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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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Abstract
Tardigrades are ubiquitous meiofauna that are especially renowned for their exceptional extremotolerance to various adverse environments, including pressure, temperature, and even ionizing radiation. This is achieved through a reversible halt of metabolism triggered by desiccation, a phenomenon called anhydrobiosis. Recent establishment of genome resources for two tardigrades, Hypsibius exemplaris and Ramazzottius varieornatus, accelerated research to uncover the molecular mechanisms behind anhydrobiosis, leading to the discovery of many tardigrade-unique proteins. This review focuses on the history, methods, discoveries, and current state and challenges regarding tardigrade genomics, with an emphasis on molecular anhydrobiology. Remaining questions and future perspectives regarding prospective approaches to fully elucidate the molecular machinery of this complex phenomenon are discussed.
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Affiliation(s)
- Kazuharu Arakawa
- Institute for Advanced Biosciences, Keio University, Daishouji, Tsuruoka, Yamagata, Japan; .,Faculty of Environment and Information Studies, Keio University, Fujisawa, Kanagawa, Japan.,Graduate School of Media and Governance, Systems Biology Program, Keio University, Fujisawa, Kanagawa, Japan.,Exploratory Research Center on Life and Living Systems (ExCELLS), National Institute of Natural Sciences, Myodaiji, Okazaki, Aichi, Japan
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Evidence for sponges as sister to all other animals from partitioned phylogenomics with mixture models and recoding. Nat Commun 2021; 12:1783. [PMID: 33741994 PMCID: PMC7979703 DOI: 10.1038/s41467-021-22074-7] [Citation(s) in RCA: 48] [Impact Index Per Article: 16.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2020] [Accepted: 02/24/2021] [Indexed: 11/08/2022] Open
Abstract
Resolving the relationships between the major lineages in the animal tree of life is necessary to understand the origin and evolution of key animal traits. Sponges, characterized by their simple body plan, were traditionally considered the sister group of all other animal lineages, implying a gradual increase in animal complexity from unicellularity to complex multicellularity. However, the availability of genomic data has sparked tremendous controversy as some phylogenomic studies support comb jellies taking this position, requiring secondary loss or independent origins of complex traits. Here we show that incorporating site-heterogeneous mixture models and recoding into partitioned phylogenomics alleviates systematic errors that hamper commonly-applied phylogenetic models. Testing on real datasets, we show a great improvement in model-fit that attenuates branching artefacts induced by systematic error. We reanalyse key datasets and show that partitioned phylogenomics does not support comb jellies as sister to other animals at either the supermatrix or partition-specific level.
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Abstract
Gastropod molluscs are among the most diverse and abundant animals in the oceans, and are successful colonizers of terrestrial and freshwater environments. Past phylogenetic efforts to resolve gastropod relationships resulted in a range of conflicting hypotheses. Here, we use phylogenomics to address deep relationships between the five major gastropod lineages—Caenogastropoda, Heterobranchia, Neritimorpha, Patellogastropoda and Vetigastropoda—and provide one congruent and well-supported topology. We substantially expand taxon sampling for outgroups and for previously underrepresented gastropod lineages, presenting new transcriptomes for neritimorphs and patellogastropods. We conduct analyses under maximum-likelihood, Bayesian inference and a coalescent-based approach, accounting for the most pervasive sources of systematic errors in large datasets: compositional heterogeneity, site heterogeneity, heterotachy, variation in evolutionary rates among genes, matrix completeness, outgroup choice and gene tree conflict. We find that vetigastropods and patellogastropods are sister taxa, and that neritimorphs are the sister group to caenogastropods and heterobranchs. We name these two major unranked clades Psilogastropoda and Angiogastropoda, respectively. We additionally provide the first genomic-scale data for internal relationships of neritimorphs and patellogastropods. Our results highlight the need for reinterpreting the evolution of morphological and developmental characters in gastropods, especially for inferring their ancestral states.
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Affiliation(s)
- Tauana Junqueira Cunha
- Museum of Comparative Zoology, Department of Organismic and Evolutionary Biology, Harvard University , 26 Oxford Street, Cambridge, MA 02138 , USA
| | - Gonzalo Giribet
- Museum of Comparative Zoology, Department of Organismic and Evolutionary Biology, Harvard University , 26 Oxford Street, Cambridge, MA 02138 , USA
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Data, time and money: evaluating the best compromise for inferring molecular phylogenies of non-model animal taxa. Mol Phylogenet Evol 2020; 142:106660. [DOI: 10.1016/j.ympev.2019.106660] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2019] [Revised: 10/17/2019] [Accepted: 10/17/2019] [Indexed: 12/15/2022]
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Lozano-Fernandez J, Giacomelli M, Fleming JF, Chen A, Vinther J, Thomsen PF, Glenner H, Palero F, Legg DA, Iliffe TM, Pisani D, Olesen J. Pancrustacean Evolution Illuminated by Taxon-Rich Genomic-Scale Data Sets with an Expanded Remipede Sampling. Genome Biol Evol 2019; 11:2055-2070. [PMID: 31270537 PMCID: PMC6684935 DOI: 10.1093/gbe/evz097] [Citation(s) in RCA: 48] [Impact Index Per Article: 9.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 06/05/2019] [Indexed: 12/26/2022] Open
Abstract
The relationships of crustaceans and hexapods (Pancrustacea) have been much discussed and partially elucidated following the emergence of phylogenomic data sets. However, major uncertainties still remain regarding the position of iconic taxa such as Branchiopoda, Copepoda, Remipedia, and Cephalocarida, and the sister group relationship of hexapods. We assembled the most taxon-rich phylogenomic pancrustacean data set to date and analyzed it using a variety of methodological approaches. We prioritized low levels of missing data and found that some clades were consistently recovered independently of the analytical approach used. These include, for example, Oligostraca and Altocrustacea. Substantial support was also found for Allotriocarida, with Remipedia as the sister of Hexapoda (i.e., Labiocarida), and Branchiopoda as the sister of Labiocarida, a clade that we name Athalassocarida (="nonmarine shrimps"). Within Allotriocarida, Cephalocarida was found as the sister of Athalassocarida. Finally, moderate support was found for Hexanauplia (Copepoda as sister to Thecostraca) in alliance with Malacostraca. Mapping key crustacean tagmosis patterns and developmental characters across the revised phylogeny suggests that the ancestral pancrustacean was relatively short-bodied, with extreme body elongation and anamorphic development emerging later in pancrustacean evolution.
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Affiliation(s)
- Jesus Lozano-Fernandez
- School of Biological Sciences, University of Bristol, United Kingdom
- School of Earth Sciences, University of Bristol, United Kingdom
- Department of Evolutionary Biology, Ecology and Environmental Sciences, and Biodiversity Research Institute (IRBio), Universitat de Barcelona, Barcelona, Spain
| | - Mattia Giacomelli
- School of Biological Sciences, University of Bristol, United Kingdom
| | - James F Fleming
- School of Earth Sciences, University of Bristol, United Kingdom
- Institute for Advanced Biosciences, Keio University, Tsuruoka, Yamagata, Japan
| | - Albert Chen
- School of Earth Sciences, University of Bristol, United Kingdom
- Department of Biology and Biochemistry, University of Bath, Bath, United Kingdom
| | - Jakob Vinther
- School of Biological Sciences, University of Bristol, United Kingdom
- School of Earth Sciences, University of Bristol, United Kingdom
| | - Philip Francis Thomsen
- Natural History Museum of Denmark, University of Copenhagen, Denmark
- Department of Bioscience, University of Aarhus, Aarhus, Denmark
| | | | - Ferran Palero
- Centro de Estudios Avanzados de Blanes (CEAB-CSIC), Blanes, Spain
- Faculty of Biology and Environmental Protection, University of Lodz, Poland
| | - David A Legg
- Department of Earth, Atmospheric, and Environmental Sciences, University of Manchester, United Kingdom
| | - Thomas M Iliffe
- Department of Marine Biology, Texas A&M University at Galveston
| | - Davide Pisani
- School of Biological Sciences, University of Bristol, United Kingdom
- School of Earth Sciences, University of Bristol, United Kingdom
| | - Jørgen Olesen
- Natural History Museum of Denmark, University of Copenhagen, Denmark
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Laumer CE, Fernández R, Lemer S, Combosch D, Kocot KM, Riesgo A, Andrade SCS, Sterrer W, Sørensen MV, Giribet G. Revisiting metazoan phylogeny with genomic sampling of all phyla. Proc Biol Sci 2019; 286:20190831. [PMID: 31288696 PMCID: PMC6650721 DOI: 10.1098/rspb.2019.0831] [Citation(s) in RCA: 123] [Impact Index Per Article: 24.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2019] [Accepted: 06/17/2019] [Indexed: 11/21/2022] Open
Abstract
Proper biological interpretation of a phylogeny can sometimes hinge on the placement of key taxa-or fail when such key taxa are not sampled. In this light, we here present the first attempt to investigate (though not conclusively resolve) animal relationships using genome-scale data from all phyla. Results from the site-heterogeneous CAT + GTR model recapitulate many established major clades, and strongly confirm some recent discoveries, such as a monophyletic Lophophorata, and a sister group relationship between Gnathifera and Chaetognatha, raising continued questions on the nature of the spiralian ancestor. We also explore matrix construction with an eye towards testing specific relationships; this approach uniquely recovers support for Panarthropoda, and shows that Lophotrochozoa (a subclade of Spiralia) can be constructed in strongly conflicting ways using different taxon- and/or orthologue sets. Dayhoff-6 recoding sacrifices information, but can also reveal surprising outcomes, e.g. full support for a clade of Lophophorata and Entoprocta + Cycliophora, a clade of Placozoa + Cnidaria, and raising support for Ctenophora as sister group to the remaining Metazoa, in a manner dependent on the gene and/or taxon sampling of the matrix in question. Future work should test the hypothesis that the few remaining uncertainties in animal phylogeny might reflect violations of the various stationarity assumptions used in contemporary inference methods.
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Affiliation(s)
- Christopher E. Laumer
- Museum of Comparative Zoology (MCZ) and Department of Organismic and Evolutionary Biology, Harvard University, 26 Oxford Street, Cambridge, MA 02138, USA
- EMBL-European Bioinformatics Institute (EBI), Wellcome Genome Campus, Hinxton CB10 1SD, UK
| | - Rosa Fernández
- Museum of Comparative Zoology (MCZ) and Department of Organismic and Evolutionary Biology, Harvard University, 26 Oxford Street, Cambridge, MA 02138, USA
- Bioinformatics & Genomics Unit, Center for Genomic Regulation, Carrer del Dr. Aiguader 88, 08003 Barcelona (Spain)
| | - Sarah Lemer
- Museum of Comparative Zoology (MCZ) and Department of Organismic and Evolutionary Biology, Harvard University, 26 Oxford Street, Cambridge, MA 02138, USA
- Marine Laboratory, University of Guam, UOG Station, Mangilao, Guam 96923, USA
| | - David Combosch
- Museum of Comparative Zoology (MCZ) and Department of Organismic and Evolutionary Biology, Harvard University, 26 Oxford Street, Cambridge, MA 02138, USA
- Marine Laboratory, University of Guam, UOG Station, Mangilao, Guam 96923, USA
| | - Kevin M. Kocot
- Department of Biological Sciences and Alabama Museum of Natural History, The University of Alabama, Campus Box 870344, Tuscaoosa, AL 35487, USA
| | - Ana Riesgo
- Department of Life Sciences, Natural History Museum of London, Cromwell Road, London SW7 5BD, UK
| | - Sónia C. S. Andrade
- Departamento de Genética e Biologia Evolutiva, IB, Universidade de São Paulo, 05508090 São Paulo, SP, Brazil
| | - Wolfgang Sterrer
- Bermuda Natural History Museum, PO Box FL 145, Flatts, FLBX, Bermuda
| | - Martin V. Sørensen
- Natural History Museum of Denmark, Universitetsparken 15, 2100 Copenhagen, Denmark
| | - Gonzalo Giribet
- Museum of Comparative Zoology (MCZ) and Department of Organismic and Evolutionary Biology, Harvard University, 26 Oxford Street, Cambridge, MA 02138, USA
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Sperling EA, Stockey RG. The Temporal and Environmental Context of Early Animal Evolution: Considering All the Ingredients of an "Explosion". Integr Comp Biol 2019; 58:605-622. [PMID: 30295813 DOI: 10.1093/icb/icy088] [Citation(s) in RCA: 57] [Impact Index Per Article: 11.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023] Open
Abstract
Animals originated and evolved during a unique time in Earth history-the Neoproterozoic Era. This paper aims to discuss (1) when landmark events in early animal evolution occurred, and (2) the environmental context of these evolutionary milestones, and how such factors may have affected ecosystems and body plans. With respect to timing, molecular clock studies-utilizing a diversity of methodologies-agree that animal multicellularity had arisen by ∼800 million years ago (Ma) (Tonian period), the bilaterian body plan by ∼650 Ma (Cryogenian), and divergences between sister phyla occurred ∼560-540 Ma (late Ediacaran). Most purported Tonian and Cryogenian animal body fossils are unlikely to be correctly identified, but independent support for the presence of pre-Ediacaran animals is recorded by organic geochemical biomarkers produced by demosponges. This view of animal origins contrasts with data from the fossil record, and the taphonomic question of why animals were not preserved (if present) remains unresolved. Neoproterozoic environments demanding small, thin, body plans, and lower abundance/rarity in populations may have played a role. Considering environmental conditions, geochemical data suggest that animals evolved in a relatively low-oxygen ocean. Here, we present new analyses of sedimentary total organic carbon contents in shales suggesting that the Neoproterozoic ocean may also have had lower primary productivity-or at least lower quantities of organic carbon reaching the seafloor-compared with the Phanerozoic. Indeed, recent modeling efforts suggest that low primary productivity is an expected corollary of a low-O2 world. Combined with an inability to inhabit productive regions in a low-O2 ocean, earliest animal communities would likely have been more food limited than generally appreciated, impacting both ecosystem structure and organismal behavior. In light of this, we propose the "fire triangle" metaphor for environmental influences on early animal evolution. Moving toward consideration of all environmental aspects of the Cambrian radiation (fuel, heat, and oxidant) will ultimately lead to a more holistic view of the event.
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Affiliation(s)
- Erik A Sperling
- Department of Geological Sciences, Stanford University, 450 Serra Mall, Building 320, Stanford, CA 94305, USA
| | - Richard G Stockey
- Department of Geological Sciences, Stanford University, 450 Serra Mall, Building 320, Stanford, CA 94305, USA
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Laumer CE, Gruber-Vodicka H, Hadfield MG, Pearse VB, Riesgo A, Marioni JC, Giribet G. Support for a clade of Placozoa and Cnidaria in genes with minimal compositional bias. eLife 2018; 7:e36278. [PMID: 30373720 PMCID: PMC6277202 DOI: 10.7554/elife.36278] [Citation(s) in RCA: 56] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2018] [Accepted: 10/11/2018] [Indexed: 12/22/2022] Open
Abstract
The phylogenetic placement of the morphologically simple placozoans is crucial to understanding the evolution of complex animal traits. Here, we examine the influence of adding new genomes from placozoans to a large dataset designed to study the deepest splits in the animal phylogeny. Using site-heterogeneous substitution models, we show that it is possible to obtain strong support, in both amino acid and reduced-alphabet matrices, for either a sister-group relationship between Cnidaria and Placozoa, or for Cnidaria and Bilateria as seen in most published work to date, depending on the orthologues selected to construct the matrix. We demonstrate that a majority of genes show evidence of compositional heterogeneity, and that support for the Cnidaria + Bilateria clade can be assigned to this source of systematic error. In interpreting these results, we caution against a peremptory reading of placozoans as secondarily reduced forms of little relevance to broader discussions of early animal evolution.
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Affiliation(s)
- Christopher E Laumer
- Wellcome Trust Sanger InstituteHinxtonUnited Kingdom
- European Molecular Biology Laboratories-European Bioinformatics InstituteHinxtonUnited Kingdom
| | | | - Michael G Hadfield
- Kewalo Marine LaboratoryPacific Biosciences Research Center and the University of Hawaii-ManoaHonoluluUnited States
| | - Vicki B Pearse
- Institute of Marine SciencesUniversity of CaliforniaSanta CruzUnited States
| | - Ana Riesgo
- Invertebrate Division, Life Sciences DepartmentThe Natural History MuseumLondonUnited Kingdom
| | - John C Marioni
- Wellcome Trust Sanger InstituteHinxtonUnited Kingdom
- European Molecular Biology Laboratories-European Bioinformatics InstituteHinxtonUnited Kingdom
- Cancer Research UK Cambridge InstituteUniversity of CambridgeCambridgeUnited Kingdom
| | - Gonzalo Giribet
- Museum of Comparative Zoology, Department of Organismic and Evolutionary BiologyHarvard UniversityCambridgeUnited States
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