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Domazet-Lošo M, Široki T, Šimičević K, Domazet-Lošo T. Macroevolutionary dynamics of gene family gain and loss along multicellular eukaryotic lineages. Nat Commun 2024; 15:2663. [PMID: 38531970 DOI: 10.1038/s41467-024-47017-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2023] [Accepted: 03/11/2024] [Indexed: 03/28/2024] Open
Abstract
The gain and loss of genes fluctuate over evolutionary time in major eukaryotic clades. However, the full profile of these macroevolutionary trajectories is still missing. To give a more inclusive view on the changes in genome complexity across the tree of life, here we recovered the evolutionary dynamics of gene family gain and loss ranging from the ancestor of cellular organisms to 352 eukaryotic species. We show that in all considered lineages the gene family content follows a common evolutionary pattern, where the number of gene families reaches the highest value at a major evolutionary and ecological transition, and then gradually decreases towards extant organisms. This supports theoretical predictions and suggests that the genome complexity is often decoupled from commonly perceived organismal complexity. We conclude that simplification by gene family loss is a dominant force in Phanerozoic genomes of various lineages, probably underpinned by intense ecological specializations and functional outsourcing.
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Affiliation(s)
- Mirjana Domazet-Lošo
- Department of Applied Computing, Faculty of Electrical Engineering and Computing, University of Zagreb, Unska 3, HR-10000, Zagreb, Croatia.
| | - Tin Široki
- Department of Applied Computing, Faculty of Electrical Engineering and Computing, University of Zagreb, Unska 3, HR-10000, Zagreb, Croatia
| | - Korina Šimičević
- Department of Applied Computing, Faculty of Electrical Engineering and Computing, University of Zagreb, Unska 3, HR-10000, Zagreb, Croatia
| | - Tomislav Domazet-Lošo
- Laboratory of Evolutionary Genetics, Division of Molecular Biology, Ruđer Bošković Institute, Bijenička cesta 54, HR-10000, Zagreb, Croatia.
- School of Medicine, Catholic University of Croatia, Ilica 242, HR-10000, Zagreb, Croatia.
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2
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Clark JW. Genome evolution in plants and the origins of innovation. THE NEW PHYTOLOGIST 2023; 240:2204-2209. [PMID: 37658677 DOI: 10.1111/nph.19242] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/14/2023] [Accepted: 08/03/2023] [Indexed: 09/03/2023]
Abstract
Plant evolution has been characterised by a series of major novelties in their vegetative and reproductive traits that have led to greater complexity. Underpinning this diversification has been the evolution of the genome. When viewed at the scale of the plant kingdom, plant genome evolution has been punctuated by conspicuous instances of gene and whole-genome duplication, horizontal gene transfer and extensive gene loss. The periods of dynamic genome evolution often coincide with the evolution of key traits, demonstrating the coevolution of plant genomes and phenotypes at a macroevolutionary scale. Conventionally, plant complexity and diversity have been considered through the lens of gene duplication and the role of gene loss in plant evolution remains comparatively unexplored. However, in light of reductive evolution across multiple plant lineages, the association between gene loss and plant phenotypic diversity warrants greater attention.
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Affiliation(s)
- James W Clark
- School of Biological Sciences, University of Bristol, Tyndall Ave, Bristol, BS8 1TQ, UK
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3
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Prokopchuk G, Butenko A, Dacks JB, Speijer D, Field MC, Lukeš J. Lessons from the deep: mechanisms behind diversification of eukaryotic protein complexes. Biol Rev Camb Philos Soc 2023; 98:1910-1927. [PMID: 37336550 PMCID: PMC10952624 DOI: 10.1111/brv.12988] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2021] [Revised: 05/30/2023] [Accepted: 06/05/2023] [Indexed: 06/21/2023]
Abstract
Genetic variation is the major mechanism behind adaptation and evolutionary change. As most proteins operate through interactions with other proteins, changes in protein complex composition and subunit sequence provide potentially new functions. Comparative genomics can reveal expansions, losses and sequence divergence within protein-coding genes, but in silico analysis cannot detect subunit substitutions or replacements of entire protein complexes. Insights into these fundamental evolutionary processes require broad and extensive comparative analyses, from both in silico and experimental evidence. Here, we combine data from both approaches and consider the gamut of possible protein complex compositional changes that arise during evolution, citing examples of complete conservation to partial and total replacement by functional analogues. We focus in part on complexes in trypanosomes as they represent one of the better studied non-animal/non-fungal lineages, but extend insights across the eukaryotes by extensive comparative genomic analysis. We argue that gene loss plays an important role in diversification of protein complexes and hence enhancement of eukaryotic diversity.
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Affiliation(s)
- Galina Prokopchuk
- Institute of Parasitology, Biology Centre, Czech Academy of SciencesBranišovská 1160/31České Budějovice37005Czech Republic
- Faculty of ScienceUniversity of South BohemiaBranišovská 1160/31České Budějovice37005Czech Republic
| | - Anzhelika Butenko
- Institute of Parasitology, Biology Centre, Czech Academy of SciencesBranišovská 1160/31České Budějovice37005Czech Republic
- Faculty of ScienceUniversity of South BohemiaBranišovská 1160/31České Budějovice37005Czech Republic
- Life Science Research Centre, Faculty of ScienceUniversity of OstravaChittussiho 983/10Ostrava71000Czech Republic
| | - Joel B. Dacks
- Institute of Parasitology, Biology Centre, Czech Academy of SciencesBranišovská 1160/31České Budějovice37005Czech Republic
- Division of Infectious Diseases, Department of MedicineUniversity of Alberta1‐124 Clinical Sciences Building, 11350‐83 AvenueEdmontonT6G 2R3AlbertaCanada
- Centre for Life's Origins and Evolution, Department of Genetics, Evolution and the EnvironmentUniversity College LondonDarwin Building, Gower StreetLondonWC1E 6BTUK
| | - Dave Speijer
- Medical Biochemistry, Amsterdam UMCUniversity of AmsterdamMeibergdreef 15Amsterdam1105 AZThe Netherlands
| | - Mark C. Field
- Institute of Parasitology, Biology Centre, Czech Academy of SciencesBranišovská 1160/31České Budějovice37005Czech Republic
- School of Life SciencesUniversity of DundeeDow StreetDundeeDD1 5EHScotlandUK
| | - Julius Lukeš
- Institute of Parasitology, Biology Centre, Czech Academy of SciencesBranišovská 1160/31České Budějovice37005Czech Republic
- Faculty of ScienceUniversity of South BohemiaBranišovská 1160/31České Budějovice37005Czech Republic
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4
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Hansen MH, Adamek M, Iftime D, Petras D, Schuseil F, Grond S, Stegmann E, Cryle MJ, Ziemert N. Resurrecting ancestral antibiotics: unveiling the origins of modern lipid II targeting glycopeptides. Nat Commun 2023; 14:7842. [PMID: 38030603 PMCID: PMC10687080 DOI: 10.1038/s41467-023-43451-4] [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: 08/10/2023] [Accepted: 11/09/2023] [Indexed: 12/01/2023] Open
Abstract
Antibiotics are central to modern medicine, and yet they are mainly the products of intra and inter-kingdom evolutionary warfare. To understand how nature evolves antibiotics around a common mechanism of action, we investigated the origins of an extremely valuable class of compounds, lipid II targeting glycopeptide antibiotics (GPAs, exemplified by teicoplanin and vancomycin), which are used as last resort for the treatment of antibiotic resistant bacterial infections. Using a molecule-centred approach and computational techniques, we first predicted the nonribosomal peptide synthetase assembly line of paleomycin, the ancestral parent of lipid II targeting GPAs. Subsequently, we employed synthetic biology techniques to produce the predicted peptide and validated its antibiotic activity. We revealed the structure of paleomycin, which enabled us to address how nature morphs a peptide antibiotic scaffold through evolution. In doing so, we obtained temporal snapshots of key selection domains in nonribosomal peptide synthesis during the biosynthetic journey from ancestral, teicoplanin-like GPAs to modern GPAs such as vancomycin. Our study demonstrates the synergy of computational techniques and synthetic biology approaches enabling us to journey back in time, trace the temporal evolution of antibiotics, and revive these ancestral molecules. It also reveals the optimisation strategies nature has applied to evolve modern GPAs, laying the foundation for future efforts to engineer this important class of antimicrobial agents.
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Affiliation(s)
- Mathias H Hansen
- Department of Biochemistry and Molecular Biology, The Monash Biomedicine Discovery Institute, Monash University, Clayton, VIC, 3800, Australia
- EMBL Australia, Monash University, Clayton, VIC, 3800, Australia
- ARC Centre of Excellence for Innovations in Peptide and Protein Science, Monash University, Clayton, VIC, 3800, Australia
| | - Martina Adamek
- Interfaculty Institute of Microbiology and Infection Medicine Tübingen, Cluster of Excellence 'Controlling Microbes to Fight Infections', University of Tübingen, Tübingen, Germany
- German Centre for Infection Research (DZIF), Partner Site Tübingen, Tübingen, Germany
- Institute for Bioinformatics and Medical Informatics (IBMI), University of Tübingen, Tübingen, Germany
| | - Dumitrita Iftime
- Interfaculty Institute of Microbiology and Infection Medicine Tübingen, Cluster of Excellence 'Controlling Microbes to Fight Infections', University of Tübingen, Tübingen, Germany
| | - Daniel Petras
- Interfaculty Institute of Microbiology and Infection Medicine Tübingen, Cluster of Excellence 'Controlling Microbes to Fight Infections', University of Tübingen, Tübingen, Germany
| | - Frauke Schuseil
- Interfaculty Institute of Microbiology and Infection Medicine Tübingen, Cluster of Excellence 'Controlling Microbes to Fight Infections', University of Tübingen, Tübingen, Germany
- German Centre for Infection Research (DZIF), Partner Site Tübingen, Tübingen, Germany
- Institute for Bioinformatics and Medical Informatics (IBMI), University of Tübingen, Tübingen, Germany
| | - Stephanie Grond
- Institute of Organic Chemistry, University of Tübingen, Tübingen, Germany
| | - Evi Stegmann
- Interfaculty Institute of Microbiology and Infection Medicine Tübingen, Cluster of Excellence 'Controlling Microbes to Fight Infections', University of Tübingen, Tübingen, Germany.
- Institute for Bioinformatics and Medical Informatics (IBMI), University of Tübingen, Tübingen, Germany.
| | - Max J Cryle
- Department of Biochemistry and Molecular Biology, The Monash Biomedicine Discovery Institute, Monash University, Clayton, VIC, 3800, Australia.
- EMBL Australia, Monash University, Clayton, VIC, 3800, Australia.
- ARC Centre of Excellence for Innovations in Peptide and Protein Science, Monash University, Clayton, VIC, 3800, Australia.
| | - Nadine Ziemert
- Interfaculty Institute of Microbiology and Infection Medicine Tübingen, Cluster of Excellence 'Controlling Microbes to Fight Infections', University of Tübingen, Tübingen, Germany.
- German Centre for Infection Research (DZIF), Partner Site Tübingen, Tübingen, Germany.
- Institute for Bioinformatics and Medical Informatics (IBMI), University of Tübingen, Tübingen, Germany.
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5
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Ruiz-Trillo I, Kin K, Casacuberta E. The Origin of Metazoan Multicellularity: A Potential Microbial Black Swan Event. Annu Rev Microbiol 2023; 77:499-516. [PMID: 37406343 DOI: 10.1146/annurev-micro-032421-120023] [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: 07/07/2023]
Abstract
The emergence of animals from their unicellular ancestors is a major evolutionary event. Thanks to the study of diverse close unicellular relatives of animals, we now have a better grasp of what the unicellular ancestor of animals was like. However, it is unclear how that unicellular ancestor of animals became the first animals. To explain this transition, two popular theories, the choanoblastaea and the synzoospore, have been proposed. We will revise and expose the flaws in these two theories while showing that, due to the limits of our current knowledge, the origin of animals is a biological black swan event. As such, the origin of animals defies retrospective explanations. Therefore, we should be extra careful not to fall for confirmation biases based on few data and, instead, embrace this uncertainty and be open to alternative scenarios. With the aim to broaden the potential explanations on how animals emerged, we here propose two novel and alternative scenarios. In any case, to find the answer to how animals evolved, additional data will be required, as will the hunt for microscopic creatures that are closely related to animals but have not yet been sampled and studied.
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Affiliation(s)
- Iñaki Ruiz-Trillo
- Institut de Biologia Evolutiva (CSIC-Universitat Pompeu Fabra), Barcelona, Spain;
- ICREA, Barcelona, Spain
| | - Koryu Kin
- Institut de Biologia Evolutiva (CSIC-Universitat Pompeu Fabra), Barcelona, Spain;
| | - Elena Casacuberta
- Institut de Biologia Evolutiva (CSIC-Universitat Pompeu Fabra), Barcelona, Spain;
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6
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Gradistics: An underappreciated dimension in evolutionary space. Biosystems 2023; 224:104844. [PMID: 36736879 DOI: 10.1016/j.biosystems.2023.104844] [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: 09/08/2022] [Revised: 01/28/2023] [Accepted: 01/30/2023] [Indexed: 02/04/2023]
Abstract
The growth of complexity is an unsolved and underappreciated problem. We consider possible causes of this growth, hypotheses testing, molecular mechanisms, complexity measures, cases of simplification, and significance for biomedicine. We focus on a general ability of regulation, which is based on the growing information storage and processing capacities, as the main proxy of complexity. Natural selection is indifferent to complexity. However, complexification can be inferred from the same first principle, on which natural selection is founded. Natural selection depends on potentially unlimited reproduction under limited environmental conditions. Because of the demographic pressure, the simple ecological niches become fulfilled and diversified (due to species splitting and divergence). Diversification increases complexity of biocenoses. After the filling and diversification of simple niches, the more complex niches can arise. This is the 'atomic orbitals' (AO) model. Complexity has many shortcomings but it has an advantage. This advantage is ability to regulatory adaptation, including behavioral, formed in the evolution by means of genetic adaptation. Regulatory adaptation is much faster than genetic one because it is based on the information previously accumulated via genetic adaptation and learning. Regulatory adaptation further increases complexity of biocenoses. This is the 'regulatory advantage' (RA) model. The comparison of both models allows testable predictions. We focus on the animal evolution because of the appearance of higher regulatory level (nervous system), which is absent in other lineages, and relevance to humans (including biomedical aspects).
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7
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Wagner HJ, Genner MJ, Partridge JC, Chung WS, Marshall NJ, Robison BH, Douglas RH. Diversity and evolution of optically complex eyes in a family of deep-sea fish: Ocular diverticula in barreleye spookfish (Opisthoproctidae). Front Ecol Evol 2022. [DOI: 10.3389/fevo.2022.1044565] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/03/2022] Open
Abstract
Several families of mesopelagic fish have tubular eyes that are usually upwardly directed. These maximise sensitivity to dim downwelling sunlight and dorsal bioluminescence, as well as facilitating the detection of dark silhouettes above the animal. Such eyes, however, have a much-reduced field of view and will not be sensitive to, for example, lateral and ventral bioluminescent stimuli. All mesopelagic Opisthoproctidae so far examined have evolved mechanisms for extending the limited visual field of their eyes using approximately ventrolaterally directed, light-sensitive, diverticula. Some genera have small rudimentary lateral retinal areas capable of detecting only unfocussed illumination. Others have more extensive structures resulting in eyes that simultaneously focus light from above onto the main retina of the tubular eye using a lens, while diverticula produce focussed images of ventrolateral illumination using either reflection or possibly refraction. These bipartite structures represent perhaps the most optically complex of all vertebrate eyes. Here we extend the limited previous data on the ocular morphology of five Opisthoproctidae (Opisthoproctus soleatus, Winteria telescopa, Dolichopteryx longipes, Rhynchohyalus natalensis, and Bathylychnops exilis) using a combination of histology and magnetic resonance imaging and provide a preliminary description of the eyes of Macropinna microstoma. We note an increase in diverticular complexity over the life span of some species and quantify the contribution of the diverticulum to the eye’s total neural output in D. longipes and R. natalensis (25 and 20%, respectively). To help understand the evolution of Opisthoproctidae ocular diversity, a phylogeny, including all the species whose eye types are known, was reconstructed using DNA sequences from 15 mitochondrial and four nuclear genes. Mapping the different types of diverticula onto this phylogeny suggests a process of repeated evolution of complex ocular morphology from more rudimentary diverticula.
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8
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Harris BJ, Clark JW, Schrempf D, Szöllősi GJ, Donoghue PCJ, Hetherington AM, Williams TA. Divergent evolutionary trajectories of bryophytes and tracheophytes from a complex common ancestor of land plants. Nat Ecol Evol 2022; 6:1634-1643. [PMID: 36175544 PMCID: PMC9630106 DOI: 10.1038/s41559-022-01885-x] [Citation(s) in RCA: 25] [Impact Index Per Article: 12.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2021] [Accepted: 08/12/2022] [Indexed: 11/16/2022]
Abstract
The origin of plants and their colonization of land fundamentally transformed the terrestrial environment. Here we elucidate the basis of this formative episode in Earth history through patterns of lineage, gene and genome evolution. We use new fossil calibrations, a relative clade age calibration (informed by horizontal gene transfer) and new phylogenomic methods for mapping gene family origins. Distinct rooting strategies resolve tracheophytes (vascular plants) and bryophytes (non-vascular plants) as monophyletic sister groups that diverged during the Cambrian, 515-494 million years ago. The embryophyte stem is characterized by a burst of gene innovation, while bryophytes subsequently experienced an equally dramatic episode of reductive genome evolution in which they lost genes associated with the elaboration of vasculature and the stomatal complex. Overall, our analyses reveal that extant tracheophytes and bryophytes are both highly derived from a more complex ancestral land plant. Understanding the origin of land plants requires tracing character evolution across a diversity of modern lineages.
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Affiliation(s)
- Brogan J Harris
- School of Biological Sciences, University of Bristol, Bristol, UK
| | - James W Clark
- School of Biological Sciences, University of Bristol, Bristol, UK
- Bristol Palaeobiology Group, School of Earth Sciences, University of Bristol, Bristol, UK
| | - Dominik Schrempf
- Department of Biological Physics, Eötvös Loránd University, Budapest, Hungary
| | - Gergely J Szöllősi
- Department of Biological Physics, Eötvös Loránd University, Budapest, Hungary
- MTA-ELTE 'Lendület' Evolutionary Genomics Research Group, Budapest, Hungary
- Institute of Evolution, Centre for Ecological Research, Budapest, Hungary
| | - Philip C J Donoghue
- Bristol Palaeobiology Group, School of Earth Sciences, University of Bristol, Bristol, UK
| | | | - Tom A Williams
- School of Biological Sciences, University of Bristol, Bristol, UK.
- Bristol Palaeobiology Group, School of Earth Sciences, University of Bristol, Bristol, UK.
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9
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Massive Loss of Transcription Factors Promotes the Initial Diversification of Placental Mammals. Int J Mol Sci 2022; 23:ijms23179720. [PMID: 36077118 PMCID: PMC9456351 DOI: 10.3390/ijms23179720] [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: 07/25/2022] [Revised: 08/22/2022] [Accepted: 08/23/2022] [Indexed: 11/17/2022] Open
Abstract
As one of the most successful group of organisms, mammals occupy a variety of niches on Earth as a result of macroevolution. Transcription factors (TFs), the fundamental regulators of gene expression, may also have evolved. To examine the relationship between TFs and mammalian macroevolution, we analyzed 140,821 de novo-identified TFs and their birth and death histories from 96 mammalian species. Gene tree vs. species tree reconciliation revealed that placental mammals experienced an upsurge in TF losses around 100 million years ago (Mya) and also near the Cretaceous–Paleogene boundary (K–Pg boundary, 66 Mya). Early Euarchontoglires, Laurasiatheria and marsupials appeared between 100 and 95 Mya and underwent initial diversification. The K-Pg boundary was associated with the massive extinction of dinosaurs, which lead to adaptive radiation of mammals. Surprisingly, TF loss decelerated, rather than accelerated, molecular evolutionary rates of their target genes. As the rate of molecular evolution is affected by the mutation rate, the proportion of neutral mutations and the population size, the decrease in molecular evolution may reflect increased functional constraints to survive target genes.
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10
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MRTF specifies a muscle-like contractile module in Porifera. Nat Commun 2022; 13:4134. [PMID: 35840552 PMCID: PMC9287330 DOI: 10.1038/s41467-022-31756-9] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2022] [Accepted: 06/30/2022] [Indexed: 12/13/2022] Open
Abstract
Muscle-based movement is a hallmark of animal biology, but the evolutionary origins of myocytes are unknown. Although believed to lack muscles, sponges (Porifera) are capable of coordinated whole-body contractions that purge debris from internal water canals. This behavior has been observed for decades, but their contractile tissues remain uncharacterized with respect to their ultrastructure, regulation, and development. We examine the sponge Ephydatia muelleri and find tissue-wide organization of a contractile module composed of actin, striated-muscle myosin II, and transgelin, and that contractions are regulated by the release of internal Ca2+ stores upstream of the myosin-light-chain-kinase (MLCK) pathway. The development of this contractile module appears to involve myocardin-related transcription factor (MRTF) as part of an environmentally inducible transcriptional complex that also functions in muscle development, plasticity, and regeneration. As an actin-regulated force-sensor, MRTF-activity offers a mechanism for how the contractile tissues that line water canals can dynamically remodel in response to flow and can re-form normally from stem-cells in the absence of the intrinsic spatial cues typical of animal embryogenesis. We conclude that the contractile module of sponge tissues shares elements of homology with contractile tissues in other animals, including muscles, indicating descent from a common, multifunctional tissue in the animal stem-lineage. Myocytes are a key cell type that enable animal movement, but their evolutionary origins remain unclear. Colgren and Nichols describe molecular and functional similarities between a contractile module in tissues of a sponge and muscle tissues in other animals, indicating a common evolutionary origin.
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11
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Wu B, Hao W, Cox MP. Reconstruction of gene innovation associated with major evolutionary transitions in the kingdom Fungi. BMC Biol 2022; 20:144. [PMID: 35706021 PMCID: PMC9202105 DOI: 10.1186/s12915-022-01346-8] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2022] [Accepted: 06/07/2022] [Indexed: 11/26/2022] Open
Abstract
Background Fungi exhibit astonishing diversity with multiple major phenotypic transitions over the kingdom’s evolutionary history. As part of this process, fungi developed hyphae, adapted to land environments (terrestrialization), and innovated their sexual structures. These changes also helped fungi establish ecological relationships with other organisms (animals and plants), but the genomic basis of these changes remains largely unknown. Results By systematically analyzing 304 genomes from all major fungal groups, together with a broad range of eukaryotic outgroups, we have identified 188 novel orthogroups associated with major changes during the evolution of fungi. Functional annotations suggest that many of these orthogroups were involved in the formation of key trait innovations in extant fungi and are functionally connected. These innovations include components for cell wall formation, functioning of the spindle pole body, polarisome formation, hyphal growth, and mating group signaling. Innovation of mitochondria-localized proteins occurred widely during fungal transitions, indicating their previously unrecognized importance. We also find that prokaryote-derived horizontal gene transfer provided a small source of evolutionary novelty with such genes involved in key metabolic pathways. Conclusions The overall picture is one of a relatively small number of novel genes appearing at major evolutionary transitions in the phylogeny of fungi, with most arising de novo and horizontal gene transfer providing only a small additional source of evolutionary novelty. Our findings contribute to an increasingly detailed portrait of the gene families that define fungal phyla and underpin core features of extant fungi. Supplementary Information The online version contains supplementary material available at 10.1186/s12915-022-01346-8.
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Affiliation(s)
- Baojun Wu
- School of Natural Sciences, Massey University, Palmerston North, 4410, New Zealand.
| | - Weilong Hao
- Department of Biological Sciences, Wayne State University, Detroit, MI, USA
| | - Murray P Cox
- School of Natural Sciences, Massey University, Palmerston North, 4410, New Zealand.
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12
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Gaia as Solaris: An Alternative Default Evolutionary Trajectory. ORIGINS LIFE EVOL B 2022; 52:129-147. [PMID: 35441955 DOI: 10.1007/s11084-022-09619-6] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2021] [Accepted: 01/21/2022] [Indexed: 01/23/2023]
Abstract
Now that we know that Earth-like planets are ubiquitous in the universe, as well as that most of them are much older than the Earth, it is justified to ask to what extent evolutionary outcomes on other such planets are similar, or indeed commensurable, to the outcomes we perceive around us. In order to assess the degree of specialty or mediocrity of our trajectory of biospheric evolution, we need to take into account recent advances in theoretical astrobiology, in particular (i) establishing the history of habitable planets' formation in the Galaxy, and (ii) understanding the crucial importance of "Gaian" feedback loops and temporal windows for the interaction of early life with its physical environment. Hereby we consider an alternative macroevolutionary pathway that may result in tight functional integration of all sub-planetary ecosystems, eventually giving rise to a true superorganism at the biospheric level. The blueprint for a possible outcome of this scenario has been masterfully provided by the great Polish novelist Stanisław Lem in his 1961 novel Solaris. In fact, Solaris offers such a persuasive and powerful case for an "extremely strong" Gaia hypothesis that it is, arguably, high time to investigate it in a discursive astrobiological and philosophical context. In addition to novel predictions in the domain of potentially detectable biosignatures, some additional cognitive and heuristic benefits of studying such extreme cases of functional integration are briefly discussed.
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13
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Schierwater B, Osigus HJ, Bergmann T, Blackstone NW, Hadrys H, Hauslage J, Humbert PO, Kamm K, Kvansakul M, Wysocki K, DeSalle R. The enigmatic Placozoa part 1: Exploring evolutionary controversies and poor ecological knowledge. Bioessays 2021; 43:e2100080. [PMID: 34472126 DOI: 10.1002/bies.202100080] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2021] [Revised: 07/21/2021] [Accepted: 08/16/2021] [Indexed: 12/13/2022]
Abstract
The placozoan Trichoplax adhaerens is a tiny hairy plate and more simply organized than any other living metazoan. After its original description by F.E. Schulze in 1883, it attracted attention as a potential model for the ancestral state of metazoan organization, the "Urmetazoon". Trichoplax lacks any kind of symmetry, organs, nerve cells, muscle cells, basal lamina, and extracellular matrix. Furthermore, the placozoan genome is the smallest (not secondarily reduced) genome of all metazoan genomes. It harbors a remarkably rich diversity of genes and has been considered the best living surrogate for a metazoan ancestor genome. The phylum Placozoa presently harbors three formally described species, while several dozen "cryptic" species are yet awaiting their description. The phylogenetic position of placozoans has recently become a contested arena for modern phylogenetic analyses and view-driven claims. Trichoplax offers unique prospects for understanding the minimal requirements of metazoan animal organization and their corresponding malfunctions.
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Affiliation(s)
- Bernd Schierwater
- Institute of Animal Ecology, University of Veterinary Medicine Hannover, Foundation, Hannover, Germany
| | - Hans-Jürgen Osigus
- Institute of Animal Ecology, University of Veterinary Medicine Hannover, Foundation, Hannover, Germany
| | - Tjard Bergmann
- Institute of Animal Ecology, University of Veterinary Medicine Hannover, Foundation, Hannover, Germany
| | - Neil W Blackstone
- Department of Biological Sciences, Northern Illinois University, DeKalb, Illinois, USA
| | - Heike Hadrys
- Institute of Animal Ecology, University of Veterinary Medicine Hannover, Foundation, Hannover, Germany
| | - Jens Hauslage
- Gravitational Biology, Institute of Aerospace Medicine, German Aerospace Center (DLR), Cologne, Germany
| | - Patrick O Humbert
- Department of Biochemistry & Genetics, La Trobe Institute for Molecular Science, La Trobe University, Melbourne, Victoria, Australia.,Research Centre for Molecular Cancer Prevention, La Trobe University, Melbourne, Victoria, 3086, Australia
| | - Kai Kamm
- Institute of Animal Ecology, University of Veterinary Medicine Hannover, Foundation, Hannover, Germany
| | - Marc Kvansakul
- Department of Biochemistry & Genetics, La Trobe Institute for Molecular Science, La Trobe University, Melbourne, Victoria, Australia.,Research Centre for Molecular Cancer Prevention, La Trobe University, Melbourne, Victoria, 3086, Australia
| | - Kathrin Wysocki
- Institute of Animal Ecology, University of Veterinary Medicine Hannover, Foundation, Hannover, Germany
| | - Rob DeSalle
- American Museum of Natural History, New York, New York, USA
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14
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El Baidouri F, Zalar P, James TY, Gladfelter AS, Amend A. Evolution and Physiology of Amphibious Yeasts. Annu Rev Microbiol 2021; 75:337-357. [PMID: 34351793 DOI: 10.1146/annurev-micro-051421-121352] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Since the emergence of the first fungi some 700 million years ago, unicellular yeast-like forms have emerged multiple times in independent lineages via convergent evolution. While tens to hundreds of millions of years separate the independent evolution of these unicellular organisms, they share remarkable phenotypic and metabolic similarities, and all have streamlined genomes. Yeasts occur in every aquatic environment yet examined. Many species are aquatic; perhaps most are amphibious. How these species have evolved to thrive in aquatic habitats is fundamental to understanding functions and evolutionary mechanisms in this unique group of fungi. Here we review the state of knowledge of the physiological and ecological diversity of amphibious yeasts and their key evolutionary adaptations enabling survival in aquatic habitats. We emphasize some genera previously thought to be exclusively terrestrial. Finally, we discuss the ability of many yeasts to survive in extreme habitats and how this might lend insight into ecological plasticity, including amphibious lifestyles. Expected final online publication date for the Annual Review of Microbiology, Volume 75 is October 2021. Please see http://www.annualreviews.org/page/journal/pubdates for revised estimates.
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Affiliation(s)
- Fouad El Baidouri
- School of Life Sciences, University of Hawai'i at Mānoa, Honolulu, Hawaii 96822, USA; , .,Harvard T.H. Chan School of Public Health, Boston, Massachusetts 02115, USA
| | - Polona Zalar
- Department of Biology, Biotechnical Faculty, University of Ljubljana, 1000 Ljubljana, Slovenia
| | - Timothy Y James
- Department of Ecology and Evolutionary Biology, University of Michigan, Ann Arbor, Michigan 48109, USA
| | - Amy S Gladfelter
- Department of Biology, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599, USA.,Marine Biological Laboratory, Woods Hole, Massachusetts 02543, USA
| | - Anthony Amend
- School of Life Sciences, University of Hawai'i at Mānoa, Honolulu, Hawaii 96822, USA; ,
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15
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Beutel RG, Friedrich F, Economo EP. Patterns of morphological simplification and innovation in the megadiverse Holometabola (Insecta). Cladistics 2021; 38:227-245. [DOI: 10.1111/cla.12483] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 06/22/2021] [Indexed: 12/22/2022] Open
Affiliation(s)
- Rolf Georg Beutel
- Entomology Group Institut für Zoologie und Evolutionsforschung Friedrich‐Schiller‐Universität Jena Erbertstrasse 1 Jena D‐07743 Germany
- Biodiversity and Biocomplexity Unit Okinawa Institute of Science and Technology Graduate University 1919‐1 Tancha, Onna‐son Kunigami‐gun Okinawa 904‐0495 Japan
| | - Frank Friedrich
- Institut für Zoologie Universität Hamburg Martin‐Luther‐King‐Platz 3 Hamburg D‐20146 Germany
| | - Evan P. Economo
- Biodiversity and Biocomplexity Unit Okinawa Institute of Science and Technology Graduate University 1919‐1 Tancha, Onna‐son Kunigami‐gun Okinawa 904‐0495 Japan
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16
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Kin K, Schaap P. Evolution of Multicellular Complexity in The Dictyostelid Social Amoebas. Genes (Basel) 2021; 12:487. [PMID: 33801615 PMCID: PMC8067170 DOI: 10.3390/genes12040487] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2021] [Revised: 03/17/2021] [Accepted: 03/20/2021] [Indexed: 12/14/2022] Open
Abstract
Multicellularity evolved repeatedly in the history of life, but how it unfolded varies greatly between different lineages. Dictyostelid social amoebas offer a good system to study the evolution of multicellular complexity, with a well-resolved phylogeny and molecular genetic tools being available. We compare the life cycles of the Dictyostelids with closely related amoebozoans to show that complex life cycles were already present in the unicellular common ancestor of Dictyostelids. We propose frost resistance as an early driver of multicellular evolution in Dictyostelids and show that the cell signalling pathways for differentiating spore and stalk cells evolved from that for encystation. The stalk cell differentiation program was further modified, possibly through gene duplication, to evolve a new cell type, cup cells, in Group 4 Dictyostelids. Studies in various multicellular organisms, including Dictyostelids, volvocine algae, and metazoans, suggest as a common principle in the evolution of multicellular complexity that unicellular regulatory programs for adapting to environmental change serve as "proto-cell types" for subsequent evolution of multicellular organisms. Later, new cell types could further evolve by duplicating and diversifying the "proto-cell type" gene regulatory networks.
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Affiliation(s)
- Koryu Kin
- School of Life Sciences, University of Dundee, Dundee DD1 5EH, UK;
- Institut de Biologia Evolutiva (CSIC-Universitat Pompeu Fabra), Passeig Marítim de la Barceloneta 37–49, 08003 Barcelona, Spain
| | - Pauline Schaap
- School of Life Sciences, University of Dundee, Dundee DD1 5EH, UK;
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17
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Zajac N, Zoller S, Seppälä K, Moi D, Dessimoz C, Jokela J, Hartikainen H, Glover N. Gene Duplication and Gain in the Trematode Atriophallophorus winterbourni Contributes to Adaptation to Parasitism. Genome Biol Evol 2021; 13:evab010. [PMID: 33484570 PMCID: PMC7936022 DOI: 10.1093/gbe/evab010] [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] [Accepted: 01/10/2021] [Indexed: 01/10/2023] Open
Abstract
Gene duplications and novel genes have been shown to play a major role in helminth adaptation to a parasitic lifestyle because they provide the novelty necessary for adaptation to a changing environment, such as living in multiple hosts. Here we present the de novo sequenced and annotated genome of the parasitic trematode Atriophallophorus winterbourni and its comparative genomic analysis to other major parasitic trematodes. First, we reconstructed the species phylogeny, and dated the split of A. winterbourni from the Opisthorchiata suborder to approximately 237.4 Ma (±120.4 Myr). We then addressed the question of which expanded gene families and gained genes are potentially involved in adaptation to parasitism. To do this, we used hierarchical orthologous groups to reconstruct three ancestral genomes on the phylogeny leading to A. winterbourni and performed a GO (Gene Ontology) enrichment analysis of the gene composition of each ancestral genome, allowing us to characterize the subsequent genomic changes. Out of the 11,499 genes in the A. winterbourni genome, as much as 24% have arisen through duplication events since the speciation of A. winterbourni from the Opisthorchiata, and as much as 31.9% appear to be novel, that is, newly acquired. We found 13 gene families in A. winterbourni to have had more than ten genes arising through these recent duplications; all of which have functions potentially relating to host behavioral manipulation, host tissue penetration, and hiding from host immunity through antigen presentation. We identified several families with genes evolving under positive selection. Our results provide a valuable resource for future studies on the genomic basis of adaptation to parasitism and point to specific candidate genes putatively involved in antagonistic host-parasite adaptation.
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Affiliation(s)
- Natalia Zajac
- Eawag, Swiss Federal Institute of Aquatic Science and Technology, Dübendorf, Switzerland
- ETH Zurich, Department of Environmental Systems Science, Institute of Integrative Biology, Zurich, Switzerland
| | - Stefan Zoller
- ETH Zurich, Department of Environmental Systems Science, Institute of Integrative Biology, Zurich, Switzerland
| | - Katri Seppälä
- Eawag, Swiss Federal Institute of Aquatic Science and Technology, Dübendorf, Switzerland
- Research Department for Limnology, University of Innsbruck, Mondsee, Austria
| | - David Moi
- Department of Computational Biology, University of Lausanne, Switzerland
- Swiss Institute of Bioinformatics, Lausanne, Switzerland
- Center for Integrative Genomics, Lausanne, Switzerland
| | - Christophe Dessimoz
- Department of Computational Biology, University of Lausanne, Switzerland
- Swiss Institute of Bioinformatics, Lausanne, Switzerland
- Center for Integrative Genomics, Lausanne, Switzerland
- Centre for Life’s Origins and Evolution, Department of Genetics Evolution and Environment, University College London, United Kingdom
- Department of Computer Science, University College London, United Kingdom
| | - Jukka Jokela
- Eawag, Swiss Federal Institute of Aquatic Science and Technology, Dübendorf, Switzerland
- ETH Zurich, Department of Environmental Systems Science, Institute of Integrative Biology, Zurich, Switzerland
| | - Hanna Hartikainen
- Eawag, Swiss Federal Institute of Aquatic Science and Technology, Dübendorf, Switzerland
- ETH Zurich, Department of Environmental Systems Science, Institute of Integrative Biology, Zurich, Switzerland
- School of Life Sciences, University of Nottingham, University Park, United Kingdom
| | - Natasha Glover
- Department of Computational Biology, University of Lausanne, Switzerland
- Swiss Institute of Bioinformatics, Lausanne, Switzerland
- Center for Integrative Genomics, Lausanne, Switzerland
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18
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Ros-Rocher N, Pérez-Posada A, Leger MM, Ruiz-Trillo I. The origin of animals: an ancestral reconstruction of the unicellular-to-multicellular transition. Open Biol 2021; 11:200359. [PMID: 33622103 PMCID: PMC8061703 DOI: 10.1098/rsob.200359] [Citation(s) in RCA: 45] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
How animals evolved from a single-celled ancestor, transitioning from a unicellular lifestyle to a coordinated multicellular entity, remains a fascinating question. Key events in this transition involved the emergence of processes related to cell adhesion, cell–cell communication and gene regulation. To understand how these capacities evolved, we need to reconstruct the features of both the last common multicellular ancestor of animals and the last unicellular ancestor of animals. In this review, we summarize recent advances in the characterization of these ancestors, inferred by comparative genomic analyses between the earliest branching animals and those radiating later, and between animals and their closest unicellular relatives. We also provide an updated hypothesis regarding the transition to animal multicellularity, which was likely gradual and involved the use of gene regulatory mechanisms in the emergence of early developmental and morphogenetic plans. Finally, we discuss some new avenues of research that will complement these studies in the coming years.
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Affiliation(s)
- Núria Ros-Rocher
- Institut de Biologia Evolutiva (CSIC-Universitat Pompeu Fabra), Passeig Marítim de la Barceloneta 37-49, 08003 Barcelona, Catalonia, Spain
| | - Alberto Pérez-Posada
- Institut de Biologia Evolutiva (CSIC-Universitat Pompeu Fabra), Passeig Marítim de la Barceloneta 37-49, 08003 Barcelona, Catalonia, Spain.,Centro Andaluz de Biología del Desarrollo (CSIC-Universidad Pablo de Olavide), Carretera de Utrera Km 1, 41013 Sevilla, Andalusia, Spain
| | - Michelle M Leger
- Institut de Biologia Evolutiva (CSIC-Universitat Pompeu Fabra), Passeig Marítim de la Barceloneta 37-49, 08003 Barcelona, Catalonia, Spain
| | - Iñaki Ruiz-Trillo
- Institut de Biologia Evolutiva (CSIC-Universitat Pompeu Fabra), Passeig Marítim de la Barceloneta 37-49, 08003 Barcelona, Catalonia, Spain.,Departament de Genètica, Microbiologia i Estadística, Institut de Recerca de la Biodiversitat, Universitat de Barcelona, Avinguda Diagonal 643, 08028 Barcelona, Catalonia, Spain.,ICREA, Passeig Lluís Companys 23, 08010 Barcelona, Catalonia, Spain
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19
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Futo M, Opašić L, Koska S, Čorak N, Široki T, Ravikumar V, Thorsell A, Lenuzzi M, Kifer D, Domazet-Lošo M, Vlahoviček K, Mijakovic I, Domazet-Lošo T. Embryo-Like Features in Developing Bacillus subtilis Biofilms. Mol Biol Evol 2021; 38:31-47. [PMID: 32871001 PMCID: PMC7783165 DOI: 10.1093/molbev/msaa217] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022] Open
Abstract
Correspondence between evolution and development has been discussed for more than two centuries. Recent work reveals that phylogeny-ontogeny correlations are indeed present in developmental transcriptomes of eukaryotic clades with complex multicellularity. Nevertheless, it has been largely ignored that the pervasive presence of phylogeny-ontogeny correlations is a hallmark of development in eukaryotes. This perspective opens a possibility to look for similar parallelisms in biological settings where developmental logic and multicellular complexity are more obscure. For instance, it has been increasingly recognized that multicellular behavior underlies biofilm formation in bacteria. However, it remains unclear whether bacterial biofilm growth shares some basic principles with development in complex eukaryotes. Here we show that the ontogeny of growing Bacillus subtilis biofilms recapitulates phylogeny at the expression level. Using time-resolved transcriptome and proteome profiles, we found that biofilm ontogeny correlates with the evolutionary measures, in a way that evolutionary younger and more diverged genes were increasingly expressed toward later timepoints of biofilm growth. Molecular and morphological signatures also revealed that biofilm growth is highly regulated and organized into discrete ontogenetic stages, analogous to those of eukaryotic embryos. Together, this suggests that biofilm formation in Bacillus is a bona fide developmental process comparable to organismal development in animals, plants, and fungi. Given that most cells on Earth reside in the form of biofilms and that biofilms represent the oldest known fossils, we anticipate that the widely adopted vision of the first life as a single-cell and free-living organism needs rethinking.
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Affiliation(s)
- Momir Futo
- Laboratory of Evolutionary Genetics, Division of Molecular Biology, Ruđer Bošković Institute, Zagreb, Croatia
| | - Luka Opašić
- Laboratory of Evolutionary Genetics, Division of Molecular Biology, Ruđer Bošković Institute, Zagreb, Croatia
- Department for Evolutionary Theory, Max Planck Institute for Evolutionary Biology, Plön, Germany
| | - Sara Koska
- Laboratory of Evolutionary Genetics, Division of Molecular Biology, Ruđer Bošković Institute, Zagreb, Croatia
| | - Nina Čorak
- Laboratory of Evolutionary Genetics, Division of Molecular Biology, Ruđer Bošković Institute, Zagreb, Croatia
| | - Tin Široki
- Faculty of Electrical Engineering and Computing, University of Zagreb, Zagreb, Croatia
| | - Vaishnavi Ravikumar
- The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Kgs. Lyngby, Denmark
| | - Annika Thorsell
- Proteomics Core Facility, Sahlgrenska Academy, University of Gothenburg, Gothenburg, Sweden
| | - Maša Lenuzzi
- Laboratory of Evolutionary Genetics, Division of Molecular Biology, Ruđer Bošković Institute, Zagreb, Croatia
- Department of Evolutionary Biology, Max Planck Institute for Developmental Biology, Tübingen, Germany
| | - Domagoj Kifer
- Faculty of Pharmacy and Biochemistry, University of Zagreb, Zagreb, Croatia
| | - Mirjana Domazet-Lošo
- Faculty of Electrical Engineering and Computing, University of Zagreb, Zagreb, Croatia
| | - Kristian Vlahoviček
- Bioinformatics Group, Division of Biology, Faculty of Science, University of Zagreb, Zagreb, Croatia
- School of Biosciences, University of Skövde, Skövde, Sweden
| | - Ivan Mijakovic
- The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Kgs. Lyngby, Denmark
- Systems and Synthetic Biology Division, Department of Biology and Biological Engineering, Chalmers University of Technology, Gothenburg, Sweden
| | - Tomislav Domazet-Lošo
- Laboratory of Evolutionary Genetics, Division of Molecular Biology, Ruđer Bošković Institute, Zagreb, Croatia
- Catholic University of Croatia, Zagreb, Croatia
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20
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Ruiz-Trillo I, de Mendoza A. Towards understanding the origin of animal development. Development 2020; 147:147/23/dev192575. [PMID: 33272929 DOI: 10.1242/dev.192575] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
Almost all animals undergo embryonic development, going from a single-celled zygote to a complex multicellular adult. We know that the patterning and morphogenetic processes involved in development are deeply conserved within the animal kingdom. However, the origins of these developmental processes are just beginning to be unveiled. Here, we focus on how the protist lineages sister to animals are reshaping our view of animal development. Most intriguingly, many of these protistan lineages display transient multicellular structures, which are governed by similar morphogenetic and gene regulatory processes as animal development. We discuss here two potential alternative scenarios to explain the origin of animal embryonic development: either it originated concomitantly at the onset of animals or it evolved from morphogenetic processes already present in their unicellular ancestors. We propose that an integrative study of several unicellular taxa closely related to animals will allow a more refined picture of how the last common ancestor of animals underwent embryonic development.
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Affiliation(s)
- Iñaki Ruiz-Trillo
- Institut de Biologia Evolutiva (CSIC-Universitat Pompeu Fabra), Passeig Marítim de la Barceloneta, 37-49, 08003 Barcelona, Spain .,Departament de Genètica, Microbiologia i Estadística, Institut de Recerca de la Biodiversitat, Universitat de Barcelona, Avinguda Diagonal 643, 08028 Barcelona, Spain.,ICREA, Pg. Lluís Companys 23, 08010 Barcelona, Spain
| | - Alex de Mendoza
- Queen Mary University of London, School of Biological and Chemical Sciences, London E1 4DQ, UK
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21
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Czekanski‐Moir JE, Rundell RJ. Endless forms most stupid, icky, and small: The preponderance of noncharismatic invertebrates as integral to a biologically sound view of life. Ecol Evol 2020; 10:12638-12649. [PMID: 33304481 PMCID: PMC7713927 DOI: 10.1002/ece3.6892] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2018] [Revised: 09/15/2020] [Accepted: 09/22/2020] [Indexed: 01/02/2023] Open
Abstract
Big, beautiful organisms are useful for biological education, increasing evolution literacy, and biodiversity conservation. But if educators gloss over the ubiquity of streamlined and miniaturized organisms, they unwittingly leave students and the public vulnerable to the idea that the primary evolutionary plot of every metazoan lineage is "progressive" and "favors" complexity. We show that simple, small, and intriguingly repulsive invertebrate animals provide a counterpoint to misconceptions about evolution. Our examples can be immediately deployed in biology courses and outreach. This context emphasizes that chordates are not the pinnacle of evolution. Rather, in the evolution of animals, miniaturization, trait loss, and lack of perfection are at least as frequent as their opposites. Teaching about invertebrate animals in a "tree thinking" context uproots evolution misconceptions (for students and the public alike), provides a mental scaffold for understanding all animals, and helps to cultivate future ambassadors and experts on these little-known, weird, and fascinating taxa.
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Affiliation(s)
- Jesse E. Czekanski‐Moir
- Department of Environmental and Forest BiologyState University of New York College of Environmental Science and ForestrySyracuseNYUSA
| | - Rebecca J. Rundell
- Department of Environmental and Forest BiologyState University of New York College of Environmental Science and ForestrySyracuseNYUSA
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22
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Wideman JG, Novick A, Muñoz-Gómez SA, Doolittle WF. Neutral evolution of cellular phenotypes. Curr Opin Genet Dev 2019; 58-59:87-94. [PMID: 31574422 DOI: 10.1016/j.gde.2019.09.004] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2019] [Revised: 09/09/2019] [Accepted: 09/11/2019] [Indexed: 12/29/2022]
Abstract
Eukaryotes exhibit a great diversity of cellular and subcellular morphologies, but their basic underlying architecture is fairly constant. All have a nucleus, Golgi, cytoskeleton, plasma membrane, vesicles, ribosomes, and all known lineages but one have mitochondrion-related organelles. Moreover, most eukaryotes undergo processes such as mitosis, meiosis, DNA recombination, and often perform feats such as phagocytosis, and amoeboid and flagellar movement. With all of these commonalities, it is obvious that eukaryotes evolved from a common ancestor, but it is not obvious how eukaryotes came to have their diverse structural phenotypes. Are these phenotypes adaptations to particular niches, their evolution dominated by positive natural selection? Or is eukaryotic cellular diversity substantially the product of neutral evolutionary processes, with adaptation either illusory or a secondary consequence? In this paper, we outline how a hierarchical view of phenotype can be used to articulate a neutral theory of phenotypic evolution, involving processes such as gene loss, gene replacement by homologues or analogues, gene duplication followed by subfunctionalization, and constructive neutral evolution. We suggest that neutral iterations of these processes followed by entrenchment of their products can explain much of the diversity of cellular, developmental, and biochemical phenotypes of unicellular eukaryotes and should be explored in addition to adaptive explanations.
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Affiliation(s)
- Jeremy G Wideman
- Centre for Mechanisms of Evolution, Arizona State University, Tempe, AZ, 85287, USA; Department of Biochemistry & Molecular Biology, Dalhousie University, Halifax, Nova Scotia, B3H 4R2, Canada.
| | - Aaron Novick
- Department of Biochemistry & Molecular Biology, Dalhousie University, Halifax, Nova Scotia, B3H 4R2, Canada; Department of Philosophy, Dalhousie University, Halifax, Nova Scotia, B3H 4R2, Canada; Department of Philosophy, Purdue University, West Lafayette, IN, 47907, USA
| | - Sergio A Muñoz-Gómez
- Department of Biochemistry & Molecular Biology, Dalhousie University, Halifax, Nova Scotia, B3H 4R2, Canada
| | - W Ford Doolittle
- Department of Biochemistry & Molecular Biology, Dalhousie University, Halifax, Nova Scotia, B3H 4R2, Canada
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23
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Should I stay or should I go? Retention and loss of components in vestigial endosymbiotic organelles. Curr Opin Genet Dev 2019; 58-59:33-39. [PMID: 31466038 DOI: 10.1016/j.gde.2019.07.013] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2019] [Revised: 06/21/2019] [Accepted: 07/19/2019] [Indexed: 01/28/2023]
Abstract
Our knowledge on the variability of the reduced forms of endosymbiotic organelles - mitochondria and plastids - is expanding rapidly, thanks to growing interest in peculiar microbial eukaryotes, along with the availability of the methods used in modern genomics and transcriptomics. The aim of this work is to highlight the most recent advances in understanding these organelles' diversity, physiology and evolution. We also outline the known mechanisms behind the convergence of traits between organelles which have undergone reduction independently, the importance of the earliest evolutionary events in determining the vestigial organelles' eventual fate, and a proposed classification of nonphotosynthetic plastids.
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24
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25
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Duclos KK, Hendrikse JL, Jamniczky HA. Investigating the evolution and development of biological complexity under the framework of epigenetics. Evol Dev 2019; 21:247-264. [PMID: 31268245 PMCID: PMC6852014 DOI: 10.1111/ede.12301] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
Biological complexity is a key component of evolvability, yet its study has been hampered by a focus on evolutionary trends of complexification and inconsistent definitions. Here, we demonstrate the utility of bringing complexity into the framework of epigenetics to better investigate its utility as a concept in evolutionary biology. We first analyze the existing metrics of complexity and explore the link between complexity and adaptation. Although recently developed metrics allow for a unified framework, they omit developmental mechanisms. We argue that a better approach to the empirical study of complexity and its evolution includes developmental mechanisms. We then consider epigenetic mechanisms and their role in shaping developmental and evolutionary trajectories, as well as the development and organization of complexity. We argue that epigenetics itself could have emerged from complexity because of a need to self‐regulate. Finally, we explore hybridization complexes and hybrid organisms as potential models for studying the association between epigenetics and complexity. Our goal is not to explain trends in biological complexity but to help develop and elucidate novel questions in the investigation of biological complexity and its evolution. This manuscript argues that biological complexity is better understood under the framework of epigenetics and that the epigenetic interactions emerge from the self‐regulation of complex systems. Hybrids are offered as models to study these properties.
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Affiliation(s)
- Kevin K Duclos
- Department of Cell Biology and Anatomy, The University of Calgary, Calgary, Alberta, Canada
| | - Jesse L Hendrikse
- Department of Community Health Sciences, The University of Calgary, Calgary, Alberta, Canada
| | - Heather A Jamniczky
- Department of Cell Biology and Anatomy, The University of Calgary, Calgary, Alberta, Canada
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26
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Bråte J, Neumann RS, Fromm B, Haraldsen AAB, Tarver JE, Suga H, Donoghue PCJ, Peterson KJ, Ruiz-Trillo I, Grini PE, Shalchian-Tabrizi K. Unicellular Origin of the Animal MicroRNA Machinery. Curr Biol 2018; 28:3288-3295.e5. [PMID: 30318349 PMCID: PMC6206976 DOI: 10.1016/j.cub.2018.08.018] [Citation(s) in RCA: 31] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2018] [Revised: 07/22/2018] [Accepted: 08/07/2018] [Indexed: 12/16/2022]
Abstract
The emergence of multicellular animals was associated with an increase in phenotypic complexity and with the acquisition of spatial cell differentiation and embryonic development. Paradoxically, this phenotypic transition was not paralleled by major changes in the underlying developmental toolkit and regulatory networks. In fact, most of these systems are ancient, established already in the unicellular ancestors of animals [1-5]. In contrast, the Microprocessor protein machinery, which is essential for microRNA (miRNA) biogenesis in animals, as well as the miRNA genes themselves produced by this Microprocessor, have not been identified outside of the animal kingdom [6]. Hence, the Microprocessor, with the key proteins Pasha and Drosha, is regarded as an animal innovation [7-9]. Here, we challenge this evolutionary scenario by investigating unicellular sister lineages of animals through genomic and transcriptomic analyses. We identify in Ichthyosporea both Drosha and Pasha (DGCR8 in vertebrates), indicating that the Microprocessor complex evolved long before the last common ancestor of animals, consistent with a pre-metazoan origin of most of the animal developmental gene elements. Through small RNA sequencing, we also discovered expressed bona fide miRNA genes in several species of the ichthyosporeans harboring the Microprocessor. A deep, pre-metazoan origin of the Microprocessor and miRNAs comply with a view that the origin of multicellular animals was not directly linked to the innovation of these key regulatory components.
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Affiliation(s)
- Jon Bråte
- Centre for Epigenetics, Development and Evolution (CEDE) and Centre for Integrative Microbial Evolution (CIME), Section for Genetics and Evolutionary Biology (EVOGENE), University of Oslo, Oslo, Norway
| | - Ralf S Neumann
- Centre for Epigenetics, Development and Evolution (CEDE) and Centre for Integrative Microbial Evolution (CIME), Section for Genetics and Evolutionary Biology (EVOGENE), University of Oslo, Oslo, Norway
| | - Bastian Fromm
- Department of Tumor Biology, Institute for Cancer Research, Norwegian Radium Hospital, Oslo University Hospital, Oslo, Norway; Science for Life Laboratory, Department of Molecular Biosciences, The Wenner-Gren Institute, Stockholm University, 10691 Stockholm, Sweden
| | - Arthur A B Haraldsen
- Centre for Epigenetics, Development and Evolution (CEDE) and Centre for Integrative Microbial Evolution (CIME), Section for Genetics and Evolutionary Biology (EVOGENE), University of Oslo, Oslo, Norway
| | - James E Tarver
- School of Earth Sciences, University of Bristol, Bristol BS8 1TQ, UK
| | - Hiroshi Suga
- Faculty of Life and Environmental Sciences, Prefectural University of Hiroshima, Nanatsuka 562, Shobara, Hiroshima 727-0023, Japan
| | | | - Kevin J Peterson
- Department of Biological Sciences, Dartmouth College, Hanover, NH 03755, USA
| | - Iñaki Ruiz-Trillo
- Institut de Biologia Evolutiva (CSIC-Universitat Pompeu Fabra), 08003 Barcelona, Spain; ICREA, 08010 Barcelona, Spain
| | - Paul E Grini
- Centre for Epigenetics, Development and Evolution (CEDE) and Centre for Integrative Microbial Evolution (CIME), Section for Genetics and Evolutionary Biology (EVOGENE), University of Oslo, Oslo, Norway
| | - Kamran Shalchian-Tabrizi
- Centre for Epigenetics, Development and Evolution (CEDE) and Centre for Integrative Microbial Evolution (CIME), Section for Genetics and Evolutionary Biology (EVOGENE), University of Oslo, Oslo, Norway.
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Cissé OH, Hauser PM. Genomics and evolution of Pneumocystis species. INFECTION GENETICS AND EVOLUTION 2018; 65:308-320. [PMID: 30138710 DOI: 10.1016/j.meegid.2018.08.015] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/30/2018] [Revised: 08/15/2018] [Accepted: 08/17/2018] [Indexed: 01/20/2023]
Abstract
The genus Pneumocystis comprises highly diversified fungal species that cause severe pneumonia in individuals with a deficient immune system. These fungi infect exclusively mammals and present a strict host species specificity. These species have co-diverged with their hosts for long periods of time (> 100 MYA). Details of their biology and evolution are fragmentary mainly because of a lack of an established long-term culture system. Recent genomic advances have unlocked new areas of research and allow new hypotheses to be tested. We review here new findings of the genomic studies in relation with the evolutionary trajectory of these fungi and discuss the impact of genomic data analysis in the context of the population genetics. The combination of slow genome decay and limited expansion of specific gene families and introns reflect intimate interactions of these species with their hosts. The evolutionary adaptation of these organisms is profoundly influenced by their population structure, which in turn is determined by intrinsic features such as their self-fertilizing mating system, high host specificity, long generation times, and transmission mode. Essential key questions concerning their adaptation and speciation remain to be answered. The next cornerstone will consist in the establishment of a long-term culture system and genetic manipulation that should allow unravelling the driving forces of Pneumocystis species evolution.
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Affiliation(s)
- Ousmane H Cissé
- Critical Care Medicine Department, NIH Clinical Center, National Institutes of Health, Bethesda, MD 20892, USA.
| | - Philippe M Hauser
- Institute of Microbiology, Lausanne University Hospital, Lausanne, Switzerland.
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Hoekstra PH, Wieringa JJ, Smets E, Chatrou LW. Floral evolution by simplification in Monanthotaxis (Annonaceae) and hypotheses for pollination system shifts. Sci Rep 2018; 8:12066. [PMID: 30104579 PMCID: PMC6089970 DOI: 10.1038/s41598-018-30607-2] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2018] [Accepted: 07/16/2018] [Indexed: 12/25/2022] Open
Abstract
Simplification by reduction has occurred many times independently in the floral evolution of angiosperms. These reductions have often been attributed to changes in reproductive biology. In the angiosperm plant family Annonaceae, most species have flowers with six petals, and many stamens and carpels. In the genus Monanthotaxis several deviations from this pattern have been observed, including flowers that contain three petals and three stamens only. New DNA sequences were generated for 42 specimens of Monanthotaxis. Five chloroplast markers and two nuclear markers for 72 out of 94 species of Monanthotaxis were used to reconstruct a phylogeny of the genus, which revealed several well-supported, morphologically distinct clades. The evolution of four quantitative and two qualitative floral characters was mapped onto this phylogeny, demonstrating a reduction in flower size and number of flower parts in Monanthotaxis. A large variation in stamen forms and numbers, strong correlations between petal size, stamen and carpel number, combined with a non-gradual mode of evolution and the sympatric co-occurrence of Monanthotaxis species from different clades suggest that the high diversity in the African rainforest of this genus is caused by switches in pollination systems.
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Affiliation(s)
- Paul H Hoekstra
- Naturalis Biodiversity Center, National Herbarium of the Netherlands, Darwinweg 2, 2300 RA, Leiden, The Netherlands. .,Wageningen University & Research, Biosystematics Group, Droevendaalsesteeg 1, 6708 PB, Wageningen, The Netherlands.
| | - Jan J Wieringa
- Naturalis Biodiversity Center, National Herbarium of the Netherlands, Darwinweg 2, 2300 RA, Leiden, The Netherlands.,Wageningen University & Research, Biosystematics Group, Droevendaalsesteeg 1, 6708 PB, Wageningen, The Netherlands
| | - Erik Smets
- Naturalis Biodiversity Center, National Herbarium of the Netherlands, Darwinweg 2, 2300 RA, Leiden, The Netherlands.,Ecology, Evolution and Biodiversity Conservation Section, KU Leuven, Kasteelpark Arenberg 31, box 2435, 3001, Leuven, Belgium
| | - Lars W Chatrou
- Wageningen University & Research, Biosystematics Group, Droevendaalsesteeg 1, 6708 PB, Wageningen, The Netherlands
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Somorjai IML, Martí-Solans J, Diaz-Gracia M, Nishida H, Imai KS, Escrivà H, Cañestro C, Albalat R. Wnt evolution and function shuffling in liberal and conservative chordate genomes. Genome Biol 2018; 19:98. [PMID: 30045756 PMCID: PMC6060547 DOI: 10.1186/s13059-018-1468-3] [Citation(s) in RCA: 27] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2018] [Accepted: 06/22/2018] [Indexed: 12/17/2022] Open
Abstract
BACKGROUND What impact gene loss has on the evolution of developmental processes, and how function shuffling has affected retained genes driving essential biological processes, remain open questions in the fields of genome evolution and EvoDevo. To investigate these problems, we have analyzed the evolution of the Wnt ligand repertoire in the chordate phylum as a case study. RESULTS We conduct an exhaustive survey of Wnt genes in genomic databases, identifying 156 Wnt genes in 13 non-vertebrate chordates. This represents the most complete Wnt gene catalog of the chordate subphyla and has allowed us to resolve previous ambiguities about the orthology of many Wnt genes, including the identification of WntA for the first time in chordates. Moreover, we create the first complete expression atlas for the Wnt family during amphioxus development, providing a useful resource to investigate the evolution of Wnt expression throughout the radiation of chordates. CONCLUSIONS Our data underscore extraordinary genomic stasis in cephalochordates, which contrasts with the liberal and dynamic evolutionary patterns of gene loss and duplication in urochordate genomes. Our analysis has allowed us to infer ancestral Wnt functions shared among all chordates, several cases of function shuffling among Wnt paralogs, as well as unique expression domains for Wnt genes that likely reflect functional innovations in each chordate lineage. Finally, we propose a potential relationship between the evolution of WntA and the evolution of the mouth in chordates.
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Affiliation(s)
- Ildikó M L Somorjai
- Biomedical Sciences Research Complex, School of Biology, University of St Andrews, North Haugh, St Andrews, KY16 9ST, Scotland, UK.
- Scottish Oceans Institute, School of Biology, University of St Andrews, East Sands, St Andrews, KY16 8LB, Scotland, UK.
| | - Josep Martí-Solans
- Departament de Genètica, , Microbiologia i Estadística, and Institut de Recerca de la Biodiversitat (IRBio), Universitat de Barcelona, Barcelona, Spain
| | - Miriam Diaz-Gracia
- Departament de Genètica, , Microbiologia i Estadística, and Institut de Recerca de la Biodiversitat (IRBio), Universitat de Barcelona, Barcelona, Spain
| | - Hiroki Nishida
- Department of Biological Sciences, Graduate School of Science, Osaka University, Toyonaka, Osaka, 560-0043, Japan
| | - Kaoru S Imai
- Department of Biological Sciences, Graduate School of Science, Osaka University, Toyonaka, Osaka, 560-0043, Japan
| | - Hector Escrivà
- Sorbonne Universités, UPMC Univ Paris 06, CNRS, Biologie Intégrative des Organismes Marins (BIOM), Observatoire Océanologique, F-66650, Banyuls/Mer, France
| | - Cristian Cañestro
- Departament de Genètica, , Microbiologia i Estadística, and Institut de Recerca de la Biodiversitat (IRBio), Universitat de Barcelona, Barcelona, Spain.
| | - Ricard Albalat
- Departament de Genètica, , Microbiologia i Estadística, and Institut de Recerca de la Biodiversitat (IRBio), Universitat de Barcelona, Barcelona, Spain.
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Richter DJ, Fozouni P, Eisen MB, King N. Gene family innovation, conservation and loss on the animal stem lineage. eLife 2018; 7:34226. [PMID: 29848444 PMCID: PMC6040629 DOI: 10.7554/elife.34226] [Citation(s) in RCA: 111] [Impact Index Per Article: 18.5] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2017] [Accepted: 05/26/2018] [Indexed: 02/06/2023] Open
Abstract
Choanoflagellates, the closest living relatives of animals, can provide unique insights into the changes in gene content that preceded the origin of animals. However, only two choanoflagellate genomes are currently available, providing poor coverage of their diversity. We sequenced transcriptomes of 19 additional choanoflagellate species to produce a comprehensive reconstruction of the gains and losses that shaped the ancestral animal gene repertoire. We identified ~1944 gene families that originated on the animal stem lineage, of which only 39 are conserved across all animals in our study. In addition, ~372 gene families previously thought to be animal-specific, including Notch, Delta, and homologs of the animal Toll-like receptor genes, instead evolved prior to the animal-choanoflagellate divergence. Our findings contribute to an increasingly detailed portrait of the gene families that defined the biology of the Urmetazoan and that may underpin core features of extant animals. All animals, from sea sponges and reef-building corals to elephants and humans, share a single common ancestor that lived over half a billion years ago. This single-celled predecessor evolved the ability to develop into a creature made up of many cells with specialized jobs. Reconstructing the steps in this evolutionary process has been difficult because the earliest animals were soft-bodied and microscopic and did not leave behind fossils that scientists can study. Though their bodies have since disintegrated, many of the instructions for building the first animals live on in genes that were passed on to life forms that still exist. Scientists are trying to retrace those genes back to the first animal by comparing the genomes of living animals with their closest relatives, the choanoflagellates. Choanoflagellates are single-celled, colony-forming organisms that live in waters around the world. Comparisons with choanoflagellates may help scientists identify which genes were necessary to help animals evolve and diversify into so many different species. So far, 1,000 animal and two choanoflagellate genomes have been sequenced. But the gene repertoires of most species of choanoflagellates have yet to be analyzed. Now, Richter et al. have cataloged the genes of 19 more species of choanoflagellates. This added information allowed them to recreate the likely gene set of the first animal and to identify genetic changes that occurred during animal evolution. The analyses showed that modern animals lost about a quarter of the genes present in their last common ancestor with choanoflagellates and gained an equal number of new genes. Richter et al. identified several dozen core animal genes that were gained and subsequently preserved throughout animal evolution. Many of these are necessary so that an embryo can develop properly, but the precise roles of some core genes remain a mystery. Most other genes that emerged in the first animals have been lost in at least one living animal. The study of Richter et al. also showed that some very important genes in animals, including genes essential for early development and genes that help the immune system detect pathogens, predate animals. These key genes trace back to animals’ last common ancestor with choanoflagellates and may have evolved new roles in animals.
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Affiliation(s)
- Daniel J Richter
- Department of Molecular and Cell Biology, Howard Hughes Medical Institute, University of California, Berkeley, Berkeley, United States.,Sorbonne Universités, UPMC Univ Paris 06, CNRS UMR 7144, Adaptation et Diversité en Milieu Marin, Équipe EPEP, Station Biologique de Roscoff, Roscoff, France
| | - Parinaz Fozouni
- Department of Molecular and Cell Biology, Howard Hughes Medical Institute, University of California, Berkeley, Berkeley, United States.,Medical Scientist Training Program, Biomedical Sciences Graduate Program, University of California, San Francisco, San Francisco, United States.,Gladstone Institutes, San Francisco, United States
| | - Michael B Eisen
- Department of Molecular and Cell Biology, Howard Hughes Medical Institute, University of California, Berkeley, Berkeley, United States
| | - Nicole King
- Department of Molecular and Cell Biology, Howard Hughes Medical Institute, University of California, Berkeley, Berkeley, United States
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31
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Belahbib H, Renard E, Santini S, Jourda C, Claverie JM, Borchiellini C, Le Bivic A. New genomic data and analyses challenge the traditional vision of animal epithelium evolution. BMC Genomics 2018; 19:393. [PMID: 29793430 PMCID: PMC5968619 DOI: 10.1186/s12864-018-4715-9] [Citation(s) in RCA: 34] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2017] [Accepted: 04/23/2018] [Indexed: 11/16/2022] Open
Abstract
Background The emergence of epithelia was the foundation of metazoan expansion. Epithelial tissues are a hallmark of metazoans deeply rooted in the evolution of their complex developmental morphogenesis processes. However, studies on the epithelial features of non-bilaterians are still sparse and it remains unclear whether the last common metazoan ancestor possessed a fully functional epithelial toolkit or if it was acquired later during metazoan evolution. Results To investigate the early evolution of animal epithelia, we sequenced the genome and transcriptomes of two new sponge species to characterize epithelial markers such as the E-cadherin complex and the polarity complexes for all classes (Calcarea, Demospongiae, Hexactinellida, Homoscleromorpha) of sponges (phylum Porifera) and compare them with their homologues in Placozoa and in Ctenophora. We found that Placozoa and most sponges possess orthologues of all essential genes encoding proteins characteristic of bilaterian epithelial cells, as well as their conserved interaction domains. In stark contrast, we found that ctenophores lack several major polarity complex components such as the Crumbs complex and Scribble. Furthermore, the E-cadherin ctenophore orthologue exhibits a divergent cytoplasmic domain making it unlikely to interact with its canonical cytoplasmic partners. Conclusions These unexpected findings challenge the current evolutionary paradigm on the emergence of epithelia. Altogether, our results raise doubt on the homology of protein complexes and structures involved in cell polarity and adhesive-type junctions between Ctenophora and Bilateria epithelia. Electronic supplementary material The online version of this article (10.1186/s12864-018-4715-9) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Hassiba Belahbib
- Structural and Genomic Information Laboratory, Aix-Marseille Université & CNRS UMR 7256, Mediterranean Institute of Microbiology (IMM FR 3479), Marseille, France
| | - Emmanuelle Renard
- Aix Marseille Univ, Univ Avignon, CNRS, IRD, UMR 7263, Mediterranean Institute of Marine and Continental Biodiversity and Ecology (IMBE), Station Marine d'Endoume, Marseille, France
| | - Sébastien Santini
- Structural and Genomic Information Laboratory, Aix-Marseille Université & CNRS UMR 7256, Mediterranean Institute of Microbiology (IMM FR 3479), Marseille, France
| | - Cyril Jourda
- Structural and Genomic Information Laboratory, Aix-Marseille Université & CNRS UMR 7256, Mediterranean Institute of Microbiology (IMM FR 3479), Marseille, France
| | - Jean-Michel Claverie
- Structural and Genomic Information Laboratory, Aix-Marseille Université & CNRS UMR 7256, Mediterranean Institute of Microbiology (IMM FR 3479), Marseille, France.
| | - Carole Borchiellini
- Aix Marseille Univ, Univ Avignon, CNRS, IRD, UMR 7263, Mediterranean Institute of Marine and Continental Biodiversity and Ecology (IMBE), Station Marine d'Endoume, Marseille, France.
| | - André Le Bivic
- Aix-Marseille University, CNRS, UMR 7288, Developmental Biology Institute of Marseille Luminy (IBDM), Marseille, France.
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Griesmann M, Chang Y, Liu X, Song Y, Haberer G, Crook MB, Billault-Penneteau B, Lauressergues D, Keller J, Imanishi L, Roswanjaya YP, Kohlen W, Pujic P, Battenberg K, Alloisio N, Liang Y, Hilhorst H, Salgado MG, Hocher V, Gherbi H, Svistoonoff S, Doyle JJ, He S, Xu Y, Xu S, Qu J, Gao Q, Fang X, Fu Y, Normand P, Berry AM, Wall LG, Ané JM, Pawlowski K, Xu X, Yang H, Spannagl M, Mayer KFX, Wong GKS, Parniske M, Delaux PM, Cheng S. Phylogenomics reveals multiple losses of nitrogen-fixing root nodule symbiosis. Science 2018; 361:science.aat1743. [DOI: 10.1126/science.aat1743] [Citation(s) in RCA: 198] [Impact Index Per Article: 33.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2018] [Accepted: 05/16/2018] [Indexed: 12/20/2022]
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33
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Nagy LG, Kovács GM, Krizsán K. Complex multicellularity in fungi: evolutionary convergence, single origin, or both? Biol Rev Camb Philos Soc 2018; 93:1778-1794. [DOI: 10.1111/brv.12418] [Citation(s) in RCA: 63] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2017] [Revised: 03/23/2018] [Accepted: 03/28/2018] [Indexed: 12/22/2022]
Affiliation(s)
- László G. Nagy
- Synthetic and Systems Biology Unit; Institute of Biochemistry, BRC-HAS, 62 Temesvári krt; 6726 Szeged Hungary
| | - Gábor M. Kovács
- Department of Plant Anatomy; Institute of Biology, Eötvös Loránd University, Pázmány Péter sétány 1/C; H-1117 Budapest Hungary
- Plant Protection Institute, Centre for Agricultural Research; Hungarian Academy of Sciences (MTA-ATK); PO Box 102, H-1525 Budapest Hungary
| | - Krisztina Krizsán
- Synthetic and Systems Biology Unit; Institute of Biochemistry, BRC-HAS, 62 Temesvári krt; 6726 Szeged Hungary
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Abstract
The kingdom Fungi comprises species that inhabit nearly all ecosystems. Fungi exist as both free-living and symbiotic unicellular and multicellular organisms with diverse morphologies. The genomes of fungi encode genes that enable them to thrive in diverse environments, invade plant and animal cells, and participate in nutrient cycling in terrestrial and aquatic ecosystems. The continuously expanding databases of fungal genome sequences have been generated by individual and large-scale efforts such as Génolevures, Broad Institute's Fungal Genome Initiative, and the 1000 Fungal Genomes Project (http://1000.fungalgenomes.org). These efforts have produced a catalog of fungal genes and genomic organization. The genomic datasets can be utilized to better understand how fungi have adapted to their lifestyles and ecological niches. Large datasets of fungal genomic and transcriptomic data have enabled the use of novel methodologies and improved the study of fungal evolution from a molecular sequence perspective. Combined with microscopes, petri dishes, and woodland forays, genome sequencing supports bioinformatics and comparative genomics approaches as important tools in the study of the biology and evolution of fungi.
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Excess of non-conservative amino acid changes in marine bacterioplankton lineages with reduced genomes. Nat Microbiol 2017; 2:17091. [PMID: 28604700 DOI: 10.1038/nmicrobiol.2017.91] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2016] [Accepted: 04/28/2017] [Indexed: 12/30/2022]
Abstract
Surface ocean waters are dominated by planktonic bacterial lineages with highly reduced genomes. The best examples are the cyanobacterial genus Prochlorococcus, the alphaproteobacterial clade SAR11 and the gammaproteobacterial clade SAR86, which together represent over 50% of the cells in surface oceans. Several studies have identified signatures of selection on these lineages in today's ocean and have postulated selection as the primary force throughout their evolutionary history. However, massive loss of genomic DNA in these lineages often occurred in the distant past, and the selective pressures underlying these ancient events have not been assessed. Here, we probe ancient selective pressures by computing %GC-corrected rates of conservative and radical nonsynonymous nucleotide substitutions. Surprisingly, we found an excess of radical changes in several of these lineages in comparison to their relatives with larger genomes. Furthermore, analyses of allelic genome sequences of several populations within these lineages consistently supported that radical replacements are more likely to be deleterious than conservative changes. Our results suggest coincidence of massive genomic DNA losses and increased power of genetic drift, but we also suggest that additional evidence independent of the nucleotide substitution analyses is needed to support a primary role of genetic drift driving ancient genome reduction of marine bacterioplankton lineages.
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Giardia intestinalis mitosomes undergo synchronized fission but not fusion and are constitutively associated with the endoplasmic reticulum. BMC Biol 2017; 15:27. [PMID: 28372543 DOI: 10.1186/s12915-017-0361-y] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2016] [Accepted: 03/01/2017] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Mitochondria of opisthokonts undergo permanent fission and fusion throughout the cell cycle. Here, we investigated the dynamics of the mitosomes, the simplest forms of mitochondria, in the anaerobic protist parasite Giardia intestinalis, a member of the Excavata supergroup of eukaryotes. The mitosomes have abandoned typical mitochondrial traits such as the mitochondrial genome and aerobic respiration and their single role known to date is the formation of iron-sulfur clusters. RESULTS In live experiments, no fusion events were observed between the mitosomes in G. intestinalis. Moreover, the organelles were highly prone to becoming heterogeneous. This suggests that fusion is either much less frequent or even absent in mitosome dynamics. Unlike in mitochondria, division of the mitosomes was absolutely synchronized and limited to mitosis. The association of the nuclear and the mitosomal division persisted during the encystation of the parasite. During the segregation of the divided mitosomes, the subset of the organelles between two G. intestinalis nuclei had a prominent role. Surprisingly, the sole dynamin-related protein of the parasite seemed not to be involved in mitosomal division. However, throughout the cell cycle, mitosomes associated with the endoplasmic reticulum (ER), although none of the known ER-tethering complexes was present. Instead, the ER-mitosome interface was occupied by the lipid metabolism enzyme long-chain acyl-CoA synthetase 4. CONCLUSIONS This study provides the first report on the dynamics of mitosomes. We show that together with the loss of metabolic complexity of mitochondria, mitosomes of G. intestinalis have uniquely streamlined their dynamics by harmonizing their division with mitosis. We propose that this might be a strategy of G. intestinalis to maintain a stable number of organelles during cell propagation. The lack of mitosomal fusion may also be related to the secondary reduction of the organelles. However, as there are currently no reports on mitochondrial fusion in the whole Excavata supergroup, it is possible that the absence of mitochondrial fusion is an ancestral trait common to all excavates.
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Expansion of the molecular and morphological diversity of Acanthamoebidae (Centramoebida, Amoebozoa) and identification of a novel life cycle type within the group. Biol Direct 2016; 11:69. [PMID: 28031045 PMCID: PMC5192571 DOI: 10.1186/s13062-016-0171-0] [Citation(s) in RCA: 45] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2016] [Accepted: 12/03/2016] [Indexed: 01/23/2023] Open
Abstract
BACKGROUND Acanthamoebidae is a "family" level amoebozoan group composed of the genera Acanthamoeba, Protacanthamoeba, and very recently Luapeleamoeba. This clade of amoebozoans has received considerable attention from the broader scientific community as Acanthamoeba spp. represent both model organisms and human pathogens. While the classical composition of the group (Acanthamoeba + Protacanthamoeba) has been well accepted due to the morphological and ultrastructural similarities of its members, the Acanthamoebidae has never been highly statistically supported in single gene phylogenetic reconstructions of Amoebozoa either by maximum likelihood (ML) or Bayesian analyses. RESULTS Here we show using a phylogenomic approach that the Acanthamoebidae is a fully supported monophyletic group within Amoebozoa with both ML and Bayesian analyses. We also expand the known range of morphological and life cycle diversity found in the Acanthamoebidae by demonstrating that the amoebozoans "Protostelium" arachisporum, Dracoamoeba jormungandri n. g. n. sp., and Vacuolamoeba acanthoformis n.g. n.sp., belong within the group. We also found that "Protostelium" pyriformis is clearly a species of Acanthamoeba making it the first reported sporocarpic member of the genus, that is, an amoeba that individually forms a walled, dormant propagule elevated by a non-cellular stalk. Our phylogenetic analyses recover a fully supported Acanthamoebidae composed of five genera. Two of these genera (Acanthamoeba and Luapeleameoba) have members that are sporocarpic. CONCLUSIONS Our results provide high statistical support for an Acanthamoebidae that is composed of five distinct genera. This study increases the known morphological diversity of this group and shows that species of Acanthamoeba can include spore-bearing stages. This further illustrates the widespread nature of spore-bearing stages across the tree of Amoebozoa. REVIEWERS This article was reviewed by Drs. Eugene Koonin, Purificacion Lopez-Garcia and Sandra Baldauf. Sandra Baldauf was nominated by Purificacion Lopez-Garcia, an Editorial Board member.
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