518120, China
- State Key Laboratory of Crop Stress Adaptation and Improvement, School of Life Sciences, Henan University, Kaifeng 475004, China
| | - Jie Wang
- Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Key Laboratory of Synthetic Biology, Laboratory of the Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen 518120, China
- College of Science, Health, Engineering and Education, Murdoch University, Murdoch, 6150 Western Australia, Australia
| | - Liyun Nie
- Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Key Laboratory of Synthetic Biology, Laboratory of the Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen 518120, China
| | - Jun Zou
- National Key Laboratory of Crop Genetic Improvement, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan 430070, China
| | - Hong An
- Bioinformatics and Analytics Core, University of Missouri, Columbia, MO, USA
| | - Zhiqiang Wu
- Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Key Laboratory of Synthetic Biology, Laboratory of the Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen 518120, China
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3
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Feng YY, Du H, Huang KY, Ran JH, Wang XQ. Reciprocal expression of MADS-box genes and DNA methylation reconfiguration initiate bisexual cones in spruce. Commun Biol 2024; 7:114. [PMID: 38242964 PMCID: PMC10799047 DOI: 10.1038/s42003-024-05786-6] [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: 07/27/2023] [Accepted: 01/05/2024] [Indexed: 01/21/2024] Open
Abstract
The naturally occurring bisexual cone of gymnosperms has long been considered a possible intermediate stage in the origin of flowers, but the mechanisms governing bisexual cone formation remain largely elusive. Here, we employed transcriptomic and DNA methylomic analyses, together with hormone measurement, to investigate the molecular mechanisms underlying bisexual cone development in the conifer Picea crassifolia. Our study reveals a "bisexual" expression profile in bisexual cones, especially in expression patterns of B-class, C-class and LEAFY genes, supporting the out of male model. GGM7 could be essential for initiating bisexual cones. DNA methylation reconfiguration in bisexual cones affects the expression of key genes in cone development, including PcDAL12, PcDAL10, PcNEEDLY, and PcHDG5. Auxin likely plays an important role in the development of female structures of bisexual cones. This study unveils the potential mechanisms responsible for bisexual cone formation in conifers and may shed light on the evolution of bisexuality.
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Affiliation(s)
- Yuan-Yuan Feng
- State Key Laboratory of Plant Diversity and Specialty Crops, Institute of Botany, Chinese Academy of Sciences, Beijing, 100093, China
- China National Botanical Garden, Beijing, 100093, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Hong Du
- State Key Laboratory of Plant Diversity and Specialty Crops, Institute of Botany, Chinese Academy of Sciences, Beijing, 100093, China
- China National Botanical Garden, Beijing, 100093, China
| | - Kai-Yuan Huang
- State Key Laboratory of Plant Diversity and Specialty Crops, Institute of Botany, Chinese Academy of Sciences, Beijing, 100093, China
- China National Botanical Garden, Beijing, 100093, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Jin-Hua Ran
- State Key Laboratory of Plant Diversity and Specialty Crops, Institute of Botany, Chinese Academy of Sciences, Beijing, 100093, China.
- China National Botanical Garden, Beijing, 100093, China.
- University of Chinese Academy of Sciences, Beijing, 100049, China.
| | - Xiao-Quan Wang
- State Key Laboratory of Plant Diversity and Specialty Crops, Institute of Botany, Chinese Academy of Sciences, Beijing, 100093, China.
- China National Botanical Garden, Beijing, 100093, China.
- University of Chinese Academy of Sciences, Beijing, 100049, China.
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4
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Wiberg RAW, Viktorin G, Schärer L. Mating strategy predicts gene presence/absence patterns in a genus of simultaneously hermaphroditic flatworms. Evolution 2022; 76:3054-3066. [PMID: 36199200 PMCID: PMC10092323 DOI: 10.1111/evo.14635] [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: 05/16/2022] [Accepted: 09/28/2022] [Indexed: 01/22/2023]
Abstract
Gene repertoire turnover is a characteristic of genome evolution. However, we lack well-replicated analyses of presence/absence patterns associated with different selection contexts. Here, we study ∼100 transcriptome assemblies across Macrostomum, a genus of simultaneously hermaphroditic flatworms exhibiting multiple convergent shifts in mating strategy and associated reproductive morphologies. Many species mate reciprocally, with partners donating and receiving sperm at the same time. Other species convergently evolved to mate by hypodermic injection of sperm into the partner. We find that for orthologous transcripts annotated as expressed in the body region containing the testes, sequences from hypodermically inseminating species diverge more rapidly from the model species, Macrostomum lignano, and have a lower probability of being observed in other species. For other annotation categories, simpler models with a constant rate of similarity decay with increasing genetic distance from M. lignano match the observed patterns well. Thus, faster rates of sequence evolution for hypodermically inseminating species in testis-region genes result in higher rates of homology detection failure, yielding a signal of rapid evolution in sequence presence/absence patterns. Our results highlight the utility of considering appropriate null models for unobserved genes, as well as associating patterns of gene presence/absence with replicated evolutionary events in a phylogenetic context.
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Affiliation(s)
- R Axel W Wiberg
- Zoological Institute, Department of Environmental Sciences, University of Basel, Basel, CH-4051, Switzerland.,Evolutionary Biology, Department of Ecology and Genetics, Evolutionary Biology Centre, Uppsala University, Uppsala, SE-75236, Sweden
| | - Gudrun Viktorin
- Zoological Institute, Department of Environmental Sciences, University of Basel, Basel, CH-4051, Switzerland
| | - Lukas Schärer
- Zoological Institute, Department of Environmental Sciences, University of Basel, Basel, CH-4051, Switzerland
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5
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Phylogeny and evolution of Cupressaceae: Updates on intergeneric relationships and new insights on ancient intergeneric hybridization. Mol Phylogenet Evol 2022; 177:107606. [PMID: 35952837 DOI: 10.1016/j.ympev.2022.107606] [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: 02/14/2022] [Revised: 07/24/2022] [Accepted: 08/04/2022] [Indexed: 11/24/2022]
Abstract
After the merger of the former Taxodiaceae and Cupressaceae s.s., currently the conifer family Cupressaceae (sensu lato) comprises seven subfamilies and 32 genera, most of which are important components of temperate and mountainous forests. With the exception of a recently published genus-level phylogeny of gymnosperms inferred from sequence analysis of 790 orthologs, previous phylogenetic studies of Cupressaceae were based mainly on morphological characters or a few molecular markers, and did not completely resolve the intergeneric relationships. In this study, we reconstructed a robust and well-resolved phylogeny of Cupressaceae represented by all 32 genera, using 1944 genes (Orthogroups) generated from transcriptome sequencing. Reticulate evolution analyses detected a possible ancient hybridization that occurred between ancestors of two subclades of Cupressoideae, including Microbiota-Platycladus-Tetraclinis (MPT) and Juniperus-Cupressus-Hesperocyparis-Callitropsis-Xanthocyparis (JCHCX), although both concatenation and coalescent trees are highly supported. Moreover, divergence time estimation and ancestral area reconstruction indicate that Cupressaceae very likely originated in Asia in the Triassic, and geographic isolation caused by continental separation drove the vicariant evolution of the two subfamilies Cupressoideae and Callitroideae in the northern and southern hemispheres, respectively. Evolutionary analyses of some morphological characters suggest that helically arranged linear-acicular leaves and imbricate bract-scale complexes represent ancestral states, and the shift from linear-acicular leaves to scale-like leaves was associated with the shift from helical to decussate arrangement. Our study sheds new light on phylogeny and evolutionary history of Cupressaceae, and strongly suggests that both dichotomous phylogenetic and reticulate evolution analyses be conducted in phylogenomic studies.
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6
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Mito-nuclear coevolution and phylogenetic artifacts: the case of bivalve mollusks. Sci Rep 2022; 12:11040. [PMID: 35773462 PMCID: PMC9247169 DOI: 10.1038/s41598-022-15076-y] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2022] [Accepted: 06/17/2022] [Indexed: 11/08/2022] Open
Abstract
Mito-nuclear phylogenetic discordance in Bivalvia is well known. In particular, the monophyly of Amarsipobranchia (Heterodonta + Pteriomorphia), retrieved from mitochondrial markers, contrasts with the monophyly of Heteroconchia (Heterodonta + Palaeoheterodonta), retrieved from nuclear markers. However, since oxidative phosphorylation nuclear markers support the Amarsipobranchia hypothesis instead of the Heteroconchia one, interacting subunits of the mitochondrial complexes ought to share the same phylogenetic signal notwithstanding the genomic source, which is different from the signal obtained from other nuclear markers. This may be a clue of coevolution between nuclear and mitochondrial genes. In this work we inferred the phylogenetic signal from mitochondrial and nuclear oxidative phosphorylation markers exploiting different phylogenetic approaches and added two more datasets for comparison: genes of the glycolytic pathway and genes related to the biogenesis of regulative small noncoding RNAs. All trees inferred from mitochondrial and nuclear subunits of the mitochondrial complexes support the monophyly of Amarsipobranchia, regardless of the phylogenetic pipeline. However, not every single marker agrees with this topology: this is clearly visible in nuclear subunits that do not directly interact with the mitochondrial counterparts. Overall, our data support the hypothesis of a coevolution between nuclear and mitochondrial genes for the oxidative phosphorylation. Moreover, we suggest a relationship between mitochondrial topology and different nucleotide composition between clades, which could be associated to the highly variable gene arrangement in Bivalvia.
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7
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Cerca J, Petersen B, Lazaro-Guevara JM, Rivera-Colón A, Birkeland S, Vizueta J, Li S, Li Q, Loureiro J, Kosawang C, Díaz PJ, Rivas-Torres G, Fernández-Mazuecos M, Vargas P, McCauley RA, Petersen G, Santos-Bay L, Wales N, Catchen JM, Machado D, Nowak MD, Suh A, Sinha NR, Nielsen LR, Seberg O, Gilbert MTP, Leebens-Mack JH, Rieseberg LH, Martin MD. The genomic basis of the plant island syndrome in Darwin's giant daisies. Nat Commun 2022; 13:3729. [PMID: 35764640 PMCID: PMC9240058 DOI: 10.1038/s41467-022-31280-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2021] [Accepted: 06/09/2022] [Indexed: 12/04/2022] Open
Abstract
The repeated, rapid and often pronounced patterns of evolutionary divergence observed in insular plants, or the ‘plant island syndrome’, include changes in leaf phenotypes, growth, as well as the acquisition of a perennial lifestyle. Here, we sequence and describe the genome of the critically endangered, Galápagos-endemic species Scalesia atractyloides Arnot., obtaining a chromosome-resolved, 3.2-Gbp assembly containing 43,093 candidate gene models. Using a combination of fossil transposable elements, k-mer spectra analyses and orthologue assignment, we identify the two ancestral genomes, and date their divergence and the polyploidization event, concluding that the ancestor of all extant Scalesia species was an allotetraploid. There are a comparable number of genes and transposable elements across the two subgenomes, and while their synteny has been mostly conserved, we find multiple inversions that may have facilitated adaptation. We identify clear signatures of selection across genes associated with vascular development, growth, adaptation to salinity and flowering time, thus finding compelling evidence for a genomic basis of the island syndrome in one of Darwin’s giant daisies. Many island plant species share a syndrome of characteristic phenotype and life history. Cerca et al. find the genomic basis of the plant island syndrome in one of Darwin’s giant daisies, while separating ancestral genomes in a chromosome-resolved polyploid assembly.
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Affiliation(s)
- José Cerca
- Department of Natural History, NTNU University Museum, Norwegian University of Science and Technology, Trondheim, Norway.
| | - Bent Petersen
- Centre for Evolutionary Hologenomics, The GLOBE Institute, Faculty of Health and Medical Sciences, University of Copenhagen, Øster Farimagsgade 5, 1353, Copenhagen, Denmark.,Centre of Excellence for Omics-Driven Computational Biodiscovery, Faculty of Applied Sciences, AIMST University, Kedah, Malaysia
| | - José Miguel Lazaro-Guevara
- Department of Botany and Biodiversity Research Centre, University of British Columbia, Vancouver, BC, V6T 1Z4, Canada
| | - Angel Rivera-Colón
- Department of Evolution, Ecology, and Behavior, University of Illinois at Urbana-Champaign, Champaign, IL, USA
| | - Siri Birkeland
- Department of Chemistry, Biotechnology and Food Science, Norwegian University of Life Sciences, Ås, Norway.,Natural History Museum, University of Oslo, Oslo, Norway
| | - Joel Vizueta
- Villum Centre for Biodiversity Genomics, Section for Ecology and Evolution, Department of Biology, University of Copenhagen, Universitetsparken 15, 2100, Copenhagen, Denmark
| | - Siyu Li
- Department of Plant Biology, University of California, Davis, Davis, CA, 95616, USA
| | - Qionghou Li
- Department of Botany and Biodiversity Research Centre, University of British Columbia, Vancouver, BC, V6T 1Z4, Canada
| | - João Loureiro
- Centre for Functional Ecology, Department of Life Sciences, University of Coimbra, Calçada Martim de Freitas, 3000-095, Coimbra, Portugal
| | - Chatchai Kosawang
- Department of Geosciences and Natural Resource Management, University of Copenhagen, Rolighedsvej 23, 1958, Frederiksberg C, Denmark
| | - Patricia Jaramillo Díaz
- Estación Científica Charles Darwin, Fundación Charles Darwin, Santa Cruz, Galápagos, Ecuador.,Department of Botany and Plant Physiology, University of Malaga, Malaga, Spain
| | - Gonzalo Rivas-Torres
- Colegio de Ciencias Biológicas y Ambientales COCIBA & Extensión Galápagos, Universidad San Francisco de Quito USFQ, Quito, 170901, Ecuador.,Galapagos Science Center, USFQ, UNC Chapel Hill, San Cristobal, Galapagos, Ecuador.,Estación de Biodiversidad Tiputini, Colegio de Ciencias Biológicas y Ambientales, Universidad San Francisco de Quito USFQ, Quito, Ecuador.,Courtesy Faculty, Department of Wildlife Ecology and Conservation, University of Florida, 110 Newins-Ziegler Hall, Gainesville, FL, 32611, USA
| | | | - Pablo Vargas
- Departamento de Biodiversidad y Conservación, Real Jardín Botánico (RJB-CSIC), Plaza de Murillo 2, 28014, Madrid, Spain
| | - Ross A McCauley
- Department of Biology, Fort Lewis College, Durango, CO, 81301, USA
| | - Gitte Petersen
- Department of Ecology, Environment and Plant Sciences, Stockholm University, SE-106 91, Stockholm, Sweden
| | - Luisa Santos-Bay
- Centre for Evolutionary Hologenomics, The GLOBE Institute, Faculty of Health and Medical Sciences, University of Copenhagen, Øster Farimagsgade 5, 1353, Copenhagen, Denmark
| | - Nathan Wales
- Department of Archaeology, University of York, York, UK
| | - Julian M Catchen
- Department of Evolution, Ecology, and Behavior, University of Illinois at Urbana-Champaign, Champaign, IL, USA
| | - Daniel Machado
- Department of Biotechnology and Food Science, Norwegian University of Science and Technology, Trondheim, 7491, Norway
| | | | - Alexander Suh
- School of Biological Sciences, University of East Anglia, Norwich Research Park, NR4 7TU, Norwich, UK.,Department of Organismal Biology, Evolutionary Biology Centre (EBC), Science for Life Laboratory, Uppsala University, 75236, Uppsala, Sweden
| | - Neelima R Sinha
- Department of Plant Biology, University of California, Davis, Davis, CA, 95616, USA
| | - Lene R Nielsen
- Department of Geosciences and Natural Resource Management, University of Copenhagen, Rolighedsvej 23, 1958, Frederiksberg C, Denmark
| | - Ole Seberg
- The Natural History Museum of Denmark, University of Copenhagen, Copenhagen, Denmark
| | - M Thomas P Gilbert
- Department of Natural History, NTNU University Museum, Norwegian University of Science and Technology, Trondheim, Norway.,Centre for Evolutionary Hologenomics, The GLOBE Institute, Faculty of Health and Medical Sciences, University of Copenhagen, Øster Farimagsgade 5, 1353, Copenhagen, Denmark
| | | | - Loren H Rieseberg
- Department of Botany and Biodiversity Research Centre, University of British Columbia, Vancouver, BC, V6T 1Z4, Canada
| | - Michael D Martin
- Department of Natural History, NTNU University Museum, Norwegian University of Science and Technology, Trondheim, Norway.
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Cuevas-Caballé C, Ferrer Obiol J, Vizueta J, Genovart M, Gonzalez-Solís J, Riutort M, Rozas J. The First Genome of the Balearic Shearwater (Puffinus mauretanicus) Provides a Valuable Resource for Conservation Genomics and Sheds Light on Adaptation to a Pelagic lifestyle. Genome Biol Evol 2022; 14:evac067. [PMID: 35524941 PMCID: PMC9117697 DOI: 10.1093/gbe/evac067] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 05/03/2022] [Indexed: 11/27/2022] Open
Abstract
The Balearic shearwater (Puffinus mauretanicus) is the most threatened seabird in Europe and a member of the most speciose group of pelagic seabirds, the order Procellariiformes, which exhibit extreme adaptations to a pelagic lifestyle. The fossil record suggests that human colonisation of the Balearic Islands resulted in a sharp decrease of the Balearic shearwater population size. Currently, populations of the species continue to be decimated mainly due to predation by introduced mammals and bycatch in longline fisheries, with some studies predicting its extinction by 2070. Here, using a combination of short and long reads, we generate the first high-quality reference genome for the Balearic shearwater, with a completeness amongst the highest across available avian species. We used this reference genome to study critical aspects relevant to the conservation status of the species and to gain insights into the adaptation to a pelagic lifestyle of the order Procellariiformes. We detected relatively high levels of genome-wide heterozygosity in the Balearic shearwater despite its reduced population size. However, the reconstruction of its historical demography uncovered an abrupt population decline potentially linked to a reduction of the neritic zone during the Penultimate Glacial Period (∼194-135 ka). Comparative genomics analyses uncover a set of candidate genes that may have played an important role into the adaptation to a pelagic lifestyle of Procellariiformes, including those for the enhancement of fishing capabilities, night vision, and the development of natriuresis. The reference genome obtained will be the crucial in the future development of genetic tools in conservation efforts for this Critically Endangered species.
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Affiliation(s)
- Cristian Cuevas-Caballé
- Departament de Genètica, Microbiologia i Estadística, Facultat de Biologia & Institut de Recerca de la Biodiversitat (IRBio), Universitat de Barcelona, Spain
| | - Joan Ferrer Obiol
- Departament de Genètica, Microbiologia i Estadística, Facultat de Biologia & Institut de Recerca de la Biodiversitat (IRBio), Universitat de Barcelona, Spain
- Department of Environmental Science and Policy, Università degli Studi di Milano (UniMi), Milan, Italy
| | - Joel Vizueta
- Departament de Genètica, Microbiologia i Estadística, Facultat de Biologia & Institut de Recerca de la Biodiversitat (IRBio), Universitat de Barcelona, Spain
- Villum Centre for Biodiversity Genomics, Section for Ecology and Evolution, Department of Biology, University of Copenhagen, Copenhagen, Denmark
| | - Meritxell Genovart
- Mediterranean Institute for Advanced Studies (IMEDEA), CSIC-UIB & Centre for Advanced Studies of Blanes (CEAB), CSIC, Esporles, Spain
| | - Jacob Gonzalez-Solís
- Departament de Biologia Evolutiva, Ecologia i Ciències Ambientals, Facultat de Biologia & Institut de Recerca de la Biodiversitat (IRBio), Universitat de Barcelona, Barcelona, Spain
| | - Marta Riutort
- Departament de Genètica, Microbiologia i Estadística, Facultat de Biologia & Institut de Recerca de la Biodiversitat (IRBio), Universitat de Barcelona, Spain
| | - Julio Rozas
- Departament de Genètica, Microbiologia i Estadística, Facultat de Biologia & Institut de Recerca de la Biodiversitat (IRBio), Universitat de Barcelona, Spain
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9
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Tumescheit C, Firth AE, Brown K. CIAlign: A highly customisable command line tool to clean, interpret and visualise multiple sequence alignments. PeerJ 2022; 10:e12983. [PMID: 35310163 PMCID: PMC8932311 DOI: 10.7717/peerj.12983] [Citation(s) in RCA: 21] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2021] [Accepted: 02/01/2022] [Indexed: 01/11/2023] Open
Abstract
Background Throughout biology, multiple sequence alignments (MSAs) form the basis of much investigation into biological features and relationships. These alignments are at the heart of many bioinformatics analyses. However, sequences in MSAs are often incomplete or very divergent, which can lead to poor alignment and large gaps. This slows down computation and can impact conclusions without being biologically relevant. Cleaning the alignment by removing common issues such as gaps, divergent sequences, large insertions and deletions and poorly aligned sequence ends can substantially improve analyses. Manual editing of MSAs is very widespread but is time-consuming and difficult to reproduce. Results We present a comprehensive, user-friendly MSA trimming tool with multiple visualisation options. Our highly customisable command line tool aims to give intervention power to the user by offering various options, and outputs graphical representations of the alignment before and after processing to give the user a clear overview of what has been removed. The main functionalities of the tool include removing regions of low coverage due to insertions, removing gaps, cropping poorly aligned sequence ends and removing sequences that are too divergent or too short. The thresholds for each function can be specified by the user and parameters can be adjusted to each individual MSA. CIAlign is designed with an emphasis on solving specific and common alignment problems and on providing transparency to the user. Conclusion CIAlign effectively removes problematic regions and sequences from MSAs and provides novel visualisation options. This tool can be used to fine-tune alignments for further analysis and processing. The tool is aimed at anyone who wishes to automatically clean up parts of an MSA and those requiring a new, accessible way of visualising large MSAs.
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Affiliation(s)
| | - Andrew E. Firth
- Department of Pathology, University of Cambridge, Cambridge, United Kingdom
| | - Katherine Brown
- Department of Pathology, University of Cambridge, Cambridge, United Kingdom
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10
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Wiberg RAW, Brand JN, Schärer L. Faster Rates of Molecular Sequence Evolution in Reproduction-Related Genes and in Species with Hypodermic Sperm Morphologies. Mol Biol Evol 2021; 38:5685-5703. [PMID: 34534329 PMCID: PMC8662610 DOI: 10.1093/molbev/msab276] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022] Open
Abstract
Sexual selection drives the evolution of many striking behaviors and morphologies and should leave signatures of selection at loci underlying these phenotypes. However, although loci thought to be under sexual selection often evolve rapidly, few studies have contrasted rates of molecular sequence evolution at such loci across lineages with different sexual selection contexts. Furthermore, work has focused on separate sexed animals, neglecting alternative sexual systems. We investigate rates of molecular sequence evolution in hermaphroditic flatworms of the genus Macrostomum. Specifically, we compare species that exhibit contrasting sperm morphologies, strongly associated with multiple convergent shifts in the mating strategy, reflecting different sexual selection contexts. Species donating and receiving sperm in every mating have sperm with bristles, likely to prevent sperm removal. Meanwhile, species that hypodermically inject sperm lack bristles, potentially as an adaptation to the environment experienced by hypodermic sperm. Combining functional annotations from the model, Macrostomum lignano, with transcriptomes from 93 congeners, we find genus-wide faster sequence evolution in reproduction-related versus ubiquitously expressed genes, consistent with stronger sexual selection on the former. Additionally, species with hypodermic sperm morphologies had elevated molecular sequence evolution, regardless of a gene's functional annotation. These genome-wide patterns suggest reduced selection efficiency following shifts to hypodermic mating, possibly due to higher selfing rates in these species. Moreover, we find little evidence for convergent amino acid changes across species. Our work not only shows that reproduction-related genes evolve rapidly also in hermaphroditic animals, but also that well-replicated contrasts of different sexual selection contexts can reveal underappreciated genome-wide effects.
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Affiliation(s)
- R Axel W Wiberg
- Department of Environmental Sciences, Zoological Institute, University of Basel, Basel, Switzerland
| | - Jeremias N Brand
- Department of Environmental Sciences, Zoological Institute, University of Basel, Basel, Switzerland
| | - Lukas Schärer
- Department of Environmental Sciences, Zoological Institute, University of Basel, Basel, Switzerland
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11
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Baker CM, Buckman-Young RS, Costa CS, Giribet G. Phylogenomic Analysis of Velvet Worms (Onychophora) Uncovers an Evolutionary Radiation in the Neotropics. Mol Biol Evol 2021; 38:5391-5404. [PMID: 34427671 PMCID: PMC8662635 DOI: 10.1093/molbev/msab251] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2023] Open
Abstract
Onychophora ("velvet worms") are charismatic soil invertebrates known for their status as a "living fossil," their phylogenetic affiliation to arthropods, and their distinctive biogeographic patterns. However, several aspects of their internal phylogenetic relationships remain unresolved, limiting our understanding of the group's evolutionary history, particularly with regard to changes in reproductive mode and dispersal ability. To address these gaps, we used RNA sequencing and phylogenomic analysis of transcriptomes to reconstruct the evolutionary relationships and infer divergence times within the phylum. We recovered a fully resolved and well-supported phylogeny for the circum-Antarctic family Peripatopsidae, which retains signals of Gondwanan vicariance and showcases the evolutionary lability of reproductive mode in the family. Within the Neotropical clade of Peripatidae, though, we found that amino acid-translated sequence data masked nearly all phylogenetic signal, resulting in highly unstable and poorly supported relationships. Analyses using nucleotide sequence data were able to resolve many more relationships, though we still saw discordant phylogenetic signal between genes, probably indicative of a rapid, mid-Cretaceous radiation in the group. Finally, we hypothesize that the unique reproductive mode of placentotrophic viviparity found in all Neotropical peripatids may have facilitated the multiple inferred instances of over-water dispersal and establishment on oceanic islands.
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Affiliation(s)
- Caitlin M Baker
- Museum of Comparative Zoology, Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, MA, USA
| | - Rebecca S Buckman-Young
- Museum of Comparative Zoology, Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, MA, USA
| | - Cristiano S Costa
- Laboratório de Sistemática e Taxonomia de Artrópodes Terrestres, Departamento de Biologia e Zoologia, Instituto de Biociências, Universidade Federal de Mato Grosso, Cuiabá, Brazil
| | - Gonzalo Giribet
- Museum of Comparative Zoology, Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, MA, USA
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12
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Chen L, Jin WT, Liu XQ, Wang XQ. New insights into the phylogeny and evolution of Podocarpaceae inferred from transcriptomic data. Mol Phylogenet Evol 2021; 166:107341. [PMID: 34740782 DOI: 10.1016/j.ympev.2021.107341] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2021] [Revised: 10/28/2021] [Accepted: 10/29/2021] [Indexed: 12/14/2022]
Abstract
Phylogenies of an increasing number of taxa have been resolved with the development of phylogenomics. However, the intergeneric relationships of Podocarpaceae, the second largest family of conifers comprising 19 genera and approximately 187 species mainly distributed in the Southern Hemisphere, have not been well disentangled in previous studies, even when genome-scale data sets were used. Here we used 993 nuclear orthologous groups (OGs) and 54 chloroplast OGs (genes), which were generated from 47 transcriptomes of Podocarpaceae and its sister group Araucariaceae, to reconstruct the phylogeny of Podocarpaceae. Our study completely resolved the intergeneric relationships of Podocarpaceae represented by all extant genera and revealed that topological conflicts among phylogenetic trees could be attributed to synonymous substitutions. Moreover, we found that two morphological traits, fleshy seed cones and flattened leaves, might be important for Podocarpaceae to adapt to angiosperm-dominated forests and thus could have promoted its species diversification. In addition, our results indicate that Podocarpaceae originated in Gondwana in the late Triassic and both vicariance and dispersal have contributed to its current biogeographic patterns. Our study provides the first robust transcriptome-based phylogeny of Podocarpaceae, an evolutionary framework important for future studies of this family.
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Affiliation(s)
- Luo Chen
- 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
| | - Wei-Tao Jin
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, Beijing 100093, China
| | - Xin-Quan Liu
- 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
| | - Xiao-Quan Wang
- 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.
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13
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Large-scale phylogenomics of the genus Macrostomum (Platyhelminthes) reveals cryptic diversity and novel sexual traits. Mol Phylogenet Evol 2021; 166:107296. [PMID: 34438051 DOI: 10.1016/j.ympev.2021.107296] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2021] [Revised: 07/01/2021] [Accepted: 08/19/2021] [Indexed: 02/07/2023]
Abstract
Free-living flatworms of the genus Macrostomum are small and transparent animals, representing attractive study organisms for a broad range of topics in evolutionary, developmental, and molecular biology. The genus includes the model organism M. lignano for which extensive molecular resources are available, and recently there is a growing interest in extending work to additional species in the genus. These endeavours are currently hindered because, even though >200 Macrostomum species have been taxonomically described, molecular phylogenetic information and geographic sampling remain limited. We report on a global sampling campaign aimed at increasing taxon sampling and geographic representation of the genus. Specifically, we use extensive transcriptome and single-locus data to generate phylogenomic hypotheses including 145 species. Across different phylogenetic methods and alignments used, we identify several consistent clades, while their exact grouping is less clear, possibly due to a radiation early in Macrostomum evolution. Moreover, we uncover a large undescribed diversity, with 94 of the studied species likely being new to science, and we identify multiple novel morphological traits. Furthermore, we identify cryptic speciation in a taxonomically challenging assemblage of species, suggesting that the use of molecular markers is a prerequisite for future work, and we describe the distribution of putative synapomorphies and suggest taxonomic revisions based on our finding. Our large-scale phylogenomic dataset now provides a robust foundation for comparative analyses of morphological, behavioural and molecular evolution in this genus.
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14
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Li JT, Lu JL, Wang HY, Fang Z, Wang XJ, Feng SW, Wang Z, Yuan T, Zhang SC, Ou SN, Yang XD, Wu ZH, Du XD, Tang LY, Liao B, Shu WS, Jia P, Liang JL. A comprehensive synthesis unveils the mysteries of phosphate-solubilizing microbes. Biol Rev Camb Philos Soc 2021; 96:2771-2793. [PMID: 34288351 PMCID: PMC9291587 DOI: 10.1111/brv.12779] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2020] [Revised: 06/30/2021] [Accepted: 07/02/2021] [Indexed: 12/22/2022]
Abstract
Phosphate-solubilizing microbes (PSMs) drive the biogeochemical cycling of phosphorus (P) and hold promise for sustainable agriculture. However, their global distribution, overall diversity and application potential remain unknown. Here, we present the first synthesis of their biogeography, diversity and utility, employing data from 399 papers published between 1981 and 2017, the results of a nationwide field survey in China consisting of 367 soil samples, and a genetic analysis of 12986 genome-sequenced prokaryotic strains. We show that at continental to global scales, the population density of PSMs in environmental samples is correlated with total P rather than pH. Remarkably, positive relationships exist between the population density of soil PSMs and available P, nitrate-nitrogen and dissolved organic carbon in soil, reflecting functional couplings between PSMs and microbes driving biogeochemical cycles of nitrogen and carbon. More than 2704 strains affiliated with at least nine archaeal, 88 fungal and 336 bacterial species were reported as PSMs. Only 2.59% of these strains have been tested for their efficiencies in improving crop growth or yield under field conditions, providing evidence that PSMs are more likely to exert positive effects on wheat growing in alkaline P-deficient soils. Our systematic genetic analysis reveals five promising PSM genera deserving much more attention.
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Affiliation(s)
- Jin-Tian Li
- Institute of Ecological Science, Guangzhou Key Laboratory of Subtropical Biodiversity and Biomonitoring, Guangdong Provincial Key Laboratory of Biotechnology for Plant Development, School of Life Sciences, South China Normal University, Guangzhou, 510631, PR China.,School of Life Sciences, Sun Yat-sen University, Guangzhou, 510275, PR China
| | - Jing-Li Lu
- Institute of Ecological Science, Guangzhou Key Laboratory of Subtropical Biodiversity and Biomonitoring, Guangdong Provincial Key Laboratory of Biotechnology for Plant Development, School of Life Sciences, South China Normal University, Guangzhou, 510631, PR China
| | - Hong-Yu Wang
- Institute of Ecological Science, Guangzhou Key Laboratory of Subtropical Biodiversity and Biomonitoring, Guangdong Provincial Key Laboratory of Biotechnology for Plant Development, School of Life Sciences, South China Normal University, Guangzhou, 510631, PR China
| | - Zhou Fang
- Institute of Ecological Science, Guangzhou Key Laboratory of Subtropical Biodiversity and Biomonitoring, Guangdong Provincial Key Laboratory of Biotechnology for Plant Development, School of Life Sciences, South China Normal University, Guangzhou, 510631, PR China
| | - Xiao-Juan Wang
- Institute of Ecological Science, Guangzhou Key Laboratory of Subtropical Biodiversity and Biomonitoring, Guangdong Provincial Key Laboratory of Biotechnology for Plant Development, School of Life Sciences, South China Normal University, Guangzhou, 510631, PR China
| | - Shi-Wei Feng
- Institute of Ecological Science, Guangzhou Key Laboratory of Subtropical Biodiversity and Biomonitoring, Guangdong Provincial Key Laboratory of Biotechnology for Plant Development, School of Life Sciences, South China Normal University, Guangzhou, 510631, PR China
| | - Zhang Wang
- Institute of Ecological Science, Guangzhou Key Laboratory of Subtropical Biodiversity and Biomonitoring, Guangdong Provincial Key Laboratory of Biotechnology for Plant Development, School of Life Sciences, South China Normal University, Guangzhou, 510631, PR China
| | - Ting Yuan
- School of Life Sciences, Sun Yat-sen University, Guangzhou, 510275, PR China
| | - Sheng-Chang Zhang
- School of Life Sciences, Sun Yat-sen University, Guangzhou, 510275, PR China
| | - Shu-Ning Ou
- Institute of Ecological Science, Guangzhou Key Laboratory of Subtropical Biodiversity and Biomonitoring, Guangdong Provincial Key Laboratory of Biotechnology for Plant Development, School of Life Sciences, South China Normal University, Guangzhou, 510631, PR China
| | - Xiao-Dan Yang
- Institute of Ecological Science, Guangzhou Key Laboratory of Subtropical Biodiversity and Biomonitoring, Guangdong Provincial Key Laboratory of Biotechnology for Plant Development, School of Life Sciences, South China Normal University, Guangzhou, 510631, PR China
| | - Zhuo-Hui Wu
- Institute of Ecological Science, Guangzhou Key Laboratory of Subtropical Biodiversity and Biomonitoring, Guangdong Provincial Key Laboratory of Biotechnology for Plant Development, School of Life Sciences, South China Normal University, Guangzhou, 510631, PR China
| | - Xiang-Deng Du
- School of Life Sciences, Sun Yat-sen University, Guangzhou, 510275, PR China
| | - Ling-Yun Tang
- School of Life Sciences, Sun Yat-sen University, Guangzhou, 510275, PR China
| | - Bin Liao
- School of Life Sciences, Sun Yat-sen University, Guangzhou, 510275, PR China
| | - Wen-Sheng Shu
- Institute of Ecological Science, Guangzhou Key Laboratory of Subtropical Biodiversity and Biomonitoring, Guangdong Provincial Key Laboratory of Biotechnology for Plant Development, School of Life Sciences, South China Normal University, Guangzhou, 510631, PR China.,Guangdong Provincial Key Laboratory of Chemical Pollution, South China Normal University, Guangzhou, 510006, PR China
| | - Pu Jia
- Institute of Ecological Science, Guangzhou Key Laboratory of Subtropical Biodiversity and Biomonitoring, Guangdong Provincial Key Laboratory of Biotechnology for Plant Development, School of Life Sciences, South China Normal University, Guangzhou, 510631, PR China
| | - Jie-Liang Liang
- Institute of Ecological Science, Guangzhou Key Laboratory of Subtropical Biodiversity and Biomonitoring, Guangdong Provincial Key Laboratory of Biotechnology for Plant Development, School of Life Sciences, South China Normal University, Guangzhou, 510631, PR China
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15
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Junker N, Gossmann TI. Adaptation-Driven Evolution of Sirtuin 1 (SIRT1), a Key Regulator of Metabolism and Aging, in Marmot Species. Front Ecol Evol 2021. [DOI: 10.3389/fevo.2021.666564] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
The sirtuin protein family plays a role in the lifespan of various species and is involved in numerous key metabolic processes. To understand the evolutionary role of sirtuins in marmots, a long-living rodent species group with remarkable metabolic shutdown during hibernation, we conducted a phylogeny-based substitution rate analysis of coding genes based on genetic information of seven marmot species. We show that sirtuin 1 (SIRT1) has evolved under positive selection in the marmot lineage. We pinpoint three amino acid changes in four different marmot species that underlie the signal of positive selection and that may favor increased longevity in marmots. Based on a computational structural analysis we can show that all three substitutions affect the secondary structure of the same region in human SIRT1. We propose that the identified region is close to the catalytic domain and that the potential structural changes may impact the catalytic activity of the enzyme and therefore might be playing a functional role in marmot's extended lifespan and metabolic shutdown.
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16
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A Novel Freshwater to Marine Evolutionary Transition Revealed within Methylophilaceae Bacteria from the Arctic Ocean. mBio 2021; 12:e0130621. [PMID: 34154421 PMCID: PMC8262872 DOI: 10.1128/mbio.01306-21] [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] [Indexed: 11/20/2022] Open
Abstract
Bacteria inhabiting polar oceans, particularly the Arctic Ocean, are less studied than those at lower latitudes. Discovering bacterial adaptations to Arctic Ocean conditions is essential for understanding responses to the accelerated environmental changes occurring in the North. The Methylophilaceae are emerging as a model for investigating the genomic basis of habitat adaptation, because related lineages are widely distributed across both freshwater and marine ecosystems. Here, we investigated Methylophilaceae diversity in the salinity-stratified surface waters of the Canada Basin, Arctic Ocean. In addition to a diversity of marine OM43 lineages, we report on the genomic characteristics and evolution of a previously undescribed Methylophilaceae clade (BS01) common to polar surface waters yet related to freshwater sediment Methylotenera species. BS01 is restricted to the lower-salinity surface waters, while OM43 is found throughout the halocline. An acidic proteome supports a marine lifestyle for BS01, but gene content shows increased metabolic versatility compared to OM43 and evidence for ongoing genome-streamlining. Phylogenetic reconstruction shows that BS01 colonized the pelagic ocean independently of OM43 via convergent evolution. Salinity adaptation and differences in one-carbon and nitrogen metabolism may play a role in niche differentiation between BS01 and OM43. In particular, urea utilization by BS01 is predicted to provide an ecological advantage over OM43 given the limited amount of inorganic nitrogen in the Canada Basin. These observations provide further evidence that the Arctic Ocean is inhabited by distinct bacterial groups and that at least one group (BS01) evolved via a freshwater to marine environmental transition.
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Leclerc M, Harrison MC, Storck V, Planas D, Amyot M, Walsh DA. Microbial Diversity and Mercury Methylation Activity in Periphytic Biofilms at a Run-of-River Hydroelectric Dam and Constructed Wetlands. mSphere 2021; 6:e00021-21. [PMID: 33731467 PMCID: PMC8546676 DOI: 10.1128/msphere.00021-21] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2021] [Accepted: 02/24/2021] [Indexed: 01/04/2023] Open
Abstract
Periphytic biofilms have the potential to greatly influence the microbial production of the neurotoxicant monomethylmercury in freshwaters although few studies have simultaneously assessed periphyton mercury methylation and demethylation rates and the microbial communities associated with these transformations. We performed a field study on periphyton from a river affected by run-of-river power plants and artificial wetlands in a boreal landscape (Québec, Canada). In situ incubations were performed on three sites using environmental concentrations of isotopically enriched monomethylmercury (MM198Hg) and inorganic mercury (200Hg) for demethylation and methylation rate measurements. Periphytic microbial communities were investigated through 16S rRNA gene analyses and metagenomic screenings for the hgcA gene, involved in mercury methylation. Positive mercury methylation rates ([5.9 ± 3.4] × 10-3 day-1) were observed only in the wetlands, and demethylation rates averaged 1.78 ± 0.21 day-1 for the three studied sites. The 16S rRNA gene analyses revealed Proteobacteria as the most abundant phylum across all sites (36.3% ± 1.4%), from which families associated with mercury methylation were mostly found in the wetland site. Metagenome screening for HgcA identified 24 different hgcA sequences in the constructed wetland site only, associated with 8 known families, where the iron-reducing Geobacteraceae were the most abundant. This work brings new information on mercury methylation in periphyton from habitats of impacted rivers, associating it mostly with putative iron-reducing bacteria.IMPORTANCE Monomethylmercury (MMHg) is a biomagnifiable neurotoxin of global concern with risks to human health mostly associated with fish consumption. Hydroelectric reservoirs are known to be sources of MMHg many years after their impoundment. Little is known, however, on run-of-river dams flooding smaller terrestrial areas, although their numbers are expected to increase considerably worldwide in decades to come. Production of MMHg is associated mostly with anaerobic processes, but Hg methylation has been shown to occur in periphytic biofilms located in oxic zones of the water column. Therefore, in this study, we investigated in situ production of MMHg by periphytic communities in habitats impacted by the construction of a run-of-river dam by combining transformation rate measurements with genomic approaches targeting hgcAB genes, responsible for mercury methylation. These results provide extended knowledge on mercury methylators in river ecosystems impacted by run-of-river dams in temperate habitats.
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Affiliation(s)
- Maxime Leclerc
- GRIL, Département de Sciences Biologiques, Université de Montréal, Montréal, Québec, Canada
- GRIL, Département de Sciences Biologiques, Université du Québec à Montréal, Montréal, Québec, Canada
| | | | - Veronika Storck
- GRIL, Département de Sciences Biologiques, Université de Montréal, Montréal, Québec, Canada
- Department of Biology, Concordia University, Montréal, Québec, Canada
| | - Dolors Planas
- GRIL, Département de Sciences Biologiques, Université du Québec à Montréal, Montréal, Québec, Canada
| | - Marc Amyot
- GRIL, Département de Sciences Biologiques, Université de Montréal, Montréal, Québec, Canada
| | - David A Walsh
- Department of Biology, Concordia University, Montréal, Québec, Canada
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18
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Irisarri I, Burki F, Whelan S. Automated Removal of Non-homologous Sequence Stretches with PREQUAL. Methods Mol Biol 2021; 2231:147-162. [PMID: 33289892 DOI: 10.1007/978-1-0716-1036-7_10] [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] [Indexed: 06/12/2023]
Abstract
Large-scale multigene datasets used in phylogenomics and comparative genomics often contain sequence errors inherited from source genomes and transcriptomes. These errors typically manifest as stretches of non-homologous characters and derive from sequencing, assembly, and/or annotation errors. The lack of automatic tools to detect and remove sequence errors leads to the propagation of these errors in large-scale datasets. PREQUAL is a command line tool that identifies and masks regions with non-homologous adjacent characters in sets of unaligned homologous sequences. PREQUAL uses a full probabilistic approach based on pair hidden Markov models. On the front end, PREQUAL is user-friendly and simple to use while also allowing full customization to adjust filtering sensitivity. It is primarily aimed at amino acid sequences but can handle protein-coding nucleotide sequences. PREQUAL is computationally efficient and shows high sensitivity and accuracy. In this chapter, we briefly introduce the motivation for PREQUAL and its underlying methodology, followed by a description of basic and advanced usage, and conclude with some notes and recommendations. PREQUAL fills an important gap in the current bioinformatics tool kit for phylogenomics, contributing toward increased accuracy and reproducibility in future studies.
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Affiliation(s)
- Iker Irisarri
- Department of Organismal Biology (Program in Systematic Biology), Uppsala University, Uppsala, Sweden.
- Department of Biodiversity and Evolutionary Biology, Museo Nacional de Ciencias Naturales, Madrid, Spain.
- Department of Applied Bioinformatics, Institute for Microbiology and Genetics, University of Göttingen, Göttingen, Germany.
| | - Fabien Burki
- Department of Organismal Biology (Program in Systematic Biology), Uppsala University, Uppsala, Sweden
- Science for Life Laboratory, Uppsala University, Uppsala, Sweden
| | - Simon Whelan
- Department of Evolutionary Genetics (Program in Evolutionary Biology), Uppsala University, Uppsala, Sweden
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19
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Abstract
Inferring phylogenetic relationships among hundreds or thousands of microbial genomes is an increasingly common task. The conventional phylogenetic approach adopts multiple sequence alignment to compare gene-by-gene, concatenated multigene or whole-genome sequences, from which a phylogenetic tree would be inferred. These alignments follow the implicit assumption of full-length contiguity among homologous sequences. However, common events in microbial genome evolution (e.g., structural rearrangements and genetic recombination) violate this assumption. Moreover, aligning hundreds or thousands of sequences is computationally intensive and not scalable to the rate at which genome data are generated. Therefore, alignment-free methods present an attractive alternative strategy. Here we describe a scalable alignment-free strategy to infer phylogenetic relationships using complete genome sequences of bacteria and archaea, based on short, subsequences of length k (k-mers). We describe how this strategy can be extended to infer evolutionary relationships beyond a tree-like structure, to better capture both vertical and lateral signals of microbial evolution.
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20
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Zrimec J, Börlin CS, Buric F, Muhammad AS, Chen R, Siewers V, Verendel V, Nielsen J, Töpel M, Zelezniak A. Deep learning suggests that gene expression is encoded in all parts of a co-evolving interacting gene regulatory structure. Nat Commun 2020; 11:6141. [PMID: 33262328 PMCID: PMC7708451 DOI: 10.1038/s41467-020-19921-4] [Citation(s) in RCA: 65] [Impact Index Per Article: 16.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2019] [Accepted: 11/02/2020] [Indexed: 12/31/2022] Open
Abstract
Understanding the genetic regulatory code governing gene expression is an important challenge in molecular biology. However, how individual coding and non-coding regions of the gene regulatory structure interact and contribute to mRNA expression levels remains unclear. Here we apply deep learning on over 20,000 mRNA datasets to examine the genetic regulatory code controlling mRNA abundance in 7 model organisms ranging from bacteria to Human. In all organisms, we can predict mRNA abundance directly from DNA sequence, with up to 82% of the variation of transcript levels encoded in the gene regulatory structure. By searching for DNA regulatory motifs across the gene regulatory structure, we discover that motif interactions could explain the whole dynamic range of mRNA levels. Co-evolution across coding and non-coding regions suggests that it is not single motifs or regions, but the entire gene regulatory structure and specific combination of regulatory elements that define gene expression levels.
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Affiliation(s)
- Jan Zrimec
- Department of Biology and Biological Engineering, Chalmers University of Technology, Kemivägen 10, SE-412 96, Gothenburg, Sweden
| | - Christoph S Börlin
- Department of Biology and Biological Engineering, Chalmers University of Technology, Kemivägen 10, SE-412 96, Gothenburg, Sweden
- Novo Nordisk Foundation Center for Biosustainability, Chalmers University of Technology, Kemivägen 10, SE-412 96, Gothenburg, Sweden
| | - Filip Buric
- Department of Biology and Biological Engineering, Chalmers University of Technology, Kemivägen 10, SE-412 96, Gothenburg, Sweden
| | - Azam Sheikh Muhammad
- Computer Science and Engineering, Chalmers University of Technology, Kemivägen 10, SE-412 96, Gothenburg, Sweden
| | - Rhongzen Chen
- Computer Science and Engineering, Chalmers University of Technology, Kemivägen 10, SE-412 96, Gothenburg, Sweden
| | - Verena Siewers
- Department of Biology and Biological Engineering, Chalmers University of Technology, Kemivägen 10, SE-412 96, Gothenburg, Sweden
- Novo Nordisk Foundation Center for Biosustainability, Chalmers University of Technology, Kemivägen 10, SE-412 96, Gothenburg, Sweden
| | - Vilhelm Verendel
- Computer Science and Engineering, Chalmers University of Technology, Kemivägen 10, SE-412 96, Gothenburg, Sweden
| | - Jens Nielsen
- Department of Biology and Biological Engineering, Chalmers University of Technology, Kemivägen 10, SE-412 96, Gothenburg, Sweden
- Novo Nordisk Foundation Center for Biosustainability, Chalmers University of Technology, Kemivägen 10, SE-412 96, Gothenburg, Sweden
| | - Mats Töpel
- Department of Marine Sciences, University of Gothenburg, Box 461, SE-405 30, Gothenburg, Sweden
- Gothenburg Global Biodiversity Center (GGBC), Box 461, 40530, Gothenburg, Sweden
| | - Aleksej Zelezniak
- Department of Biology and Biological Engineering, Chalmers University of Technology, Kemivägen 10, SE-412 96, Gothenburg, Sweden.
- Science for Life Laboratory, Tomtebodavägen 23a, SE-171 65, Stockholm, Sweden.
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21
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Du H, Ran JH, Feng YY, Wang XQ. The flattened and needlelike leaves of the pine family (Pinaceae) share a conserved genetic network for adaxial-abaxial polarity but have diverged for photosynthetic adaptation. BMC Evol Biol 2020; 20:131. [PMID: 33028198 PMCID: PMC7542717 DOI: 10.1186/s12862-020-01694-5] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2020] [Accepted: 09/21/2020] [Indexed: 11/10/2022] Open
Abstract
Background Leaves have highly diverse morphologies. However, with an evolutionary history of approximately 200 million years, leaves of the pine family are relatively monotonous and often collectively called “needles”, although they vary in length, width and cross-section shapes. It would be of great interest to determine whether Pinaceae leaves share similar morpho-physiological features and even consistent developmental and adaptive mechanisms. Results Based on a detailed morpho-anatomical study of leaves from all 11 Pinaceae genera, we particularly investigated the expression patterns of adaxial-abaxial polarity genes in two types of leaves (needlelike and flattened) and compared their photosynthetic capacities. We found that the two types of leaves share conserved spatial patterning of vasculatures and genetic networks for adaxial-abaxial polarity, although they display different anatomical structures in the mesophyll tissue differentiation and distribution direction. In addition, the species with needlelike leaves exhibited better photosynthetic capacity than the species with flattened leaves. Conclusions Our study provides the first evidence for the existence of a conserved genetic module controlling adaxial-abaxial polarity in the development of different Pinaceae leaves.
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Affiliation(s)
- Hong Du
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, the Chinese Academy of Sciences, 20 Nanxincun, Xiangshan, Beijing, 100093, China
| | - Jin-Hua Ran
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, the Chinese Academy of Sciences, 20 Nanxincun, Xiangshan, Beijing, 100093, China.,University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Yuan-Yuan Feng
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, the Chinese Academy of Sciences, 20 Nanxincun, Xiangshan, Beijing, 100093, China.,University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Xiao-Quan Wang
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, the Chinese Academy of Sciences, 20 Nanxincun, Xiangshan, Beijing, 100093, China. .,University of Chinese Academy of Sciences, Beijing, 100049, China.
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22
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Portik DM, Wiens JJ. Do Alignment and Trimming Methods Matter for Phylogenomic (UCE) Analyses? Syst Biol 2020; 70:440-462. [PMID: 32797207 DOI: 10.1093/sysbio/syaa064] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2019] [Revised: 08/02/2020] [Accepted: 08/03/2020] [Indexed: 11/14/2022] Open
Abstract
Alignment is a crucial issue in molecular phylogenetics because different alignment methods can potentially yield very different topologies for individual genes. But it is unclear if the choice of alignment methods remains important in phylogenomic analyses, which incorporate data from hundreds or thousands of genes. For example, problematic biases in alignment might be multiplied across many loci, whereas alignment errors in individual genes might become irrelevant. The issue of alignment trimming (i.e., removing poorly aligned regions or missing data from individual genes) is also poorly explored. Here, we test the impact of 12 different combinations of alignment and trimming methods on phylogenomic analyses. We compare these methods using published phylogenomic data from ultraconserved elements (UCEs) from squamate reptiles (lizards and snakes), birds, and tetrapods. We compare the properties of alignments generated by different alignment and trimming methods (e.g., length, informative sites, missing data). We also test whether these data sets can recover well-established clades when analyzed with concatenated (RAxML) and species-tree methods (ASTRAL-III), using the full data ($\sim $5000 loci) and subsampled data sets (10% and 1% of loci). We show that different alignment and trimming methods can significantly impact various aspects of phylogenomic data sets (e.g., length, informative sites). However, these different methods generally had little impact on the recovery and support values for well-established clades, even across very different numbers of loci. Nevertheless, our results suggest several "best practices" for alignment and trimming. Intriguingly, the choice of phylogenetic methods impacted the phylogenetic results most strongly, with concatenated analyses recovering significantly more well-established clades (with stronger support) than the species-tree analyses. [Alignment; concatenated analysis; phylogenomics; sequence length heterogeneity; species-tree analysis; trimming].
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Affiliation(s)
- Daniel M Portik
- Department of Ecology and Evolutionary Biology, University of Arizona, Tucson, AZ 85721, USA.,California Academy of Sciences, San Francisco, CA 94118, USA
| | - John J Wiens
- Department of Ecology and Evolutionary Biology, University of Arizona, Tucson, AZ 85721, USA
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23
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Schwentner M, Rabet N, Richter S, Giribet G, Padhye S, Cart JF, Bonillo C, Rogers DC. Phylogeny and Biogeography of Spinicaudata (Crustacea: Branchiopoda). Zool Stud 2020; 59:e44. [PMID: 33365101 PMCID: PMC7746975 DOI: 10.6620/zs.2020.59-44] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2019] [Accepted: 03/09/2020] [Indexed: 12/24/2022]
Abstract
Spinicaudata (spiny clam shrimp) is a taxon of Branchiopoda occurring since the Devonian and today it occurs nearly globally in temporary water bodies. We present the most species-rich phylogenetic analyses of this taxon based on four molecular loci: COI, 16S rRNA, EF1α and 28S rRNA. Our results support previous findings that Cyzicidae sensu lato is paraphyletic. To render Cyzicidae monophyletic we establish a fourth extant spinicaudatan family to accommodate Eocyzicus. Within Cyzicidae, none of the genera Cyzicus, Caenestheria or Caenestheriella are monophyletic, and the morphological characters used to define these genera (condyle length and rostrum shape) are not associated with well-delimited clades within Cyzicidae. There is insufficient resolution to elucidate the relationships within Leptestheriidae. However, there is sufficient evidence to show that the leptestheriid genera Eoleptestheria and Leptestheria are non-monophyletic, and there is no support for the genus Leptestheriella. Molecular clock analyses suggest that the wide geographic distribution of many spinicaudatan taxa across multiple continents is largely based on vicariance associated with the break-up of Pangea and Gondwana. Trans-oceanic dispersal has occurred in some taxa (e.g., Eulimnadia and within Leptestheriidae) but has been relatively rare. Our results highlight the need to revise the taxonomy of Cyzicidae and Leptestheriidae and provide evidence that the global spinicaudatan diversity may be underestimated due to the presence of numerous cryptic species. We establish Eocyzicidae fam. nov. to accommodate the genus Eocyzicus. Consequently, Cyzicidae comprises only two genera -Cyzicus and Ozestheria. Ozestheria occurs also in Africa and Asia and Ozestheria pilosa new comb. is assigned to this genus.
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Affiliation(s)
- Martin Schwentner
- Center of Natural History, Universität Hamburg, Hamburg, Germany. E-mail: (Schwentner)
- Naturhistorisches Museum, Vienna, Austria
| | - Nicolas Rabet
- Sorbonne Université, Muséum national d'Histoire naturelle, Biologie des organismes et écosystèmes aquatiques (BOREA), CNRS, IRD, Université de Caen Basse-Normandie, CP26 75231, 43 rue Cuvier Paris Cedex 05, France. E-mail: (Rabet), (Bonillo)
| | - Stefan Richter
- Allgemeine und Spezielle Zoologie, Universität Rostock, Rostock, Germany. E-mail: (Richter)
| | - Gonzalo Giribet
- Museum of Comparative Zoology, Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, Massachusetts, USA. E-mail: (Giribet)
| | - Sameer Padhye
- Systematics, Ecology & Conservation Lab, Zoo Outreach Organization, Coimbatore, Tamil Nadu, India. E-mail: (Padhye)
| | | | - Céline Bonillo
- Sorbonne Université, Muséum national d'Histoire naturelle, Biologie des organismes et écosystèmes aquatiques (BOREA), CNRS, IRD, Université de Caen Basse-Normandie, CP26 75231, 43 rue Cuvier Paris Cedex 05, France. E-mail: (Rabet), (Bonillo)
| | - D Christopher Rogers
- Kansas Biological Survey, and The Biodiversity Institute, The University of Kansas, Higuchi Hall, 2101 Constant Avenue, Lawrence, KS 66047-3759, USA. E-mail: (Rogers)
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24
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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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25
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Lucentini L, Plazzi F, Sfriso AA, Pizzirani C, Sfriso A, Chiesa S. Additional taxonomic coverage of the doubly uniparental inheritance in bivalves: Evidence of sex‐linked heteroplasmy in the razor clam
Solen marginatus
Pulteney, 1799, but not in the lagoon cockle
Cerastoderma glaucum
(Bruguière, 1789). J ZOOL SYST EVOL RES 2020. [DOI: 10.1111/jzs.12386] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Livia Lucentini
- Department of Chemistry, Biology and Biotechnologies University of Perugia Perugia Italy
| | - Federico Plazzi
- Department of Biological, Geological and Environmental Sciences University of Bologna Bologna Italy
| | - Andrea Augusto Sfriso
- Department of Chemical and Pharmaceuticals Sciences University of Ferrara Ferrara Italy
| | - Claudia Pizzirani
- Department of Chemistry, Biology and Biotechnologies University of Perugia Perugia Italy
| | - Adriano Sfriso
- Department of Environmental Sciences, Informatics and Statistics Ca' Foscari University of Venice Venice Italy
| | - Stefania Chiesa
- Department of Molecular Sciences and Nanosystems Ca' Foscari University of Venice Venice Italy
- ISPRA Institute for Environmental Protection and Research Rome Italy
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26
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Shedding light: a phylotranscriptomic perspective illuminates the origin of photosymbiosis in marine bivalves. BMC Evol Biol 2020; 20:50. [PMID: 32357841 PMCID: PMC7195748 DOI: 10.1186/s12862-020-01614-7] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2019] [Accepted: 04/15/2020] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Photosymbiotic associations between metazoan hosts and photosynthetic dinoflagellates are crucial to the trophic and structural integrity of many marine ecosystems, including coral reefs. Although extensive efforts have been devoted to study the short-term ecological interactions between coral hosts and their symbionts, long-term evolutionary dynamics of photosymbiosis in many marine animals are not well understood. Within Bivalvia, the second largest class of mollusks, obligate photosymbiosis is found in two marine lineages: the giant clams (subfamily Tridacninae) and the heart cockles (subfamily Fraginae), both in the family Cardiidae. Morphologically, giant clams show relatively conservative shell forms whereas photosymbiotic fragines exhibit a diverse suite of anatomical adaptations including flattened shells, leafy mantle extensions, and lens-like microstructural structures. To date, the phylogenetic relationships between these two subfamilies remain poorly resolved, and it is unclear whether photosymbiosis in cardiids originated once or twice. RESULTS In this study, we establish a backbone phylogeny for Cardiidae utilizing RNASeq-based transcriptomic data from Tridacninae, Fraginae and other cardiids. A variety of phylogenomic approaches were used to infer the relationship between the two groups. Our analyses found conflicting gene signals and potential rapid divergence among the lineages. Overall, results support a sister group relationship between Tridacninae and Fraginae, which diverged during the Cretaceous. Although a sister group relationship is recovered, ancestral state reconstruction using maximum likelihood-based methods reveals two independent origins of photosymbiosis, one at the base of Tridacninae and the other within a symbiotic Fraginae clade. CONCLUSIONS The newly revealed common ancestry between Tridacninae and Fraginae brings a possibility that certain genetic, metabolic, and/or anatomical exaptations existed in their last common ancestor, which promoted both lineages to independently establish photosymbiosis, possibly in response to the modern expansion of reef habitats.
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27
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Wong TKF, Kalyaanamoorthy S, Meusemann K, Yeates DK, Misof B, Jermiin LS. A minimum reporting standard for multiple sequence alignments. NAR Genom Bioinform 2020; 2:lqaa024. [PMID: 33575581 PMCID: PMC7671350 DOI: 10.1093/nargab/lqaa024] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Grants] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2020] [Revised: 03/12/2020] [Accepted: 03/30/2020] [Indexed: 12/19/2022] Open
Abstract
Multiple sequence alignments (MSAs) play a pivotal role in studies of molecular sequence data, but nobody has developed a minimum reporting standard (MRS) to quantify the completeness of MSAs in terms of completely specified nucleotides or amino acids. We present an MRS that relies on four simple completeness metrics. The metrics are implemented in AliStat, a program developed to support the MRS. A survey of published MSAs illustrates the benefits and unprecedented transparency offered by the MRS.
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Affiliation(s)
- Thomas K F Wong
- Land & Water, CSIRO, Canberra, ACT 2601, Australia
- Research School of Biology, Australian National University, Canberra, ACT 2600, Australia
| | - Subha Kalyaanamoorthy
- Land & Water, CSIRO, Canberra, ACT 2601, Australia
- Department of Chemistry, University of Waterloo, Waterloo, ON N2L 3G1, Canada
| | - Karen Meusemann
- Australian National Insect Collection, CSIRO National Research Collections Australia, Canberra, ACT 2601, Australia
- Zoologisches Forschungsmuseum Alexander Koenig, 53113 Bonn, Germany
- Evolutionsbiologie & Ökologie, Institut für Biologie I, Albert-Ludwigs-Universität Freiburg, 79085 Freiburg im Breisgau, Germany
| | - David K Yeates
- Australian National Insect Collection, CSIRO National Research Collections Australia, Canberra, ACT 2601, Australia
| | - Bernhard Misof
- Zoologisches Forschungsmuseum Alexander Koenig, 53113 Bonn, Germany
| | - Lars S Jermiin
- Land & Water, CSIRO, Canberra, ACT 2601, Australia
- Research School of Biology, Australian National University, Canberra, ACT 2600, Australia
- School of Biology and Environmental Science, University College Dublin, Belfield, Dublin 4, Ireland
- Earth Institute, University College Dublin, Belfield, Dublin 4 Ireland
- To whom correspondence should be addressed.
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28
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Lemer S, Bieler R, Giribet G. Resolving the relationships of clams and cockles: dense transcriptome sampling drastically improves the bivalve tree of life. Proc Biol Sci 2020; 286:20182684. [PMID: 30963927 PMCID: PMC6408618 DOI: 10.1098/rspb.2018.2684] [Citation(s) in RCA: 30] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
Bivalvia has been the subject of extensive recent phylogenetic work to attempt resolving either the backbone of the bivalve tree using transcriptomic data, or the tips using morpho-anatomical data and up to five genetic markers. Yet the first approach lacked decisive taxon sampling and the second failed to resolve many interfamilial relationships, especially within the diverse clade Imparidentia. Here we combine dense taxon sampling with 108 deep-sequenced Illumina-based transcriptomes to provide resolution in nodes that required additional study. We designed specific data matrices to address the poorly resolved relationships within Imparidentia. Our results support the overall backbone of the bivalve tree, the monophyly of Bivalvia and all its main nodes, although the monophyly of Protobranchia remains less clear. Likewise, the inter-relationships of the six main bivalve clades were fully supported. Within Imparidentia, resolution increases when analysing Imparidentia-specific matrices. Lucinidae, Thyasiridae and Gastrochaenida represent three early branches. Gastrochaenida is sister group to all remaining imparidentians, which divide into six orders. Neoheterodontei is always fully supported, and consists of Sphaeriida, Myida and Venerida, with the latter now also containing Mactroidea, Ungulinoidea and Chamidae, a family particularly difficult to place in earlier work. Overall, our study, by using densely sampled transcriptomes, provides the best-resolved bivalve phylogeny to date.
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Affiliation(s)
- Sarah Lemer
- 1 University of Guam Marine Laboratory , 303 University Drive, UOG Station, Mangilao, GU 96923 , USA.,2 Museum of Comparative Zoology, Department of Organismic and Evolutionary Biology, Harvard University , 26 Oxford Street, Cambridge, MA 02138 , USA
| | - Rüdiger Bieler
- 3 Integrative Research Center, Field Museum of Natural History , 1400 South Lake Shore Drive, Chicago, IL 60605 , USA
| | - Gonzalo Giribet
- 2 Museum of Comparative Zoology, Department of Organismic and Evolutionary Biology, Harvard University , 26 Oxford Street, Cambridge, MA 02138 , USA
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29
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Maldonado E, Antunes A. LMAP_S: Lightweight Multigene Alignment and Phylogeny eStimation. BMC Bioinformatics 2019; 20:739. [PMID: 31888452 PMCID: PMC6937843 DOI: 10.1186/s12859-019-3292-5] [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: 01/04/2019] [Accepted: 11/26/2019] [Indexed: 01/22/2023] Open
Abstract
Background Recent advances in genome sequencing technologies and the cost drop in high-throughput sequencing continue to give rise to a deluge of data available for downstream analyses. Among others, evolutionary biologists often make use of genomic data to uncover phenotypic diversity and adaptive evolution in protein-coding genes. Therefore, multiple sequence alignments (MSA) and phylogenetic trees (PT) need to be estimated with optimal results. However, the preparation of an initial dataset of multiple sequence file(s) (MSF) and the steps involved can be challenging when considering extensive amount of data. Thus, it becomes necessary the development of a tool that removes the potential source of error and automates the time-consuming steps of a typical workflow with high-throughput and optimal MSA and PT estimations. Results We introduce LMAP_S (Lightweight Multigene Alignment and Phylogeny eStimation), a user-friendly command-line and interactive package, designed to handle an improved alignment and phylogeny estimation workflow: MSF preparation, MSA estimation, outlier detection, refinement, consensus, phylogeny estimation, comparison and editing, among which file and directory organization, execution, manipulation of information are automated, with minimal manual user intervention. LMAP_S was developed for the workstation multi-core environment and provides a unique advantage for processing multiple datasets. Our software, proved to be efficient throughout the workflow, including, the (unlimited) handling of more than 20 datasets. Conclusions We have developed a simple and versatile LMAP_S package enabling researchers to effectively estimate multiple datasets MSAs and PTs in a high-throughput fashion. LMAP_S integrates more than 25 software providing overall more than 65 algorithm choices distributed in five stages. At minimum, one FASTA file is required within a single input directory. To our knowledge, no other software combines MSA and phylogeny estimation with as many alternatives and provides means to find optimal MSAs and phylogenies. Moreover, we used a case study comparing methodologies that highlighted the usefulness of our software. LMAP_S has been developed as an open-source package, allowing its integration into more complex open-source bioinformatics pipelines. LMAP_S package is released under GPLv3 license and is freely available at https://lmap-s.sourceforge.io/.
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Affiliation(s)
- Emanuel Maldonado
- CIIMAR/CIMAR - Interdisciplinary Centre of Marine and Environmental Research, University of Porto, Terminal de Cruzeiros do Porto de Leixões, Av. General Norton de Matos, s/n, 4450-208, Porto, Portugal
| | - Agostinho Antunes
- CIIMAR/CIMAR - Interdisciplinary Centre of Marine and Environmental Research, University of Porto, Terminal de Cruzeiros do Porto de Leixões, Av. General Norton de Matos, s/n, 4450-208, Porto, Portugal. .,Department of Biology, Faculty of Sciences, University of Porto, Rua do Campo Alegre, 4169-007, Porto, Portugal.
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30
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Du Y, Wu S, Edwards SV, Liu L. The effect of alignment uncertainty, substitution models and priors in building and dating the mammal tree of life. BMC Evol Biol 2019; 19:203. [PMID: 31694538 PMCID: PMC6833305 DOI: 10.1186/s12862-019-1534-9] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2019] [Accepted: 10/21/2019] [Indexed: 11/29/2022] Open
Abstract
BACKGROUND The flood of genomic data to help build and date the tree of life requires automation at several critical junctures, most importantly during sequence assembly and alignment. It is widely appreciated that automated alignment protocols can yield inaccuracies, but the relative impact of various sources error on phylogenomic analysis is not yet known. This study employs an updated mammal data set of 5162 coding loci sampled from 90 species to evaluate the effects of alignment uncertainty, substitution models, and fossil priors on gene tree, species tree, and divergence time estimation. Additionally, a novel coalescent likelihood ratio test is introduced for comparing competing species trees against a given set of gene trees. RESULTS The aligned DNA sequences of 5162 loci from 90 species were trimmed and filtered using trimAL and two filtering protocols. The final dataset contains 4 sets of alignments - before trimming, after trimming, filtered by a recently proposed pipeline, and further filtered by comparing ML gene trees for each locus with the concatenation tree. Our analyses suggest that the average discordance among the coalescent trees is significantly smaller than that among the concatenation trees estimated from the 4 sets of alignments or with different substitution models. There is no significant difference among the divergence times estimated with different substitution models. However, the divergence dates estimated from the alignments after trimming are more recent than those estimated from the alignments before trimming. CONCLUSIONS Our results highlight that alignment uncertainty of the updated mammal data set and the choice of substitution models have little impact on tree topologies yielded by coalescent methods for species tree estimation, whereas they are more influential on the trees made by concatenation. Given the choice of calibration scheme and clock models, divergence time estimates are robust to the choice of substitution models, but removing alignments deemed problematic by trimming algorithms can lead to more recent dates. Although the fossil prior is important in divergence time estimation, Bayesian estimates of divergence times in this data set are driven primarily by the sequence data.
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Affiliation(s)
- Yan Du
- Department of Statistics, University of Georgia, 310 Herty Drive, Athens, GA 30606 USA
| | - Shaoyuan Wu
- Jiangsu Key Laboratory of Phylogenomics & Comparative Genomics, School of Life Sciences, Jiangsu Normal University, Xuzhou, Jiangsu 221116 People’s Republic of China
| | - Scott V. Edwards
- Department of Organismic & Evolutionary Biology, Museum of Comparative Zoology, Harvard University, Cambridge, MA 02138 USA
| | - Liang Liu
- Liang Liu, Department of Statistics and Institute of Bioinformatics, University of Georgia, 310 Herty Drive, Athens, GA 30606 USA
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31
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Ali RH, Bogusz M, Whelan S. Identifying Clusters of High Confidence Homologies in Multiple Sequence Alignments. Mol Biol Evol 2019; 36:2340-2351. [PMID: 31209473 PMCID: PMC6933875 DOI: 10.1093/molbev/msz142] [Citation(s) in RCA: 52] [Impact Index Per Article: 10.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022] Open
Abstract
Multiple sequence alignment (MSA) is ubiquitous in evolution and bioinformatics. MSAs are usually taken to be a known and fixed quantity on which to perform downstream analysis despite extensive evidence that MSA accuracy and uncertainty affect results. These errors are known to cause a wide range of problems for downstream evolutionary inference, ranging from false inference of positive selection to long branch attraction artifacts. The most popular approach to dealing with this problem is to remove (filter) specific columns in the MSA that are thought to be prone to error. Although popular, this approach has had mixed success and several studies have even suggested that filtering might be detrimental to phylogenetic studies. We present a graph-based clustering method to address MSA uncertainty and error in the software Divvier (available at https://github.com/simonwhelan/Divvier), which uses a probabilistic model to identify clusters of characters that have strong statistical evidence of shared homology. These clusters can then be used to either filter characters from the MSA (partial filtering) or represent each of the clusters in a new column (divvying). We validate Divvier through its performance on real and simulated benchmarks, finding Divvier substantially outperforms existing filtering software by retaining more true pairwise homologies calls and removing more false positive pairwise homologies. We also find that Divvier, in contrast to other filtering tools, can alleviate long branch attraction artifacts induced by MSA and reduces the variation in tree estimates caused by MSA uncertainty.
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Affiliation(s)
- Raja Hashim Ali
- Department of Evolutionary Biology, Evolutionary Biology Centre, Uppsala University, Uppsala, Sweden
- Faculty of Computer Science and Engineering, Ghulam Ishaq Khan Institute of Engineering Sciences and Technology, Topi, Pakistan
| | - Marcin Bogusz
- Department of Evolutionary Biology, Evolutionary Biology Centre, Uppsala University, Uppsala, Sweden
| | - Simon Whelan
- Department of Evolutionary Biology, Evolutionary Biology Centre, Uppsala University, Uppsala, Sweden
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32
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Jones KE, Fér T, Schmickl RE, Dikow RB, Funk VA, Herrando‐Moraira S, Johnston PR, Kilian N, Siniscalchi CM, Susanna A, Slovák M, Thapa R, Watson LE, Mandel JR. An empirical assessment of a single family-wide hybrid capture locus set at multiple evolutionary timescales in Asteraceae. APPLICATIONS IN PLANT SCIENCES 2019; 7:e11295. [PMID: 31667023 PMCID: PMC6814182 DOI: 10.1002/aps3.11295] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/27/2019] [Accepted: 09/05/2019] [Indexed: 05/23/2023]
Abstract
PREMISE Hybrid capture with high-throughput sequencing (Hyb-Seq) is a powerful tool for evolutionary studies. The applicability of an Asteraceae family-specific Hyb-Seq probe set and the outcomes of different phylogenetic analyses are investigated here. METHODS Hyb-Seq data from 112 Asteraceae samples were organized into groups at different taxonomic levels (tribe, genus, and species). For each group, data sets of non-paralogous loci were built and proportions of parsimony informative characters estimated. The impacts of analyzing alternative data sets, removing long branches, and type of analysis on tree resolution and inferred topologies were investigated in tribe Cichorieae. RESULTS Alignments of the Asteraceae family-wide Hyb-Seq locus set were parsimony informative at all taxonomic levels. Levels of resolution and topologies inferred at shallower nodes differed depending on the locus data set and the type of analysis, and were affected by the presence of long branches. DISCUSSION The approach used to build a Hyb-Seq locus data set influenced resolution and topologies inferred in phylogenetic analyses. Removal of long branches improved the reliability of topological inferences in maximum likelihood analyses. The Astereaceae Hyb-Seq probe set is applicable at multiple taxonomic depths, which demonstrates that probe sets do not necessarily need to be lineage-specific.
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Affiliation(s)
- Katy E. Jones
- Botanischer Garten und Botanisches Museum BerlinFreie Universität BerlinKönigin‐Luise‐Str. 6–814195BerlinGermany
| | - Tomáš Fér
- Department of BotanyFaculty of ScienceCharles UniversityBenátská 2CZ 12800PragueCzech Republic
| | - Roswitha E. Schmickl
- Department of BotanyFaculty of ScienceCharles UniversityBenátská 2CZ 12800PragueCzech Republic
- Institute of BotanyThe Czech Academy of SciencesZámek 1CZ 25243PrůhoniceCzech Republic
| | - Rebecca B. Dikow
- Data Science LabOffice of the Chief Information OfficerSmithsonian InstitutionWashingtonD.C.20013‐7012USA
| | - Vicki A. Funk
- Department of BotanyNational Museum of Natural HistorySmithsonian InstitutionWashingtonD.C.20013‐7012USA
| | | | - Paul R. Johnston
- Freie Universität BerlinEvolutionary BiologyBerlinGermany
- Berlin Center for Genomics in Biodiversity ResearchBerlinGermany
- Leibniz‐Institute of Freshwater Ecology and Inland Fisheries (IGB)BerlinGermany
| | - Norbert Kilian
- Botanischer Garten und Botanisches Museum BerlinFreie Universität BerlinKönigin‐Luise‐Str. 6–814195BerlinGermany
| | - Carolina M. Siniscalchi
- Department of Biological SciencesUniversity of MemphisMemphisTennessee38152USA
- Center for BiodiversityUniversity of MemphisMemphisTennessee38152USA
| | - Alfonso Susanna
- Botanic Institute of Barcelona (IBB‐CSIC‐ICUB)Pg. del Migdia s.n.ES 08038BarcelonaSpain
| | - Marek Slovák
- Department of BotanyFaculty of ScienceCharles UniversityBenátská 2CZ 12800PragueCzech Republic
- Plant Science and Biodiversity CentreSlovak Academy of SciencesSK‐84523BratislavaSlovakia
| | - Ramhari Thapa
- Department of Biological SciencesUniversity of MemphisMemphisTennessee38152USA
- Center for BiodiversityUniversity of MemphisMemphisTennessee38152USA
| | - Linda E. Watson
- Department of Plant Biology, Ecology, and EvolutionOklahoma State UniversityStillwaterOklahoma74078USA
| | - Jennifer R. Mandel
- Department of Biological SciencesUniversity of MemphisMemphisTennessee38152USA
- Center for BiodiversityUniversity of MemphisMemphisTennessee38152USA
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Tran P, Ramachandran A, Khawasik O, Beisner BE, Rautio M, Huot Y, Walsh DA. Microbial life under ice: Metagenome diversity and in situ activity of Verrucomicrobia in seasonally ice-covered Lakes. Environ Microbiol 2019; 20:2568-2584. [PMID: 29921005 DOI: 10.1111/1462-2920.14283] [Citation(s) in RCA: 51] [Impact Index Per Article: 10.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2018] [Accepted: 05/15/2018] [Indexed: 01/25/2023]
Abstract
Northern lakes are ice-covered for a large part of the year, yet our understanding of microbial diversity and activity during winter lags behind that of the ice-free period. In this study, we investigated under-ice diversity and metabolism of Verrucomicrobia in seasonally ice-covered lakes in temperate and boreal regions of Quebec, Canada using 16S rRNA sequencing, metagenomics and metatranscriptomics. Verrucomicrobia, particularly the V1, V3 and V4 subdivisions, were abundant during ice-covered periods. A diversity of Verrucomicrobia genomes were reconstructed from Quebec lake metagenomes. Several genomes were associated with the ice-covered period and were represented in winter metatranscriptomes, supporting the notion that Verrucomicrobia are metabolically active under ice. Verrucomicrobia transcriptome analysis revealed a range of metabolisms potentially occurring under ice, including carbohydrate degradation, glycolate utilization, scavenging of chlorophyll degradation products, and urea use. Genes for aerobic sulfur and hydrogen oxidation were expressed, suggesting chemolithotrophy may be an adaptation to conditions where labile carbon may be limited. The expression of genes for flagella biosynthesis and chemotaxis was detected, suggesting Verrucomicrobia may be actively sensing and responding to winter nutrient pulses, such as phytoplankton blooms. These results increase our understanding on the diversity and metabolic processes occurring under ice in northern lakes ecosystems.© 2018 Society for Applied Microbiology and John Wiley & Sons Ltd.
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Affiliation(s)
- Patricia Tran
- Department of Biology, Concordia University, 7141 Sherbrooke St. West, Montreal, Quebec, H4B 1R6, Canada.,Groupe de Recherche Interuniversitaire en Limnologie et Environnement Aquatique (GRIL), Montréal, Québec, Canada
| | - Arthi Ramachandran
- Department of Biology, Concordia University, 7141 Sherbrooke St. West, Montreal, Quebec, H4B 1R6, Canada
| | - Ola Khawasik
- Department of Biology, Concordia University, 7141 Sherbrooke St. West, Montreal, Quebec, H4B 1R6, Canada
| | - Beatrix E Beisner
- Groupe de Recherche Interuniversitaire en Limnologie et Environnement Aquatique (GRIL), Montréal, Québec, Canada.,Département des Sciences Biologiques, Université du Québec à Montréal, Montreal, Québec, Canada
| | - Milla Rautio
- Groupe de Recherche Interuniversitaire en Limnologie et Environnement Aquatique (GRIL), Montréal, Québec, Canada.,Département des Sciences Fondamentales, Université du Québec à Chicoutimi, Chicoutimi, Québec, Canada
| | - Yannick Huot
- Groupe de Recherche Interuniversitaire en Limnologie et Environnement Aquatique (GRIL), Montréal, Québec, Canada.,Département de Géomatique Appliquée, Université de Sherbrooke, Sherbrooke, Québec, Canada
| | - David A Walsh
- Department of Biology, Concordia University, 7141 Sherbrooke St. West, Montreal, Quebec, H4B 1R6, Canada.,Groupe de Recherche Interuniversitaire en Limnologie et Environnement Aquatique (GRIL), Montréal, Québec, Canada
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Laso-Pérez R, Hahn C, van Vliet DM, Tegetmeyer HE, Schubotz F, Smit NT, Pape T, Sahling H, Bohrmann G, Boetius A, Knittel K, Wegener G. Anaerobic Degradation of Non-Methane Alkanes by " Candidatus Methanoliparia" in Hydrocarbon Seeps of the Gulf of Mexico. mBio 2019; 10:e01814-19. [PMID: 31431553 PMCID: PMC6703427 DOI: 10.1128/mbio.01814-19] [Citation(s) in RCA: 41] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2019] [Accepted: 07/24/2019] [Indexed: 11/20/2022] Open
Abstract
Crude oil and gases in the seabed provide an important energy source for subsurface microorganisms. We investigated the role of archaea in the anaerobic degradation of non-methane alkanes in deep-sea oil seeps from the Gulf of Mexico. We identified microscopically the ethane and short-chain alkane oxidizers "Candidatus Argoarchaeum" and "Candidatus Syntrophoarchaeum" forming consortia with bacteria. Moreover, we found that the sediments contain large numbers of cells from the archaeal clade "Candidatus Methanoliparia," which was previously proposed to perform methanogenic alkane degradation. "Ca. Methanoliparia" occurred abundantly as single cells attached to oil droplets in sediments without apparent bacterial or archaeal partners. Metagenome-assembled genomes of "Ca. Methanoliparia" encode a complete methanogenesis pathway including a canonical methyl-coenzyme M reductase (MCR) but also a highly divergent MCR related to those of alkane-degrading archaea and pathways for the oxidation of long-chain alkyl units. Its metabolic genomic potential and its global detection in hydrocarbon reservoirs suggest that "Ca. Methanoliparia" is an important methanogenic alkane degrader in subsurface environments, producing methane by alkane disproportionation as a single organism.IMPORTANCE Oil-rich sediments from the Gulf of Mexico were found to contain diverse alkane-degrading groups of archaea. The symbiotic, consortium-forming "Candidatus Argoarchaeum" and "Candidatus Syntrophoarchaeum" are likely responsible for the degradation of ethane and short-chain alkanes, with the help of sulfate-reducing bacteria. "Ca. Methanoliparia" occurs as single cells associated with oil droplets. These archaea encode two phylogenetically different methyl-coenzyme M reductases that may allow this organism to thrive as a methanogen on a substrate of long-chain alkanes. Based on a library survey, we show that "Ca. Methanoliparia" is frequently detected in oil reservoirs and may be a key agent in the transformation of long-chain alkanes to methane. Our findings provide evidence for the important and diverse roles of archaea in alkane-rich marine habitats and support the notion of a significant functional versatility of the methyl coenzyme M reductase.
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Affiliation(s)
- Rafael Laso-Pérez
- Max-Planck Institute for Marine Microbiology, Bremen, Germany
- Alfred Wegener Institute Helmholtz Center for Polar and Marine Research, Bremerhaven, Germany
- MARUM, Center for Marine Environmental Sciences and Department of Geosciences, University of Bremen, Bremen, Germany
| | - Cedric Hahn
- Max-Planck Institute for Marine Microbiology, Bremen, Germany
| | - Daan M van Vliet
- Laboratory of Microbiology, Wageningen University and Research, Wageningen, The Netherlands
| | - Halina E Tegetmeyer
- Alfred Wegener Institute Helmholtz Center for Polar and Marine Research, Bremerhaven, Germany
- Center for Biotechnology, Bielefeld University, Bielefeld, Germany
| | - Florence Schubotz
- MARUM, Center for Marine Environmental Sciences and Department of Geosciences, University of Bremen, Bremen, Germany
| | - Nadine T Smit
- MARUM, Center for Marine Environmental Sciences and Department of Geosciences, University of Bremen, Bremen, Germany
| | - Thomas Pape
- MARUM, Center for Marine Environmental Sciences and Department of Geosciences, University of Bremen, Bremen, Germany
| | - Heiko Sahling
- MARUM, Center for Marine Environmental Sciences and Department of Geosciences, University of Bremen, Bremen, Germany
| | - Gerhard Bohrmann
- MARUM, Center for Marine Environmental Sciences and Department of Geosciences, University of Bremen, Bremen, Germany
| | - Antje Boetius
- Max-Planck Institute for Marine Microbiology, Bremen, Germany
- Alfred Wegener Institute Helmholtz Center for Polar and Marine Research, Bremerhaven, Germany
- MARUM, Center for Marine Environmental Sciences and Department of Geosciences, University of Bremen, Bremen, Germany
| | - Katrin Knittel
- Max-Planck Institute for Marine Microbiology, Bremen, Germany
| | - Gunter Wegener
- Max-Planck Institute for Marine Microbiology, Bremen, Germany
- Alfred Wegener Institute Helmholtz Center for Polar and Marine Research, Bremerhaven, Germany
- MARUM, Center for Marine Environmental Sciences and Department of Geosciences, University of Bremen, Bremen, Germany
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35
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Gossmann TI, Shanmugasundram A, Börno S, Duvaux L, Lemaire C, Kuhl H, Klages S, Roberts LD, Schade S, Gostner JM, Hildebrand F, Vowinckel J, Bichet C, Mülleder M, Calvani E, Zelezniak A, Griffin JL, Bork P, Allaine D, Cohas A, Welch JJ, Timmermann B, Ralser M. Ice-Age Climate Adaptations Trap the Alpine Marmot in a State of Low Genetic Diversity. Curr Biol 2019; 29:1712-1720.e7. [PMID: 31080084 PMCID: PMC6538971 DOI: 10.1016/j.cub.2019.04.020] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2018] [Revised: 02/16/2019] [Accepted: 04/09/2019] [Indexed: 12/30/2022]
Abstract
Some species responded successfully to prehistoric changes in climate [1, 2], while others failed to adapt and became extinct [3]. The factors that determine successful climate adaptation remain poorly understood. We constructed a reference genome and studied physiological adaptations in the Alpine marmot (Marmota marmota), a large ground-dwelling squirrel exquisitely adapted to the "ice-age" climate of the Pleistocene steppe [4, 5]. Since the disappearance of this habitat, the rodent persists in large numbers in the high-altitude Alpine meadow [6, 7]. Genome and metabolome showed evidence of adaptation consistent with cold climate, affecting white adipose tissue. Conversely, however, we found that the Alpine marmot has levels of genetic variation that are among the lowest for mammals, such that deleterious mutations are less effectively purged. Our data rule out typical explanations for low diversity, such as high levels of consanguineous mating, or a very recent bottleneck. Instead, ancient demographic reconstruction revealed that genetic diversity was lost during the climate shifts of the Pleistocene and has not recovered, despite the current high population size. We attribute this slow recovery to the marmot's adaptive life history. The case of the Alpine marmot reveals a complicated relationship between climatic changes, genetic diversity, and conservation status. It shows that species of extremely low genetic diversity can be very successful and persist over thousands of years, but also that climate-adapted life history can trap a species in a persistent state of low genetic diversity.
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Affiliation(s)
- Toni I Gossmann
- University of Sheffield, Department of Animal and Plant Sciences, Sheffield S10 2TN, UK; Bielefeld University, Department of Animal Behaviour, 33501 Bielefeld, Germany
| | - Achchuthan Shanmugasundram
- Molecular Biology of Metabolism Laboratory, The Francis Crick Institute, 1 Midland Road, London NW1 1AT, UK; Centre for Genomic Research, Institute of Integrative Biology, University of Liverpool, Biosciences Building, Crown Street, Liverpool L69 7ZB, UK
| | - Stefan Börno
- Max Planck Institute for Molecular Genetics, Sequencing Core Facility, Ihnestrasse 73, 14195 Berlin, Germany
| | - Ludovic Duvaux
- IRHS, Université d'Angers, INRA, Agrocampus-Ouest, SFR 4207 QuaSaV, 49071 Beaucouzé, France; BIOGECO, INRA, Université de Bordeaux, 69 Route d'Arcachon, 33612 Cestas, France
| | - Christophe Lemaire
- IRHS, Université d'Angers, INRA, Agrocampus-Ouest, SFR 4207 QuaSaV, 49071 Beaucouzé, France
| | - Heiner Kuhl
- Max Planck Institute for Molecular Genetics, Sequencing Core Facility, Ihnestrasse 73, 14195 Berlin, Germany; Department of Ecophysiology and Aquaculture, Leibniz-Institute of Freshwater Ecology and Inland Fisheries, 12587 Berlin, Germany
| | - Sven Klages
- Max Planck Institute for Molecular Genetics, Sequencing Core Facility, Ihnestrasse 73, 14195 Berlin, Germany
| | - Lee D Roberts
- Department of Biochemistry and Cambridge Systems Biology Centre, University of Cambridge, 80 Tennis Court Road, Cambridge CB2 1GA, UK; Leeds Institute of Cardiovascular and Metabolic Medicine, University of Leeds, Leeds LS2 9JT, UK
| | - Sophia Schade
- Max Planck Institute for Molecular Genetics, Sequencing Core Facility, Ihnestrasse 73, 14195 Berlin, Germany
| | - Johanna M Gostner
- Division of Medical Biochemistry, Medical University of Innsbruck, 6020 Innsbruck, Austria
| | - Falk Hildebrand
- European Molecular Biology Laboratory (EMBL), 69117 Heidelberg, Germany; Earlham Institute, Norwich Research Park, Norwich NR4 7UZ, UK; Gut Health and Microbes Programme, Quadram Institute, Norwich Research Park, Norwich NR4 7UQ, UK
| | - Jakob Vowinckel
- Department of Biochemistry and Cambridge Systems Biology Centre, University of Cambridge, 80 Tennis Court Road, Cambridge CB2 1GA, UK
| | | | - Michael Mülleder
- Department of Biochemistry and Cambridge Systems Biology Centre, University of Cambridge, 80 Tennis Court Road, Cambridge CB2 1GA, UK; Department of Biochemistry, Charitè, Am Chariteplatz 1, 10117 Berlin, Germany
| | - Enrica Calvani
- Molecular Biology of Metabolism Laboratory, The Francis Crick Institute, 1 Midland Road, London NW1 1AT, UK; Department of Biochemistry and Cambridge Systems Biology Centre, University of Cambridge, 80 Tennis Court Road, Cambridge CB2 1GA, UK
| | - Aleksej Zelezniak
- Molecular Biology of Metabolism Laboratory, The Francis Crick Institute, 1 Midland Road, London NW1 1AT, UK; Department of Biology and Biological Engineering, Chalmers University of Technology, 412 96 Göteborg, Sweden; Science for Life Laboratory, KTH - Royal Institute of Technology, Stockholm 171 65, Sweden
| | - Julian L Griffin
- Department of Biochemistry and Cambridge Systems Biology Centre, University of Cambridge, 80 Tennis Court Road, Cambridge CB2 1GA, UK
| | - Peer Bork
- European Molecular Biology Laboratory (EMBL), 69117 Heidelberg, Germany; Max-Delbrück-Centre for Molecular Medicine, 13092 Berlin, Germany; Molecular Medicine Partnership Unit, 69120 Heidelberg, Germany
| | - Dominique Allaine
- Université de Lyon, F-69000, Lyon; Université Lyon 1; CNRS, UMR 5558, Laboratoire de Biométrie et Biologie Evolutive, 69622 Villeurbanne, France
| | - Aurélie Cohas
- Université de Lyon, F-69000, Lyon; Université Lyon 1; CNRS, UMR 5558, Laboratoire de Biométrie et Biologie Evolutive, 69622 Villeurbanne, France
| | - John J Welch
- Department of Genetics, University of Cambridge, Cambridge CB2 3EH, UK
| | - Bernd Timmermann
- Max Planck Institute for Molecular Genetics, Sequencing Core Facility, Ihnestrasse 73, 14195 Berlin, Germany
| | - Markus Ralser
- Molecular Biology of Metabolism Laboratory, The Francis Crick Institute, 1 Midland Road, London NW1 1AT, UK; Department of Biochemistry and Cambridge Systems Biology Centre, University of Cambridge, 80 Tennis Court Road, Cambridge CB2 1GA, UK; Department of Biochemistry, Charitè, Am Chariteplatz 1, 10117 Berlin, Germany.
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36
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Ran JH, Shen TT, Wang MM, Wang XQ. Phylogenomics resolves the deep phylogeny of seed plants and indicates partial convergent or homoplastic evolution between Gnetales and angiosperms. Proc Biol Sci 2019; 285:rspb.2018.1012. [PMID: 29925623 DOI: 10.1098/rspb.2018.1012] [Citation(s) in RCA: 77] [Impact Index Per Article: 15.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2018] [Accepted: 05/24/2018] [Indexed: 02/04/2023] Open
Abstract
After decades of molecular phylogenetic studies, the deep phylogeny of gymnosperms has not been resolved, and the phylogenetic placement of Gnetales remains one of the most controversial issues in seed plant evolution. To resolve the deep phylogeny of seed plants and to address the sources of phylogenetic conflict, we conducted a phylotranscriptomic study with a sampling of all 13 families of gymnosperms and main lineages of angiosperms. Multiple datasets containing up to 1 296 042 sites across 1308 loci were analysed, using concatenation and coalescence approaches. Our study generated a consistent and well-resolved phylogeny of seed plants, which places Gnetales as sister to Pinaceae and thus supports the Gnepine hypothesis. Cycads plus Ginkgo is sister to the remaining gymnosperms. We also found that Gnetales and angiosperms have similar molecular evolutionary rates, which are much higher than those of other gymnosperms. This implies that Gnetales and angiosperms might have experienced similar selective pressures in evolutionary histories. Convergent molecular evolution or homoplasy is partially responsible for the phylogenetic conflicts in seed plants. Our study provides a robustly reconstructed backbone phylogeny that is important for future molecular and morphological studies of seed plants, in particular gymnosperms, in the light of evolution.
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Affiliation(s)
- Jin-Hua Ran
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, Beijing 100093, People's Republic of China
| | - Ting-Ting Shen
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, Beijing 100093, People's Republic of China
| | - Ming-Ming Wang
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, Beijing 100093, People's Republic of China
| | - Xiao-Quan Wang
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, Beijing 100093, People's Republic of China .,University of Chinese Academy of Sciences, Beijing 100049, People's Republic of China
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37
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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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38
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Karr TL, Southern H, Rosenow MA, Gossmann TI, Snook RR. The Old and the New: Discovery Proteomics Identifies Putative Novel Seminal Fluid Proteins in Drosophila. Mol Cell Proteomics 2019; 18:S23-S33. [PMID: 30760537 PMCID: PMC6427231 DOI: 10.1074/mcp.ra118.001098] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2018] [Revised: 02/11/2019] [Indexed: 12/11/2022] Open
Abstract
Seminal fluid proteins (SFPs), the nonsperm component of male ejaculates produced by male accessory glands, are viewed as central mediators of reproductive fitness. SFPs effect both male and female post-mating functions and show molecular signatures of rapid adaptive evolution. Although Drosophila melanogaster, is the dominant insect model for understanding SFP evolution, understanding of SFP evolutionary causes and consequences require additional comparative analyses of close and distantly related taxa. Although SFP identification was historically challenging, advances in label-free quantitative proteomics expands the scope of studying other systems to further advance the field. Focused studies of SFPs has so far overlooked the proteomes of male reproductive glands and their inherent complex protein networks for which there is little information on the overall signals of molecular evolution. Here we applied label-free quantitative proteomics to identify the accessory gland proteome and secretome in Drosophila pseudoobscura,, a close relative of D. melanogaster,, and use the dataset to identify both known and putative novel SFPs. Using this approach, we identified 163 putative SFPs, 32% of which overlapped with previously identified D. melanogaster, SFPs and show that SFPs with known extracellular annotation evolve more rapidly than other proteins produced by or contained within the accessory gland. Our results will further the understanding of the evolution of SFPs and the underlying male accessory gland proteins that mediate reproductive fitness of the sexes.
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Affiliation(s)
- Timothy L Karr
- From the ‡Center for Mechanisms of Evolution, The Biodesign Institute, Arizona State University, Tempe, Arizona;.
| | - Helen Southern
- Department of Animal and Plant Sciences, University of Sheffield, Sheffield, UK
| | | | - Toni I Gossmann
- Department of Animal and Plant Sciences, University of Sheffield, Sheffield, UK
| | - Rhonda R Snook
- Department of Zoology, Stockholm University, Stockholm, Sweden.
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Muñoz-Gómez SA, Hess S, Burger G, Lang BF, Susko E, Slamovits CH, Roger AJ. An updated phylogeny of the Alphaproteobacteria reveals that the parasitic Rickettsiales and Holosporales have independent origins. eLife 2019; 8:e42535. [PMID: 30789345 PMCID: PMC6447387 DOI: 10.7554/elife.42535] [Citation(s) in RCA: 63] [Impact Index Per Article: 12.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2018] [Accepted: 02/21/2019] [Indexed: 11/13/2022] Open
Abstract
The Alphaproteobacteria is an extraordinarily diverse and ancient group of bacteria. Previous attempts to infer its deep phylogeny have been plagued with methodological artefacts. To overcome this, we analyzed a dataset of 200 single-copy and conserved genes and employed diverse strategies to reduce compositional artefacts. Such strategies include using novel dataset-specific profile mixture models and recoding schemes, and removing sites, genes and taxa that are compositionally biased. We show that the Rickettsiales and Holosporales (both groups of intracellular parasites of eukaryotes) are not sisters to each other, but instead, the Holosporales has a derived position within the Rhodospirillales. A synthesis of our results also leads to an updated proposal for the higher-level taxonomy of the Alphaproteobacteria. Our robust consensus phylogeny will serve as a framework for future studies that aim to place mitochondria, and novel environmental diversity, within the Alphaproteobacteria.
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Affiliation(s)
- Sergio A Muñoz-Gómez
- Department of Biochemistry and Molecular BiologyDalhousie UniversityHalifaxCanada
- Centre for Comparative Genomics and Evolutionary BioinformaticsDalhousie UniversityHalifaxCanada
| | - Sebastian Hess
- Department of Biochemistry and Molecular BiologyDalhousie UniversityHalifaxCanada
- Centre for Comparative Genomics and Evolutionary BioinformaticsDalhousie UniversityHalifaxCanada
- Institute of ZoologyUniversity of CologneCologneGermany
| | - Gertraud Burger
- Department of Biochemistry, Robert-Cedergren Center in Bioinformatics and GenomicsUniversité de MontréalMontrealCanada
| | - B Franz Lang
- Department of Biochemistry, Robert-Cedergren Center in Bioinformatics and GenomicsUniversité de MontréalMontrealCanada
| | - Edward Susko
- Centre for Comparative Genomics and Evolutionary BioinformaticsDalhousie UniversityHalifaxCanada
- Department of Mathematics and StatisticsDalhousie UniversityHalifaxCanada
| | - Claudio H Slamovits
- Department of Biochemistry and Molecular BiologyDalhousie UniversityHalifaxCanada
- Centre for Comparative Genomics and Evolutionary BioinformaticsDalhousie UniversityHalifaxCanada
| | - Andrew J Roger
- Department of Biochemistry and Molecular BiologyDalhousie UniversityHalifaxCanada
- Centre for Comparative Genomics and Evolutionary BioinformaticsDalhousie UniversityHalifaxCanada
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40
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Muñoz-Gómez SA, Hess S, Burger G, Lang BF, Susko E, Slamovits CH, Roger AJ. An updated phylogeny of the Alphaproteobacteria reveals that the parasitic Rickettsiales and Holosporales have independent origins. eLife 2019; 8. [PMID: 30789345 DOI: 10.7554/elife.42535.001] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2018] [Accepted: 02/21/2019] [Indexed: 05/20/2023] Open
Abstract
The Alphaproteobacteria is an extraordinarily diverse and ancient group of bacteria. Previous attempts to infer its deep phylogeny have been plagued with methodological artefacts. To overcome this, we analyzed a dataset of 200 single-copy and conserved genes and employed diverse strategies to reduce compositional artefacts. Such strategies include using novel dataset-specific profile mixture models and recoding schemes, and removing sites, genes and taxa that are compositionally biased. We show that the Rickettsiales and Holosporales (both groups of intracellular parasites of eukaryotes) are not sisters to each other, but instead, the Holosporales has a derived position within the Rhodospirillales. A synthesis of our results also leads to an updated proposal for the higher-level taxonomy of the Alphaproteobacteria. Our robust consensus phylogeny will serve as a framework for future studies that aim to place mitochondria, and novel environmental diversity, within the Alphaproteobacteria.
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Affiliation(s)
- Sergio A Muñoz-Gómez
- Department of Biochemistry and Molecular Biology, Dalhousie University, Halifax, Canada
- Centre for Comparative Genomics and Evolutionary Bioinformatics, Dalhousie University, Halifax, Canada
| | - Sebastian Hess
- Department of Biochemistry and Molecular Biology, Dalhousie University, Halifax, Canada
- Centre for Comparative Genomics and Evolutionary Bioinformatics, Dalhousie University, Halifax, Canada
- Institute of Zoology, University of Cologne, Cologne, Germany
| | - Gertraud Burger
- Department of Biochemistry, Robert-Cedergren Center in Bioinformatics and Genomics, Université de Montréal, Montreal, Canada
| | - B Franz Lang
- Department of Biochemistry, Robert-Cedergren Center in Bioinformatics and Genomics, Université de Montréal, Montreal, Canada
| | - Edward Susko
- Centre for Comparative Genomics and Evolutionary Bioinformatics, Dalhousie University, Halifax, Canada
- Department of Mathematics and Statistics, Dalhousie University, Halifax, Canada
| | - Claudio H Slamovits
- Department of Biochemistry and Molecular Biology, Dalhousie University, Halifax, Canada
- Centre for Comparative Genomics and Evolutionary Bioinformatics, Dalhousie University, Halifax, Canada
| | - Andrew J Roger
- Department of Biochemistry and Molecular Biology, Dalhousie University, Halifax, Canada
- Centre for Comparative Genomics and Evolutionary Bioinformatics, Dalhousie University, Halifax, Canada
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41
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Di Franco A, Poujol R, Baurain D, Philippe H. Evaluating the usefulness of alignment filtering methods to reduce the impact of errors on evolutionary inferences. BMC Evol Biol 2019; 19:21. [PMID: 30634908 PMCID: PMC6330419 DOI: 10.1186/s12862-019-1350-2] [Citation(s) in RCA: 64] [Impact Index Per Article: 12.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2018] [Accepted: 01/02/2019] [Indexed: 11/10/2022] Open
Abstract
Background Multiple Sequence Alignments (MSAs) are the starting point of molecular evolutionary analyses. Errors in MSAs generate a non-historical signal that can lead to incorrect inferences. Therefore, numerous efforts have been made to reduce the impact of alignment errors, by improving alignment algorithms and by developing methods to filter out poorly aligned regions. However, MSAs do not only contain alignment errors, but also primary sequence errors. Such errors may originate from sequencing errors, from assembly errors, or from erroneous structural annotations (such as incorrect intron/exon boundaries). Even though their existence is acknowledged, the impact of primary sequence errors on evolutionary inference is poorly characterized. Results In a first step to fill this gap, we have developed a program called HmmCleaner, which detects and eliminates these errors from MSAs. It uses profile hidden Markov models (pHMM) to identify sequence segments that poorly fit their MSA and selectively removes them. We assessed its performances using > 700 amino-acid MSAs from prokaryotes and eukaryotes, in which we introduced several types of simulated primary sequence errors. The sensitivity of HmmCleaner towards simulated primary sequence errors was > 95%. In a second step, we compared the impact of segment filtering software (HmmCleaner and PREQUAL) relative to commonly used block-filtering software (BMGE and TrimAI) on evolutionary analyses. Using real data from vertebrates, we observed that segment-filtering methods improve the quality of evolutionary inference more than the currently used block-filtering methods. The formers were especially effective at improving branch length inferences, and at reducing false positive rate during detection of positive selection. Conclusions Segment filtering methods such as HmmCleaner accurately detect simulated primary sequence errors. Our results suggest that these errors are more detrimental than alignment errors. However, they also show that stochastic (sampling) error is predominant in single-gene evolutionary inferences. Therefore, we argue that MSA filtering should focus on segment instead of block removal and that more studies are required to find the optimal balance between accuracy improvement and stochastic error increase brought by data removal. Electronic supplementary material The online version of this article (10.1186/s12862-019-1350-2) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Arnaud Di Franco
- Station d'Ecologie Théorique et Expérimentale de Moulis, CNRS, Moulis, France
| | - Raphaël Poujol
- Département de Biochimie, Centre Robert-Cedergren, Université de Montréal, Montréal, Québec, Canada
| | - Denis Baurain
- InBioS-PhytoSYSTEMS, Unité de Phylogénomique des Eucaryotes, Université de Liège, Liège, Belgium
| | - Hervé Philippe
- Station d'Ecologie Théorique et Expérimentale de Moulis, CNRS, Moulis, France. .,Département de Biochimie, Centre Robert-Cedergren, Université de Montréal, Montréal, Québec, Canada.
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42
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High-Throughput Reconstruction of Ancestral Protein Sequence, Structure, and Molecular Function. Methods Mol Biol 2019; 1851:135-170. [PMID: 30298396 DOI: 10.1007/978-1-4939-8736-8_8] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Ancestral protein sequence reconstruction is a powerful technique for explicitly testing hypotheses about the evolution of molecular function, allowing researchers to meticulously dissect how historical changes in protein sequence impacted functional repertoire by altering the protein's 3D structure. These techniques have provided concrete, experimentally validated insights into ancient evolutionary processes and help illuminate the complex relationship between protein sequence, structure, and function. Inferring the protein family phylogenies on which ancestral sequence reconstruction depends and reconstructing the sequences, themselves, are amenable to high-throughput computational analysis. However, determining the structures of ancestral-reconstructed proteins and characterizing their functions typically rely on time-consuming and expensive laboratory analyses, limiting most current studies to examining a relatively small number of specific hypotheses. For this reason, we have little detailed, unbiased information about how molecular function evolves across large protein family phylogenies. Here we describe a generalized protocol that integrates ancestral sequence reconstruction with structural homology modeling and structure-based molecular affinity prediction to characterize historical changes in protein function across families with thousands of individual sequences. We highlight key steps in the analysis protocol requiring particularly careful attention to avoid introducing potential errors as well as steps for which computationally efficient subroutines can be substituted for more intensive approaches, allowing researchers to scale the analysis up or down, depending on available resources and requirements for reproducibility and scientific rigor. In our view, this approach provides a compelling compliment to more laboratory-intensive procedures, generating important contextual information that can help guide detailed experiments.
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Herman JL. Enhancing Statistical Multiple Sequence Alignment and Tree Inference Using Structural Information. Methods Mol Biol 2019; 1851:183-214. [PMID: 30298398 DOI: 10.1007/978-1-4939-8736-8_10] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/08/2023]
Abstract
For highly divergent sequences, there is often insufficient information to reliably construct alignments and phylogenetic trees. Since protein structure may be strongly conserved despite large divergences in sequence, structural information can be used to help identify homology in such cases.While there exist well-studied models of sequence evolution, structurally informed alignment methods have typically made use of geometric measures of deviation that do not take into account the underlying mutational processes. In order to integrate structural information into sequence-based evolutionary models, we recently developed a stochastic model of structural evolution on a phylogenetic tree and implemented this as the StructAlign plugin for the StatAlign statistical alignment package.In this chapter, we will outline the types of analyses that can be carried out using StructAlign, illustrating how the inclusion of structural information can be used to inform joint estimation of alignments and trees. StructAlign can also be used to infer branch-specific rates of structural evolution, and analysis of an example globin dataset highlights strong variation in the inferred rate across the tree. While structure is more highly conserved within clades, the rate of structural divergence as a function of sequence variation is larger between functionally divergent proteins. Allowing for the rate of structural divergence to vary over the tree results in an improved fit to the empirically observed pairwise RMSD values.
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Affiliation(s)
- Joseph L Herman
- Department of Biomedical Informatics, Harvard Medical School, Boston, MA, USA.
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44
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Ashkenazy H, Sela I, Levy Karin E, Landan G, Pupko T. Multiple Sequence Alignment Averaging Improves Phylogeny Reconstruction. Syst Biol 2018; 68:117-130. [PMID: 29771363 DOI: 10.1093/sysbio/syy036] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2017] [Accepted: 05/09/2018] [Indexed: 01/11/2023] Open
Abstract
The classic methodology of inferring a phylogenetic tree from sequence data is composed of two steps. First, a multiple sequence alignment (MSA) is computed. Then, a tree is reconstructed assuming the MSA is correct. Yet, inferred MSAs were shown to be inaccurate and alignment errors reduce tree inference accuracy. It was previously proposed that filtering unreliable alignment regions can increase the accuracy of tree inference. However, it was also demonstrated that the benefit of this filtering is often obscured by the resulting loss of phylogenetic signal. In this work we explore an approach, in which instead of relying on a single MSA, we generate a large set of alternative MSAs and concatenate them into a single SuperMSA. By doing so, we account for phylogenetic signals contained in columns that are not present in the single MSA computed by alignment algorithms. Using simulations, we demonstrate that this approach results, on average, in more accurate trees compared to 1) using an unfiltered MSA and 2) using a single MSA with weights assigned to columns according to their reliability. Next, we explore in which regions of the MSA space our approach is expected to be beneficial. Finally, we provide a simple criterion for deciding whether or not the extra effort of computing a SuperMSA and inferring a tree from it is beneficial. Based on these assessments, we expect our methodology to be useful for many cases in which diverged sequences are analyzed. The option to generate such a SuperMSA is available at http://guidance.tau.ac.il.
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Affiliation(s)
- Haim Ashkenazy
- Department of Cell Research and Immunology, George S. Wise Faculty of Life Sciences, Tel Aviv University, Ramat Aviv 69978, Tel Aviv, Israel
| | - Itamar Sela
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD 20894, USA
| | - Eli Levy Karin
- Department of Cell Research and Immunology, George S. Wise Faculty of Life Sciences, Tel Aviv University, Ramat Aviv 69978, Tel Aviv, Israel.,Department of Molecular Biology & Ecology of Plants, George S. Wise Faculty of Life Sciences, Tel Aviv University, Tel Aviv 69978, Israel
| | - Giddy Landan
- Institute of Microbiology, Christian-Albrechts-University of Kiel, 24118 Kiel, Germany
| | - Tal Pupko
- Department of Cell Research and Immunology, George S. Wise Faculty of Life Sciences, Tel Aviv University, Ramat Aviv 69978, Tel Aviv, Israel
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45
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Phylogeny and evolutionary history of Pinaceae updated by transcriptomic analysis. Mol Phylogenet Evol 2018; 129:106-116. [DOI: 10.1016/j.ympev.2018.08.011] [Citation(s) in RCA: 43] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2018] [Revised: 06/21/2018] [Accepted: 08/20/2018] [Indexed: 11/19/2022]
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46
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Corcoran P, Gossmann TI, Barton HJ, Slate J, Zeng K. Determinants of the Efficacy of Natural Selection on Coding and Noncoding Variability in Two Passerine Species. Genome Biol Evol 2018; 9:2987-3007. [PMID: 29045655 PMCID: PMC5714183 DOI: 10.1093/gbe/evx213] [Citation(s) in RCA: 33] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 10/16/2017] [Indexed: 02/06/2023] Open
Abstract
Population genetic theory predicts that selection should be more effective when the effective population size (Ne) is larger, and that the efficacy of selection should correlate positively with recombination rate. Here, we analyzed the genomes of ten great tits and ten zebra finches. Nucleotide diversity at 4-fold degenerate sites indicates that zebra finches have a 2.83-fold larger Ne. We obtained clear evidence that purifying selection is more effective in zebra finches. The proportion of substitutions at 0-fold degenerate sites fixed by positive selection (α) is high in both species (great tit 48%; zebra finch 64%) and is significantly higher in zebra finches. When α was estimated on GC-conservative changes (i.e., between A and T and between G and C), the estimates reduced in both species (great tit 22%; zebra finch 53%). A theoretical model presented herein suggests that failing to control for the effects of GC-biased gene conversion (gBGC) is potentially a contributor to the overestimation of α, and that this effect cannot be alleviated by first fitting a demographic model to neutral variants. We present the first estimates in birds for α in the untranslated regions, and found evidence for substantial adaptive changes. Finally, although purifying selection is stronger in high-recombination regions, we obtained mixed evidence for α increasing with recombination rate, especially after accounting for gBGC. These results highlight that it is important to consider the potential confounding effects of gBGC when quantifying selection and that our understanding of what determines the efficacy of selection is incomplete.
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Affiliation(s)
- Pádraic Corcoran
- Department of Animal and Plant Sciences, University of Sheffield, South Yorkshire, United Kingdom
| | - Toni I Gossmann
- Department of Animal and Plant Sciences, University of Sheffield, South Yorkshire, United Kingdom
| | - Henry J Barton
- Department of Animal and Plant Sciences, University of Sheffield, South Yorkshire, United Kingdom
| | | | - Jon Slate
- Department of Animal and Plant Sciences, University of Sheffield, South Yorkshire, United Kingdom
| | - Kai Zeng
- Department of Animal and Plant Sciences, University of Sheffield, South Yorkshire, United Kingdom
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47
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Laumer CE, Gruber-Vodicka H, Hadfield MG, Pearse VB, Riesgo A, Marioni JC, Giribet G. Support for a clade of Placozoa and Cnidaria in genes with minimal compositional bias. eLife 2018; 7:e36278. [PMID: 30373720 PMCID: PMC6277202 DOI: 10.7554/elife.36278] [Citation(s) in RCA: 56] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2018] [Accepted: 10/11/2018] [Indexed: 12/22/2022] Open
Abstract
The phylogenetic placement of the morphologically simple placozoans is crucial to understanding the evolution of complex animal traits. Here, we examine the influence of adding new genomes from placozoans to a large dataset designed to study the deepest splits in the animal phylogeny. Using site-heterogeneous substitution models, we show that it is possible to obtain strong support, in both amino acid and reduced-alphabet matrices, for either a sister-group relationship between Cnidaria and Placozoa, or for Cnidaria and Bilateria as seen in most published work to date, depending on the orthologues selected to construct the matrix. We demonstrate that a majority of genes show evidence of compositional heterogeneity, and that support for the Cnidaria + Bilateria clade can be assigned to this source of systematic error. In interpreting these results, we caution against a peremptory reading of placozoans as secondarily reduced forms of little relevance to broader discussions of early animal evolution.
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Affiliation(s)
- Christopher E Laumer
- Wellcome Trust Sanger InstituteHinxtonUnited Kingdom
- European Molecular Biology Laboratories-European Bioinformatics InstituteHinxtonUnited Kingdom
| | | | - Michael G Hadfield
- Kewalo Marine LaboratoryPacific Biosciences Research Center and the University of Hawaii-ManoaHonoluluUnited States
| | - Vicki B Pearse
- Institute of Marine SciencesUniversity of CaliforniaSanta CruzUnited States
| | - Ana Riesgo
- Invertebrate Division, Life Sciences DepartmentThe Natural History MuseumLondonUnited Kingdom
| | - John C Marioni
- Wellcome Trust Sanger InstituteHinxtonUnited Kingdom
- European Molecular Biology Laboratories-European Bioinformatics InstituteHinxtonUnited Kingdom
- Cancer Research UK Cambridge InstituteUniversity of CambridgeCambridgeUnited Kingdom
| | - Gonzalo Giribet
- Museum of Comparative Zoology, Department of Organismic and Evolutionary BiologyHarvard UniversityCambridgeUnited States
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Hernández-González IL, Moreno-Hagelsieb G, Olmedo-Álvarez G. Environmentally-driven gene content convergence and the Bacillus phylogeny. BMC Evol Biol 2018; 18:148. [PMID: 30285626 PMCID: PMC6171248 DOI: 10.1186/s12862-018-1261-7] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2017] [Accepted: 09/13/2018] [Indexed: 01/28/2023] Open
Abstract
Background Members of the Bacillus genus have been isolated from a variety of environments. However, the relationship between potential metabolism and the niche from which bacteria of this genus have been isolated has not been extensively studied. The existence of a monophyletic aquatic Bacillus group, composed of members isolated from both marine and fresh water has been proposed. Here, we present a phylogenetic/phylogenomic analysis to investigate the potential relationship between the environment from which group members have been isolated and their evolutionary origin. We also carried out hierarchical clustering based on functional content to test for potential environmental effects on the genetic content of these bacteria. Results The phylogenetic reconstruction showed that Bacillus strains classified as aquatic have evolutionary origins in different lineages. Although we observed the presence of a clade consisting exclusively of aquatic Bacillus, it is not comprised of the same strains previously reported. In contrast to phylogeny, clustering based on the functional categories of the encoded proteomes resulted in groups more compatible with the environments from which the organisms were isolated. This evidence suggests a detectable environmental influence on bacterial genetic content, despite their different evolutionary origins. Conclusion Our results suggest that aquatic Bacillus species have polyphyletic origins, but exhibit convergence at the gene content level. Electronic supplementary material The online version of this article (10.1186/s12862-018-1261-7) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Ismael L Hernández-González
- Department of Genetic Engineering, CINVESTAV-Irapuato, Km. 9.6 Libramiento Norte, Carr. Irapuato-Leon, Irapuato, 36824, Guanajuato, Mexico
| | - Gabriel Moreno-Hagelsieb
- Department of Biology, Wilfrid Laurier University, 75 University Ave. W., Waterloo, N2L 3C5, Ontario, Canada.
| | - Gabriela Olmedo-Álvarez
- Department of Genetic Engineering, CINVESTAV-Irapuato, Km. 9.6 Libramiento Norte, Carr. Irapuato-Leon, Irapuato, 36824, Guanajuato, Mexico.
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Schwentner M, Richter S, Rogers DC, Giribet G. Tetraconatan phylogeny with special focus on Malacostraca and Branchiopoda: highlighting the strength of taxon-specific matrices in phylogenomics. Proc Biol Sci 2018; 285:20181524. [PMID: 30135168 PMCID: PMC6125901 DOI: 10.1098/rspb.2018.1524] [Citation(s) in RCA: 52] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2018] [Accepted: 07/18/2018] [Indexed: 01/12/2023] Open
Abstract
Understanding the evolution of Tetraconata or Pancrustacea-the clade that includes crustaceans and insects-requires a well-resolved hypothesis regarding the relationships within and among its constituent taxa. Here, we assembled a taxon-rich phylogenomic dataset focusing on crustacean lineages based solely on genomes and new-generation Illumina-generated transcriptomes, including 89 representatives of Tetraconata. This constitutes, to our knowledge, the first phylogenomic study specifically addressing internal relationships of Malacostraca (with 26 species included) and Branchiopoda (36 species). Seven matrices comprising 81-684 orthogroups and 17 690-242 530 amino acid positions were assembled and analysed under five different analytical approaches. To maximize gene occupancy and to improve resolution, taxon-specific matrices were designed for Malacostraca and Branchiopoda. Key tetraconatan taxa (i.e. Oligostraca, Multicrustacea, Branchiopoda, Malacostraca, Thecostraca, Copepoda and Hexapoda) were monophyletic and well supported. Within Branchiopoda, Phyllopoda, Diplostraca, Cladoceromorpha and Cladocera were monophyletic. Within Malacostraca, the clades Eumalacostraca, Decapoda and Reptantia were well supported. Recovery of Caridoida or Peracarida was highly dependent on the analysis for the complete matrix, but it was consistently monophyletic in the malacostracan-specific matrices. From such examples, we demonstrate that taxon-specific matrices and particular evolutionary models and analytical methods, namely CAT-GTR and Dayhoff recoding, outperform other approaches in resolving certain recalcitrant nodes in phylogenomic analyses.
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Affiliation(s)
- Martin Schwentner
- Museum of Comparative Zoology, Department of Organismic and Evolutionary Biology, Harvard University, 26 Oxford Street, Cambridge, MA 02138, USA
- Centrum of Natural History, Universität Hamburg, Martin-Luther-King-Platz 3, 20146 Hamburg, Germany
| | - Stefan Richter
- Allgemeine und Spezielle Zoologie, Universität Rostock, Universitätsplatz 2, 18055 Rostock, Germany
| | - D Christopher Rogers
- Kansas Biological Survey, Kansas University, Higuchi Hall, 2101 Constant Avenue, Lawrence, KS 66047, USA
| | - Gonzalo Giribet
- Museum of Comparative Zoology, Department of Organismic and Evolutionary Biology, Harvard University, 26 Oxford Street, Cambridge, MA 02138, USA
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50
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Narasumani M, Harrison PM. Discerning evolutionary trends in post-translational modification and the effect of intrinsic disorder: Analysis of methylation, acetylation and ubiquitination sites in human proteins. PLoS Comput Biol 2018; 14:e1006349. [PMID: 30096183 PMCID: PMC6105011 DOI: 10.1371/journal.pcbi.1006349] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2018] [Revised: 08/22/2018] [Accepted: 07/07/2018] [Indexed: 11/18/2022] Open
Abstract
Intrinsically disordered regions (IDRs) of proteins play significant biological functional roles despite lacking a well-defined 3D structure. For example, IDRs provide efficient housing for large numbers of post-translational modification (PTM) sites in eukaryotic proteins. Here, we study the distribution of more than 15,000 experimentally determined human methylation, acetylation and ubiquitination sites (collectively termed 'MAU' sites) in ordered and disordered regions, and analyse their conservation across 380 eukaryotic species. Conservation signals for the maintenance and novel emergence of MAU sites are examined at 11 evolutionary levels from the whole eukaryotic domain down to the ape superfamily, in both ordered and disordered regions. We discover that MAU PTM is a major driver of conservation for arginines and lysines in both ordered and disordered regions, across the 11 levels, most significantly across the mammalian clade. Conservation of human methylatable arginines is very strongly favoured for ordered regions rather than for disordered, whereas methylatable lysines are conserved in either set of regions, and conservation of acetylatable and ubiquitinatable lysines is favoured in disordered over ordered. Notably, we find evidence for the emergence of new lysine MAU sites in disordered regions of proteins in deuterostomes and mammals, and in ordered regions after the dawn of eutherians. For histones specifically, MAU sites demonstrate an idiosyncratic significant conservation pattern that is evident since the last common ancestor of mammals. Similarly, folding-on-binding (FB) regions are highly enriched for MAU sites relative to either ordered or disordered regions, with ubiquitination sites in FBs being highly conserved at all evolutionary levels back as far as mammals. This investigation clearly demonstrates the complex patterns of PTM evolution across the human proteome and that it is necessary to consider conservation of sequence features at multiple evolutionary levels in order not to get an incomplete or misleading picture.
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