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Wang D, Qiang Y, Guo J, Vannier J, Song Z, Peng J, Zhang B, Sun J, Yu Y, Zhang Y, Zhang T, Yang X, Han J. Early evolution of the ecdysozoan body plan. eLife 2024; 13:RP94709. [PMID: 38976315 PMCID: PMC11231812 DOI: 10.7554/elife.94709] [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] [Indexed: 07/09/2024] Open
Abstract
Extant ecdysozoans (moulting animals) are represented by a great variety of soft-bodied or articulated organisms that may or may not have appendages. However, controversies remain about the vermiform nature (i.e. elongated and tubular) of their ancestral body plan. We describe here Beretella spinosa gen. et sp. nov. a tiny (maximal length 3 mm) ecdysozoan from the lowermost Cambrian, Yanjiahe Formation, South China, characterized by an unusual sack-like appearance, single opening, and spiny ornament. Beretella spinosa gen. et sp. nov has no equivalent among animals, except Saccorhytus coronarius, also from the basal Cambrian. Phylogenetic analyses resolve both fossil species as a sister group (Saccorhytida) to all known Ecdysozoa, thus suggesting that ancestral ecdysozoans may have been non-vermiform animals. Saccorhytids are likely to represent an early off-shot along the stem-line Ecdysozoa. Although it became extinct during the Cambrian, this animal lineage provides precious insight into the early evolution of Ecdysozoa and the nature of the earliest representatives of the group.
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Affiliation(s)
- Deng Wang
- State Key Laboratory of Continental Dynamics, Shaanxi Key Laboratory of Early Life & Environments and Department of Geology, Northwest University, Xi'an, China
| | - Yaqin Qiang
- School of Earth Science and Resources, Key Laboratory of Western China's Mineral Resources and Geological Engineering, Ministry of Education, Chang'an University, Xi'an, China
| | - Junfeng Guo
- School of Earth Science and Resources, Key Laboratory of Western China's Mineral Resources and Geological Engineering, Ministry of Education, Chang'an University, Xi'an, China
| | - Jean Vannier
- Université de Lyon, Université Claude Bernard Lyon 1, ENS de Lyon, CNRS, Laboratoire de Géologie de Lyon: Terre, Planètes, Environnement (CNRS-UMR 5276), Villeurbanne, France
| | - Zuchen Song
- School of Earth Science and Resources, Key Laboratory of Western China's Mineral Resources and Geological Engineering, Ministry of Education, Chang'an University, Xi'an, China
| | - Jiaxin Peng
- School of Earth Science and Resources, Key Laboratory of Western China's Mineral Resources and Geological Engineering, Ministry of Education, Chang'an University, Xi'an, China
| | - Boyao Zhang
- School of Earth Science and Resources, Key Laboratory of Western China's Mineral Resources and Geological Engineering, Ministry of Education, Chang'an University, Xi'an, China
| | - Jie Sun
- State Key Laboratory of Continental Dynamics, Shaanxi Key Laboratory of Early Life & Environments and Department of Geology, Northwest University, Xi'an, China
- School of Earth Science and Resources, Key Laboratory of Western China's Mineral Resources and Geological Engineering, Ministry of Education, Chang'an University, Xi'an, China
| | - Yilun Yu
- Institute of Vertebrate Paleontology and Paleoanthropology, Chinese Academy of Sciences, Beijing, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Yiheng Zhang
- School of Information Science and Technology, Northwest University, Xi'an, China
| | - Tao Zhang
- School of Information Science and Technology, Northwest University, Xi'an, China
| | - Xiaoguang Yang
- State Key Laboratory of Continental Dynamics, Shaanxi Key Laboratory of Early Life & Environments and Department of Geology, Northwest University, Xi'an, China
| | - Jian Han
- State Key Laboratory of Continental Dynamics, Shaanxi Key Laboratory of Early Life & Environments and Department of Geology, Northwest University, Xi'an, China
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2
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Huan P, Liu B. The gastropod Lottia peitaihoensis as a model to study the body patterning of trochophore larvae. Evol Dev 2024; 26:e12456. [PMID: 37667429 DOI: 10.1111/ede.12456] [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: 04/13/2023] [Revised: 07/03/2023] [Accepted: 08/18/2023] [Indexed: 09/06/2023]
Abstract
The body patterning of trochophore larvae is important for understanding spiralian evolution and the origin of the bilateral body plan. However, considerable variations are observed among spiralian lineages, which have adopted varied strategies to develop trochophore larvae or even omit a trochophore stage. Some spiralians, such as patellogastropod mollusks, are suggested to exhibit ancestral traits by producing equal-cleaving fertilized eggs and possessing "typical" trochophore larvae. In recent years, we developed a potential model system using the patellogastropod Lottia peitaihoensis (= Lottia goshimai). Here, we introduce how the species were selected and establish sources and techniques, including gene knockdown, ectopic gene expression, and genome editing. Investigations on this species reveal essential aspects of trochophore body patterning, including organizer signaling, molecular and cellular processes connecting the various developmental functions of the organizer, the specification and behaviors of the endomesoderm and ectomesoderm, and the characteristic dorsoventral decoupling of Hox expression. These findings enrich the knowledge of trochophore body patterning and have important implications regarding the evolution of spiralians as well as bilateral body plans.
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Affiliation(s)
- Pin Huan
- CAS and Shandong Province Key Laboratory of Experimental Marine Biology, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Baozhong Liu
- CAS and Shandong Province Key Laboratory of Experimental Marine Biology, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, China
- University of Chinese Academy of Sciences, Beijing, China
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3
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Zhang Z, Zhang Z, Holmer L, Topper TP, Pan B, Li G. Evolution and diversity of biomineralized columnar architecture in early Cambrian phosphatic-shelled brachiopods. eLife 2024; 12:RP88855. [PMID: 38597930 PMCID: PMC11006422 DOI: 10.7554/elife.88855] [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] [Indexed: 04/11/2024] Open
Abstract
Biologically-controlled mineralization producing organic-inorganic composites (hard skeletons) by metazoan biomineralizers has been an evolutionary innovation since the earliest Cambrian. Among them, linguliform brachiopods are one of the key invertebrates that secrete calcium phosphate minerals to build their shells. One of the most distinct shell structures is the organo-phosphatic cylindrical column exclusive to phosphatic-shelled brachiopods, including both crown and stem groups. However, the complexity, diversity, and biomineralization processes of these microscopic columns are far from clear in brachiopod ancestors. Here, exquisitely well-preserved columnar shell ultrastructures are reported for the first time in the earliest eoobolids Latusobolus xiaoyangbaensis gen. et sp. nov. and Eoobolus acutulus sp. nov. from the Cambrian Series 2 Shuijingtuo Formation of South China. The hierarchical shell architectures, epithelial cell moulds, and the shape and size of cylindrical columns are scrutinised in these new species. Their calcium phosphate-based biomineralized shells are mainly composed of stacked sandwich columnar units. The secretion and construction of the stacked sandwich model of columnar architecture, which played a significant role in the evolution of linguliforms, is highly biologically controlled and organic-matrix mediated. Furthermore, a continuous transformation of anatomic features resulting from the growth of diverse columnar shells is revealed between Eoobolidae, Lingulellotretidae, and Acrotretida, shedding new light on the evolutionary growth and adaptive innovation of biomineralized columnar architecture among early phosphatic-shelled brachiopods during the Cambrian explosion.
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Affiliation(s)
- Zhiliang Zhang
- State Key Laboratory of Palaeobiology and Stratigraphy, Nanjing Institute of Geology and Palaeontology, Chinese Academy of Sciences, Nanjing, China
- School of Natural Sciences, Macquarie University, Macquarie Park, Australia
| | - Zhifei Zhang
- State Key Laboratory of Continental Dynamics, Shaanxi Key Laboratory of Early Life & Environments, Department of Geology, Northwest University, Xi'an, China
| | - Lars Holmer
- Institute of Earth Sciences, Palaeobiology, Uppsala University, Uppsala, Sweden
| | - Timothy P Topper
- State Key Laboratory of Continental Dynamics, Shaanxi Key Laboratory of Early Life & Environments, Department of Geology, Northwest University, Xi'an, China
- Department of Palaeobiology, Swedish Museum of Natural History Stockholm, Stockholm, Sweden
| | - Bing Pan
- State Key Laboratory of Palaeobiology and Stratigraphy, Nanjing Institute of Geology and Palaeontology, Chinese Academy of Sciences, Nanjing, China
| | - Guoxiang Li
- State Key Laboratory of Palaeobiology and Stratigraphy, Nanjing Institute of Geology and Palaeontology, Chinese Academy of Sciences, Nanjing, China
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4
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Yang X, Aguado MT, Helm C, Zhang Z, Bleidorn C. New fossil of Gaoloufangchaeta advances the origin of Errantia (Annelida) to the early Cambrian. ROYAL SOCIETY OPEN SCIENCE 2024; 11:231580. [PMID: 38601033 PMCID: PMC11004674 DOI: 10.1098/rsos.231580] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/23/2023] [Revised: 02/27/2024] [Accepted: 02/28/2024] [Indexed: 04/12/2024]
Abstract
Molecular clock estimates suggest the origin of Annelida dates back to the Ediacaran period, which is in discordance with the first appearance of this taxon in the early Cambrian, as evidenced by the fossil records of stem-group and basally branching crown-group annelids. Using new material from the early Cambrian Guanshan biota (Cambrian Series 2, Stage 4), we re-interpret Gaoloufangchaeta bifurcus Zhao, Li & Selden, 2023, as the earliest known errantian annelid. Gaoloufangchaeta has a prominent anterior end bearing three pairs of putatively sensory appendages and a pair of anterior eyes; a muscular eversible pharynx with papillae is identified. The presence of enlarged parapodia with acicula-like structures and long capillary chaetae suggests a pelagic lifestyle for this taxon. Our phylogenetic analyses recover Gaoloufangchaeta within the Phyllodocida (Pleistoannelida, Errantia), extending the origin of Errantia back to the early Cambrian. Our data are in line with the hypothesis that Annelida diverged before the Cambrian and indicate both morphological and ecological diversification of annelids in the early Cambrian.
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Affiliation(s)
- Xiaoyu Yang
- Yunnan Key Laboratory for Palaeobiology, Institute of Palaeontology, Yunnan University, Kunming650500, People's Republic of China
- Animal Evolution and Biodiversity, Georg-August-Universität Göttingen, Göttingen37073, Germany
| | - M. Teresa Aguado
- Animal Evolution and Biodiversity, Georg-August-Universität Göttingen, Göttingen37073, Germany
| | - Conrad Helm
- Animal Evolution and Biodiversity, Georg-August-Universität Göttingen, Göttingen37073, Germany
| | - Zhiqian Zhang
- School of Fine Arts, Yunnan Normal University, Kunming650500, People's Republic of China
| | - Christoph Bleidorn
- Animal Evolution and Biodiversity, Georg-August-Universität Göttingen, Göttingen37073, Germany
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Xiang X, Vilar Gomez AA, Blomberg SP, Yuan H, Degnan BM, Degnan SM. Potential for host-symbiont communication via neurotransmitters and neuromodulators in an aneural animal, the marine sponge Amphimedon queenslandica. Front Neural Circuits 2023; 17:1250694. [PMID: 37841893 PMCID: PMC10570526 DOI: 10.3389/fncir.2023.1250694] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2023] [Accepted: 09/12/2023] [Indexed: 10/17/2023] Open
Abstract
Interkingdom signalling within a holobiont allows host and symbionts to communicate and to regulate each other's physiological and developmental states. Here we show that a suite of signalling molecules that function as neurotransmitters and neuromodulators in most animals with nervous systems, specifically dopamine and trace amines, are produced exclusively by the bacterial symbionts of the demosponge Amphimedon queenslandica. Although sponges do not possess a nervous system, A. queenslandica expresses rhodopsin class G-protein-coupled receptors that are structurally similar to dopamine and trace amine receptors. When sponge larvae, which express these receptors, are exposed to agonists and antagonists of bilaterian dopamine and trace amine receptors, we observe marked changes in larval phototactic swimming behaviour, consistent with the sponge being competent to recognise and respond to symbiont-derived trace amine signals. These results indicate that monoamines synthesised by bacterial symbionts may be able to influence the physiology of the host sponge.
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Affiliation(s)
| | | | | | | | | | - Sandie M. Degnan
- Centre for Marine Science, School of the Environment, The University of Queensland, Brisbane, QLD, Australia
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6
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Posnien N, Hunnekuhl VS, Bucher G. Gene expression mapping of the neuroectoderm across phyla - conservation and divergence of early brain anlagen between insects and vertebrates. eLife 2023; 12:e92242. [PMID: 37750868 PMCID: PMC10522337 DOI: 10.7554/elife.92242] [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: 09/07/2023] [Accepted: 09/18/2023] [Indexed: 09/27/2023] Open
Abstract
Gene expression has been employed for homologizing body regions across bilateria. The molecular comparison of vertebrate and fly brains has led to a number of disputed homology hypotheses. Data from the fly Drosophila melanogaster have recently been complemented by extensive data from the red flour beetle Tribolium castaneum with its more insect-typical development. In this review, we revisit the molecular mapping of the neuroectoderm of insects and vertebrates to reconsider homology hypotheses. We claim that the protocerebrum is non-segmental and homologous to the vertebrate fore- and midbrain. The boundary between antennal and ocular regions correspond to the vertebrate mid-hindbrain boundary while the deutocerebrum represents the anterior-most ganglion with serial homology to the trunk. The insect head placode is shares common embryonic origin with the vertebrate adenohypophyseal placode. Intriguingly, vertebrate eyes develop from a different region compared to the insect compound eyes calling organ homology into question. Finally, we suggest a molecular re-definition of the classic concepts of archi- and prosocerebrum.
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Affiliation(s)
- Nico Posnien
- Department of Developmental Biology, Johann-Friedrich-Blumenbach Institute, University GoettingenGöttingenGermany
| | - Vera S Hunnekuhl
- Department of Evolutionary Developmental Genetics, Johann-Friedrich-Blumenbach Institute, University of GöttingenGöttingenGermany
| | - Gregor Bucher
- Department of Evolutionary Developmental Genetics, Johann-Friedrich-Blumenbach Institute, University of GöttingenGöttingenGermany
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7
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Bravo González-Blas C, De Winter S, Hulselmans G, Hecker N, Matetovici I, Christiaens V, Poovathingal S, Wouters J, Aibar S, Aerts S. SCENIC+: single-cell multiomic inference of enhancers and gene regulatory networks. Nat Methods 2023; 20:1355-1367. [PMID: 37443338 PMCID: PMC10482700 DOI: 10.1038/s41592-023-01938-4] [Citation(s) in RCA: 85] [Impact Index Per Article: 85.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2022] [Accepted: 06/06/2023] [Indexed: 07/15/2023]
Abstract
Joint profiling of chromatin accessibility and gene expression in individual cells provides an opportunity to decipher enhancer-driven gene regulatory networks (GRNs). Here we present a method for the inference of enhancer-driven GRNs, called SCENIC+. SCENIC+ predicts genomic enhancers along with candidate upstream transcription factors (TFs) and links these enhancers to candidate target genes. To improve both recall and precision of TF identification, we curated and clustered a motif collection with more than 30,000 motifs. We benchmarked SCENIC+ on diverse datasets from different species, including human peripheral blood mononuclear cells, ENCODE cell lines, melanoma cell states and Drosophila retinal development. Next, we exploit SCENIC+ predictions to study conserved TFs, enhancers and GRNs between human and mouse cell types in the cerebral cortex. Finally, we use SCENIC+ to study the dynamics of gene regulation along differentiation trajectories and the effect of TF perturbations on cell state. SCENIC+ is available at scenicplus.readthedocs.io .
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Affiliation(s)
- Carmen Bravo González-Blas
- VIB Center for Brain & Disease Research, Leuven, Belgium
- Department of Human Genetics, KU Leuven, Leuven, Belgium
| | - Seppe De Winter
- VIB Center for Brain & Disease Research, Leuven, Belgium
- Department of Human Genetics, KU Leuven, Leuven, Belgium
| | - Gert Hulselmans
- VIB Center for Brain & Disease Research, Leuven, Belgium
- Department of Human Genetics, KU Leuven, Leuven, Belgium
| | - Nikolai Hecker
- VIB Center for Brain & Disease Research, Leuven, Belgium
- Department of Human Genetics, KU Leuven, Leuven, Belgium
| | - Irina Matetovici
- VIB Center for Brain & Disease Research, Leuven, Belgium
- VIB Tech Watch, VIB Headquarters, Ghent, Belgium
| | - Valerie Christiaens
- VIB Center for Brain & Disease Research, Leuven, Belgium
- Department of Human Genetics, KU Leuven, Leuven, Belgium
| | | | - Jasper Wouters
- VIB Center for Brain & Disease Research, Leuven, Belgium
- Department of Human Genetics, KU Leuven, Leuven, Belgium
| | - Sara Aibar
- VIB Center for Brain & Disease Research, Leuven, Belgium
- Department of Human Genetics, KU Leuven, Leuven, Belgium
| | - Stein Aerts
- VIB Center for Brain & Disease Research, Leuven, Belgium.
- Department of Human Genetics, KU Leuven, Leuven, Belgium.
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Vroomans RMA, Colizzi ES. Evolution of selfish multicellularity: collective organisation of individual spatio-temporal regulatory strategies. BMC Ecol Evol 2023; 23:35. [PMID: 37468829 PMCID: PMC10357660 DOI: 10.1186/s12862-023-02133-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2022] [Accepted: 06/12/2023] [Indexed: 07/21/2023] Open
Abstract
BACKGROUND The unicellular ancestors of modern-day multicellular organisms were remarkably complex. They had an extensive set of regulatory and signalling genes, an intricate life cycle and could change their behaviour in response to environmental changes. At the transition to multicellularity, some of these behaviours were co-opted to organise the development of the nascent multicellular organism. Here, we focus on the transition to multicellularity before the evolution of stable cell differentiation, to reveal how the emergence of clusters affects the evolution of cell behaviour. RESULTS We construct a computational model of a population of cells that can evolve the regulation of their behavioural state - either division or migration - and study both a unicellular and a multicellular context. Cells compete for reproduction and for resources to survive in a seasonally changing environment. We find that the evolution of multicellularity strongly determines the co-evolution of cell behaviour, by altering the competition dynamics between cells. When adhesion cannot evolve, cells compete for survival by rapidly migrating towards resources before dividing. When adhesion evolves, emergent collective migration alleviates the pressure on individual cells to reach resources. This allows individual cells to maximise their own replication. Migrating adhesive clusters display striking patterns of spatio-temporal cell state changes that visually resemble animal development. CONCLUSIONS Our model demonstrates how emergent selection pressures at the onset of multicellularity can drive the evolution of cellular behaviour to give rise to developmental patterns.
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Affiliation(s)
- Renske M A Vroomans
- Informatics Institute, University of Amsterdam, Amsterdam, Netherlands.
- Origins Center, Groningen, Netherlands.
- Sainsbury Laboratory, University of Cambridge, Cambridge, UK.
| | - Enrico Sandro Colizzi
- Origins Center, Groningen, Netherlands
- Sainsbury Laboratory, University of Cambridge, Cambridge, UK
- Mathematical Institute, Leiden University, Leiden, Netherlands
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9
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A comment on the article Jaques et al. "Origin and evolution of animal multicellularity in light of phylogenomics and cancer genetics ". MEDICAL ONCOLOGY (NORTHWOOD, LONDON, ENGLAND) 2022; 40:38. [PMID: 36460873 DOI: 10.1007/s12032-022-01868-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/30/2022] [Accepted: 10/03/2022] [Indexed: 12/04/2022]
Abstract
For developmental biologists, the work of Jaques et al. is quite surprising. It suggests that cancer genetics and cancer phylogenomics may contribute to the origin and evolution of multicellularity in animals. My commentary complements the work of Jaques et al. from the perspective of evolutionary life cycle biology and recalls the statement of Douglas H. Erwin, who said that understanding life cycle evolution is (equally) crucial to subsequent steps [1].
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10
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Holmes JD, Budd GE. Reassessing a cryptic history of early trilobite evolution. Commun Biol 2022; 5:1177. [PMCID: PMC9636250 DOI: 10.1038/s42003-022-04146-6] [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: 07/05/2022] [Accepted: 10/20/2022] [Indexed: 11/06/2022] Open
Abstract
Trilobites are an iconic Paleozoic group of biomineralizing marine euarthropods that appear abruptly in the fossil record (c. 521 million years ago) during the Cambrian ‘explosion’. This sudden appearance has proven controversial ever since Darwin puzzled over the lack of pre-trilobitic fossils in the Origin of Species, and it has generally been assumed that trilobites must have an unobserved cryptic evolutionary history reaching back into the Precambrian. Here we review the assumptions behind this model, and suggest that a cryptic history creates significant difficulties, including the invocation of rampant convergent evolution of biomineralized structures and the abandonment of the synapomorphies uniting the clade. We show that a vicariance explanation for early Cambrian trilobite palaeobiogeographic patterns is inconsistent with factors controlling extant marine invertebrate distributions, including the increasingly-recognized importance of long-distance dispersal. We suggest that survivorship bias may explain the initial rapid diversification of trilobites, and conclude that the group’s appearance at c. 521 Ma closely reflects their evolutionary origins. A reassessment of early trilobite phylogenetic relationships and palaeobiogeographic patterns suggests that a cryptic evolutionary history is unlikely for this group. The abrupt appearance of trilobites is likely to closely reflect their evolutionary origins, and may be explained by survivorship biases inherent in the fossil record.
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Affiliation(s)
- James D. Holmes
- grid.8993.b0000 0004 1936 9457Department of Earth Sciences, Palaeobiology, Uppsala University, Villavägen 16, Uppsala, 752 36 Sweden
| | - Graham E. Budd
- grid.8993.b0000 0004 1936 9457Department of Earth Sciences, Palaeobiology, Uppsala University, Villavägen 16, Uppsala, 752 36 Sweden
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11
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Zhang Y, Zhang X, Liu C. Asynchronized cell division in embryo‐like fossils from the Ediacaran Zhenba microfossil assemblage. Evol Dev 2022; 24:189-195. [DOI: 10.1111/ede.12423] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2022] [Revised: 08/26/2022] [Accepted: 09/04/2022] [Indexed: 11/30/2022]
Affiliation(s)
- Yuan Zhang
- Department of Geology, State Key Laboratory of Continental Dynamics, and Shaanxi Key Laboratory of Early Life and Environments Northwest University Xi'an China
| | - Xingliang Zhang
- Department of Geology, State Key Laboratory of Continental Dynamics, and Shaanxi Key Laboratory of Early Life and Environments Northwest University Xi'an China
- Nanjing Institute of Geology and Paleontology Chinese Academy of Sciences Nanjing China
| | - Cong Liu
- Department of Geology, State Key Laboratory of Continental Dynamics, and Shaanxi Key Laboratory of Early Life and Environments Northwest University Xi'an China
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12
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Yuan H, Hatleberg WL, Degnan BM, Degnan SM. Gene activation of metazoan Fox transcription factors at the onset of metamorphosis in the marine demosponge Amphimedon queenslandica. Dev Growth Differ 2022; 64:455-468. [PMID: 36155915 PMCID: PMC9828451 DOI: 10.1111/dgd.12812] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2022] [Revised: 09/13/2022] [Accepted: 09/14/2022] [Indexed: 01/12/2023]
Abstract
Transcription factors encoded by the Forkhead (Fox) gene family have diverse, sometimes conserved, regulatory roles in eumetazoan development, immunity, and physiology. Although this gene family includes members that predate the origin of the animal kingdom, the majority of metazoan Fox genes evolved after the divergence of animals and choanoflagellates. Here, we characterize the composition, structure, and expression of Fox genes in the marine demosponge Amphimedon queenslandica to better understand the origin and evolution of this family. The Fox gene repertoire in A. queenslandica appears to be similar to the ancestral metazoan Fox gene family. All 17 A. queenslandica Fox genes are differentially expressed during development and in adult cell types. Remarkably, eight of these, all of which appear to be metazoan-specific, are induced within just 1 h of larval settlement and commencement of metamorphosis. Gene co-expression analyses suggest that these eight Fox genes regulate developmental and physiological processes similar to their roles in other animals. These findings are consistent with Fox genes playing deeply ancestral roles in animal development and physiology, including in response to changes in the external environment.
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Affiliation(s)
- Huifang Yuan
- School of Biological Sciences and Centre for Marine ScienceUniversity of QueenslandBrisbaneQueenslandAustralia
| | - William L. Hatleberg
- School of Biological Sciences and Centre for Marine ScienceUniversity of QueenslandBrisbaneQueenslandAustralia,Present address:
Department of Biological SciencesCarnegie Mellon UniversityPittsburghPennsylvaniaUSA
| | - Bernard M. Degnan
- School of Biological Sciences and Centre for Marine ScienceUniversity of QueenslandBrisbaneQueenslandAustralia
| | - Sandie M. Degnan
- School of Biological Sciences and Centre for Marine ScienceUniversity of QueenslandBrisbaneQueenslandAustralia
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13
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Luo C, Pei Y, Richoz S, Li Q, Reitner J. Identification and Current Palaeobiological Understanding of “Keratosa”-Type Nonspicular Demosponge Fossils in Carbonates: With a New Example from the Lowermost Triassic, Armenia. Life (Basel) 2022; 12:life12091348. [PMID: 36143387 PMCID: PMC9502394 DOI: 10.3390/life12091348] [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: 07/18/2022] [Revised: 08/14/2022] [Accepted: 08/23/2022] [Indexed: 12/02/2022] Open
Abstract
Structures similar to fossilized nonspicular demosponges have been reported in carbonates throughout the Phanerozoic and recently in rocks dating back to 890 Ma ago. Interpretation of these records is increasingly influential to our understanding of metazoans in multiple aspects, including their early evolution, the ecology in fossil reefs, and recovery after mass extinction events. Here, we propose six identification criteria of “Keratosa”-type nonspicular demosponge fossils based on the well-established taphonomical models and their biological characteristics. Besides, sponge fossils of this kind from the lowermost Triassic of Chanakhchi (Armenia) are described with a 3-D reconstruction to exemplify the application of these criteria in recognition of such organisms. Subsequently, the state-of-the-art understanding of the taxonomy and evolution of these fossil sponges, a previously poorly addressed topic, is summarized. The morphology of the Triassic Chanakhchi fossils indicates an affinity with verongimorphs, a group that may have evolved by Cambrian Age 3. Other than that, further efforts are encouraged to forge quantitative criteria based on the here proposed descriptive version and to explore the taxonomic diversity and evolutionary details of these fossil nonspicular demosponges.
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Affiliation(s)
- Cui Luo
- State Key Laboratory of Palaeobiology and Stratigraphy, Nanjing Institute of Geology and Palaeontology and Center for Excellence in Life and Paleoenvironment, Chinese Academy of Sciences, Nanjing 210008, China
- Correspondence: (C.L.); (J.R.)
| | - Yu Pei
- Department of Geosciences, University of Tübingen, 72076 Tübingen, Germany
| | - Sylvain Richoz
- Department of Geology, Lund University, Sölvegatan 12, 223 62 Lund, Sweden
| | - Qijian Li
- State Key Laboratory of Palaeobiology and Stratigraphy, Nanjing Institute of Geology and Palaeontology and Center for Excellence in Life and Paleoenvironment, Chinese Academy of Sciences, Nanjing 210008, China
| | - Joachim Reitner
- Department of Geobiology, Centre of Geosciences, University of Göttingen, Goldschmidtstraße 3, 37073 Göttingen, Germany
- Göttingen Academy of Science and Humanities, Theaterstraße 7, 37077 Göttingen, Germany
- Correspondence: (C.L.); (J.R.)
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14
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Jacques F, Baratchart E, Pienta KJ, Hammarlund EU. Origin and evolution of animal multicellularity in the light of phylogenomics and cancer genetics. Med Oncol 2022; 39:160. [PMID: 35972622 PMCID: PMC9381480 DOI: 10.1007/s12032-022-01740-w] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2022] [Accepted: 04/23/2022] [Indexed: 11/07/2022]
Abstract
The rise of animals represents a major but enigmatic event in the evolutionary history of life. In recent years, numerous studies have aimed at understanding the genetic basis of this transition. However, genome comparisons of diverse animal and protist lineages suggest that the appearance of gene families that were previously considered animal specific indeed preceded animals. Animals' unicellular relatives, such as choanoflagellates, ichthyosporeans, and filastereans, demonstrate complex life cycles including transient multicellularity as well as genetic toolkits for temporal cell differentiation, cell-to-cell communication, apoptosis, and cell adhesion. This has warranted further exploration of the genetic basis underlying transitions in cellular organization. An alternative model for the study of transitions in cellular organization is tumors, which exploit physiological programs that characterize both unicellularity and multicellularity. Tumor cells, for example, switch adhesion on and off, up- or downregulate specific cell differentiation states, downregulate apoptosis, and allow cell migration within tissues. Here, we use insights from both the fields of phylogenomics and tumor biology to review the evolutionary history of the regulatory systems of multicellularity and discuss their overlap. We claim that while evolutionary biology has contributed to an increased understanding of cancer, broad investigations into tissue-normal and transformed-can also contribute the framework for exploring animal evolution.
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Affiliation(s)
- Florian Jacques
- Tissue Development and Evolution (TiDE), Department of Laboratory Medicine, Lund University, Lund, Sweden
- Department of Laboratory Medicine, Lund Stem Cell Center, Lund University, Lund, Sweden
| | - Etienne Baratchart
- Tissue Development and Evolution (TiDE), Department of Laboratory Medicine, Lund University, Lund, Sweden
- Department of Laboratory Medicine, Lund Stem Cell Center, Lund University, Lund, Sweden
| | - Kenneth J Pienta
- The Cancer Ecology Center, Brady Urological Institute, Johns Hopkins School of Medicine, Baltimore, USA
| | - Emma U Hammarlund
- Tissue Development and Evolution (TiDE), Department of Laboratory Medicine, Lund University, Lund, Sweden.
- Department of Laboratory Medicine, Lund Stem Cell Center, Lund University, Lund, Sweden.
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15
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Martynov AV, Korshunova TA. Renewed perspectives on the sedentary-pelagic last common bilaterian ancestor. CONTRIBUTIONS TO ZOOLOGY 2022. [DOI: 10.1163/18759866-bja10034] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
Abstract
Abstract
Various evaluations of the last common bilaterian ancestor (lcba) currently suggest that it resembled either a microscopic, non-segmented motile adult; or, on the contrary, a complex segmented adult motile urbilaterian. These fundamental inconsistencies remain largely unexplained. A majority of multidisciplinary data regarding sedentary adult ancestral bilaterian organization is overlooked. The sedentary-pelagic model is supported now by a number of novel developmental, paleontological and molecular phylogenetic data: (1) data in support of sedentary sponges, in the adult stage, as sister to all other Metazoa; (2) a similarity of molecular developmental pathways in both adults and larvae across sedentary sponges, cnidarians, and bilaterians; (3) a cnidarian-bilaterian relationship, including a unique sharing of a bona fide Hox-gene cluster, of which the evolutionary appearance does not connect directly to a bilaterian motile organization; (4) the presence of sedentary and tube-dwelling representatives of the main bilaterian clades in the early Cambrian; (5) an absence of definite taxonomic attribution of Ediacaran taxa reconstructed as motile to any true bilaterian phyla; (6) a similarity of tube morphology (and the clear presence of a protoconch-like apical structure of the Ediacaran sedentary Cloudinidae) among shells of the early Cambrian, and later true bilaterians, such as semi-sedentary hyoliths and motile molluscs; (7) recent data that provide growing evidence for a complex urbilaterian, despite a continuous molecular phylogenetic controversy. The present review compares the main existing models and reconciles the sedentary model of an urbilaterian and the model of a larva-like lcba with a unified sedentary(adult)-pelagic(larva) model of the lcba.
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Affiliation(s)
- Alexander V. Martynov
- Zoological Museum, Moscow State University, Bolshaya Nikitskaya Str. 6, 125009 Moscow, Russia,
| | - Tatiana A. Korshunova
- Koltzov Institute of Developmental Biology RAS, 26 Vavilova Str., 119334 Moscow, Russia
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16
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Moczek AP. When the end modifies its means: the origins of novelty and the evolution of innovation. Biol J Linn Soc Lond 2022. [DOI: 10.1093/biolinnean/blac061] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
Abstract
Abstract
The origin of novel complex traits constitutes a central yet largely unresolved challenge in evolutionary biology. Intriguingly, many of the most promising breakthroughs in understanding the genesis of evolutionary novelty in recent years have occurred not in evolutionary biology itself, but through the comparative study of development and, more recently, the interface of developmental biology and ecology. Here, I discuss how these insights are changing our understanding of what matters in the origin of novel, complex traits in ontogeny and evolution. Specifically, my essay has two major objectives. First, I discuss how the nature of developmental systems biases the production of phenotypic variation in the face of novel or stressful environments toward functional, integrated and, possibly, adaptive variants. This, in turn, allows the production of novel phenotypes to precede (rather than follow) changes in genotype and allows developmental processes that are the product of past evolution to shape evolutionary change that has yet to occur. Second, I explore how this nature of developmental systems has itself evolved over time, increasing the repertoire of ontogenies to pursue a wider range of objectives across an expanding range of conditions, thereby creating an increasingly extensive affordance landscape in development and developmental evolution. Developmental systems and their evolution can thus be viewed as dynamic processes that modify their own means across ontogeny and phylogeny. The study of these dynamics necessitates more than the strict reductionist approach that currently dominates the fields of developmental and evolutionary developmental biology.
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Affiliation(s)
- Armin P Moczek
- Department of Biology, Indiana University , Bloomington, IN , USA
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17
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Ozernyuk ND, Isaeva VV. Early Stages of Animal Mesoderm Evolution. Russ J Dev Biol 2022. [DOI: 10.1134/s1062360422020096] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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18
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Distinguishing Evolutionary Conservation from Derivedness. Life (Basel) 2022; 12:life12030440. [PMID: 35330191 PMCID: PMC8954198 DOI: 10.3390/life12030440] [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: 02/22/2022] [Revised: 03/14/2022] [Accepted: 03/14/2022] [Indexed: 11/17/2022] Open
Abstract
While the concept of “evolutionary conservation” has enabled biologists to explain many ancestral features and traits, it has also frequently been misused to evaluate the degree of changes from a common ancestor, or “derivedness”. We propose that the distinction of these two concepts allows us to properly understand phenotypic and organismal evolution. From a methodological aspect, “conservation” mainly considers genes or traits which species have in common, while “derivedness” additionally covers those that are not commonly shared, such as novel or lost traits and genes to evaluate changes from the time of divergence from a common ancestor. Due to these differences, while conservation-oriented methods are effective in identifying ancestral features, they may be prone to underestimating the overall changes accumulated during the evolution of certain lineages. Herein, we describe our recently developed method, “transcriptomic derivedness index”, for estimating the phenotypic derivedness of embryos with a molecular approach using the whole-embryonic transcriptome as a phenotype. Although echinoderms are often considered as highly derived species, our analyses with this method showed that their embryos, at least at the transcriptomic level, may not be much more derived than those of chordates. We anticipate that the future development of derivedness-oriented methods could provide quantitative indicators for finding highly/lowly evolvable traits.
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19
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Zamora S, Rahman IA, Sumrall CD, Gibson AP, Thompson JR. Cambrian edrioasteroid reveals new mechanism for secondary reduction of the skeleton in echinoderms. Proc Biol Sci 2022; 289:20212733. [PMID: 35232240 PMCID: PMC8889179 DOI: 10.1098/rspb.2021.2733] [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] [Indexed: 12/22/2022] Open
Abstract
Echinoderms are characterized by a distinctive high-magnesium calcite endoskeleton as adults, but elements of this have been drastically reduced in some groups. Herein, we describe a new pentaradial echinoderm, Yorkicystis haefneri n. gen. n. sp., which provides, to our knowledge, the oldest evidence of secondary non-mineralization of the echinoderm skeleton. This material was collected from the Cambrian Kinzers Formation in York (Pennsylvania, USA) and is dated as ca 510 Ma. Detailed morphological observations demonstrate that the ambulacra (i.e. axial region) are composed of flooring and cover plates, but the rest of the body (i.e. extraxial region) is preserved as a dark film and lacks any evidence of skeletal plating. Moreover, X-ray fluorescence analysis reveals that the axial region is elevated in iron. Based on our morphological and chemical data and on taphonomic comparisons with other fossils from the Kinzers Formation, we infer that the axial region was originally calcified, while the extraxial region was non-mineralized. Phylogenetic analyses recover Yorkicystis as an edrioasteroid, indicating that this partial absence of skeleton resulted from a secondary reduction. We hypothesize that skeletal reduction resulted from lack of expression of the skeletogenic gene regulatory network in the extraxial body wall during development. Secondary reduction of the skeleton in Yorkicystis might have allowed for greater flexibility of the body wall.
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Affiliation(s)
- Samuel Zamora
- Instituto Geológico y Minero de España (IGME-CSIC), C/Manuel Lasala, 44, 9°B, 50006 Zaragoza, Spain.,Grupo Aragosaurus-IUCA, Área de Paleontología, Facultad de Ciencias, Universidad de Zaragoza, Zaragoza, Spain
| | - Imran A Rahman
- Department of Earth Sciences, The Natural History Museum, Cromwell Road, London SW7 5BD, UK.,Oxford University Museum of Natural History, Parks Road, Oxford OX1 3PW, UK
| | - Colin D Sumrall
- Department of Earth and Planetary Sciences, University of Tennessee, Knoxville, TN 37996-1526, USA
| | - Adam P Gibson
- Department of Medical Physics and Biomedical Engineering and Institute for Sustainable Heritage, University College London, Gower Street, London WC1E 6BT, UK
| | - Jeffrey R Thompson
- Department of Earth Sciences, The Natural History Museum, Cromwell Road, London SW7 5BD, UK.,UCL Centre for Life's Origins and Evolution, University College London, Gower Street, London WC1E 6BT, UK
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20
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The Evolution of Biomineralization through the Co-Option of Organic Scaffold Forming Networks. Cells 2022; 11:cells11040595. [PMID: 35203246 PMCID: PMC8870065 DOI: 10.3390/cells11040595] [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: 01/16/2022] [Revised: 02/07/2022] [Accepted: 02/08/2022] [Indexed: 12/05/2022] Open
Abstract
Biomineralization is the process in which organisms use minerals to generate hard structures like teeth, skeletons and shells. Biomineralization is proposed to have evolved independently in different phyla through the co-option of pre-existing developmental programs. Comparing the gene regulatory networks (GRNs) that drive biomineralization in different species could illuminate the molecular evolution of biomineralization. Skeletogenesis in the sea urchin embryo was extensively studied and the underlying GRN shows high conservation within echinoderms, larval and adult skeletogenesis. The organic scaffold in which the calcite skeletal elements form in echinoderms is a tubular compartment generated by the syncytial skeletogenic cells. This is strictly different than the organic cartilaginous scaffold that vertebrates mineralize with hydroxyapatite to make their bones. Here I compare the GRNs that drive biomineralization and tubulogenesis in echinoderms and in vertebrates. The GRN that drives skeletogenesis in the sea urchin embryo shows little similarity to the GRN that drives bone formation and high resemblance to the GRN that drives vertebrates’ vascular tubulogenesis. On the other hand, vertebrates’ bone-GRNs show high similarity to the GRNs that operate in the cells that generate the cartilage-like tissues of basal chordate and invertebrates that do not produce mineralized tissue. These comparisons suggest that biomineralization in deuterostomes evolved through the phylum specific co-option of GRNs that control distinct organic scaffolds to mineralization.
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21
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Cooke GJ, Marsh DR, Walsh C, Black B, Lamarque JF. A revised lower estimate of ozone columns during Earth's oxygenated history. ROYAL SOCIETY OPEN SCIENCE 2022; 9:211165. [PMID: 35070343 PMCID: PMC8728182 DOI: 10.1098/rsos.211165] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/09/2021] [Accepted: 11/25/2021] [Indexed: 05/17/2023]
Abstract
The history of molecular oxygen (O2) in Earth's atmosphere is still debated; however, geological evidence supports at least two major episodes where O2 increased by an order of magnitude or more: the Great Oxidation Event (GOE) and the Neoproterozoic Oxidation Event. O2 concentrations have likely fluctuated (between 10-3 and 1.5 times the present atmospheric level) since the GOE ∼2.4 Gyr ago, resulting in a time-varying ozone (O3) layer. Using a three-dimensional chemistry-climate model, we simulate changes in O3 in Earth's atmosphere since the GOE and consider the implications for surface habitability, and glaciation during the Mesoproterozoic. We find lower O3 columns (reduced by up to 4.68 times for a given O2 level) compared to previous work; hence, higher fluxes of biologically harmful UV radiation would have reached the surface. Reduced O3 leads to enhanced tropospheric production of the hydroxyl radical (OH) which then substantially reduces the lifetime of methane (CH4). We show that a CH4 supported greenhouse effect during the Mesoproterozoic is highly unlikely. The reduced O3 columns we simulate have important implications for astrobiological and terrestrial habitability, demonstrating the relevance of three-dimensional chemistry-climate simulations when assessing paleoclimates and the habitability of faraway worlds.
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Affiliation(s)
- G. J. Cooke
- School of Physics and Astronomy, University of Leeds, Leeds LS2 9JT, UK
| | - D. R. Marsh
- School of Physics and Astronomy, University of Leeds, Leeds LS2 9JT, UK
- National Center for Atmospheric Research, Boulder, CO 80301, USA
| | - C. Walsh
- School of Physics and Astronomy, University of Leeds, Leeds LS2 9JT, UK
| | - B. Black
- Department of Earth and Planetary Sciences, Rutgers University, Piscataway, NJ, USA
- Department of Earth and Atmospheric Sciences, CUNY City College, New York, NY, USA
| | - J.-F. Lamarque
- National Center for Atmospheric Research, Boulder, CO 80301, USA
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22
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Abstract
In his prominent book Regeneration (1901), T.H. Morgan's collected and synthesized theoretical and experimental findings from a diverse array of regenerating animals and plants. Through his endeavor, he introduced a new way to study regeneration and its evolution, setting a conceptual framework that still guides today's research and that embraces the contemporary evolutionary and developmental approaches.In the first part of the chapter, we summarize Morgan's major tenets and use it as a narrative thread to advocate interpreting regenerative biology through the theoretical tools provided by evolution and developmental biology, but also to highlight potential caveats resulting from the rapid proliferation of comparative studies and from the expansion of experimental laboratory models. In the second part, we review some experimental evo-devo approaches, highlighting their power and some of their interpretative dangers. Finally, in order to further understand the evolution of regenerative abilities, we portray an adaptive perspective on the evolution of regeneration and suggest a framework for investigating the adaptive nature of regeneration.
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Affiliation(s)
| | - Alexandre Alié
- Sorbonne Université, CNRS, Laboratoire de Biologie du Développement de Villefranche-sur-Mer (LBDV), Villefranche-sur-Mer, France
| | - Stefano Tiozzo
- Sorbonne Université, CNRS, Laboratoire de Biologie du Développement de Villefranche-sur-Mer (LBDV), Villefranche-sur-Mer, France.
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23
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Ponz-Segrelles G, Ribeiro RP, Aguado MT. Monsters reveal patterns: bifurcated annelids and their implications for the study of development and evolution. Biol Rev Camb Philos Soc 2021; 97:896-922. [PMID: 34931440 DOI: 10.1111/brv.12826] [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: 06/24/2021] [Revised: 12/03/2021] [Accepted: 12/06/2021] [Indexed: 11/30/2022]
Abstract
During recent decades, the study of anatomical anomalies has been of great relevance for research on development and its evolution. Yet most animal groups have never been studied under this perspective. In annelids, one of the most common and remarkable anomalies is anteroposterior axis bifurcation, that is animals that have two or more heads and/or tails. Bifurcated annelids were first described in the 18th century and have been occasionally reported since then. However, these animals have rarely been considered other than curiosities, one-off anomalies, or monsters, and a condensed but comprehensive analysis of this phenomenon is lacking. Such an analysis of the existing knowledge is necessary for addressing the different patterns of annelid bifurcation, as well as to understand possible developmental mechanisms behind them and their evolution. In this review we summarize reports of annelid bifurcation published during the last 275 years and the wide variety of anatomies they present. Our survey reveals bifurcation as a widespread phenomenon found all over the annelid tree. Moreover, it also shows that bifurcations can be classified into different types according to anatomy (lateral versus dorsoventral) or developmental origin (embryonic versus postembryonic, the latter occurring in relation to regeneration, reproduction, or growth). Regarding embryos, three different types of bifurcation can be found: conjoined twins (in clitellates); Janus embryos (two posterior ends with a single head which shows duplicated structures); and duplicitas cruciata embryos (with anterior and posterior bifurcation with a 90° rotation). In adults, we show that while lateral bifurcation can result in well-integrated phenotypes, dorsoventral bifurcation cannot since it requires the discontinuity of at least some internal organs. The relevance of this distinction is highlighted in the case of the Ribbon Clade, a group of syllid annelids in which some species reproduce by collateral and successive gemmiparity (which involves dorsoventral bifurcation), while others grow by branching laterally. Although most known cases of bifurcation came from accidental findings in the wild or were unintentionally produced, experimental studies resulting in the induction of bifurcation of both embryos and adults are also reviewed. In embryos, these experimental studies show how mechanical or chemical disruption of the zygote can result in bifurcation. In adults, the ventral nervous system and the digestive tract seem to play a role in the induction of bifurcation. Based on the reviewed evidence, we argue that the long-forgotten study of annelid developmental anomalies should be incorporated into the growing field of annelid EvoDevo and examined with modern techniques and perspectives.
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Affiliation(s)
- Guillermo Ponz-Segrelles
- Departamento de Biología, Facultad de Ciencias, Universidad Autónoma de Madrid, Darwin, 2, Madrid, 28049, Spain
| | - Rannyele P Ribeiro
- Departamento de Biología, Facultad de Ciencias, Universidad Autónoma de Madrid, Darwin, 2, Madrid, 28049, Spain.,Marine Biological Laboratory, 7 MBL Street, Woods Hole, MA, 02543, U.S.A
| | - M Teresa Aguado
- Biodiversitätsmuseum, Animal Evolution & Biodiversity, Georg-August-Universität Göttingen, Untere Karspüle 2, Göttingen, 37073, Germany
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24
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Abstract
Bryozoans (also known as ectoprocts or moss animals) are aquatic, dominantly sessile, filter-feeding lophophorates that construct an organic or calcareous modular colonial (clonal) exoskeleton1–3. The presence of six major orders of bryozoans with advanced polymorphisms in lower Ordovician rocks strongly suggests a Cambrian origin for the largest and most diverse lophophorate phylum2,4–8. However, a lack of convincing bryozoan fossils from the Cambrian period has hampered resolution of the true origins and character assembly of the earliest members of the group. Here we interpret the millimetric, erect, bilaminate, secondarily phosphatized fossil Protomelission gatehousei9 from the early Cambrian of Australia and South China as a potential stem-group bryozoan. The monomorphic zooid capsules, modular construction, organic composition and simple linear budding growth geometry represent a mixture of organic Gymnolaemata and biomineralized Stenolaemata character traits, with phylogenetic analyses identifying P. gatehousei as a stem-group bryozoan. This aligns the origin of phylum Bryozoa with all other skeletonized phyla in Cambrian Age 3, pushing back its first occurrence by approximately 35 million years. It also reconciles the fossil record with molecular clock estimations of an early Cambrian origination and subsequent Ordovician radiation of Bryozoa following the acquisition of a carbonate skeleton10–13. Interpretation of the early Cambrian fossil Protomelission gatehousei9 as a potential stem-group bryozoan realigns the fossil record with molecular clock estimations of the origins of Bryozoa.
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25
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Bryozoan fossils found at last in deposits from the Cambrian period. Nature 2021; 599:203-204. [PMID: 34707263 DOI: 10.1038/d41586-021-02874-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
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26
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Growth of Biological Complexity from Prokaryotes to Hominids Reflected in the Human Genome. Int J Mol Sci 2021; 22:ijms222111640. [PMID: 34769071 PMCID: PMC8583824 DOI: 10.3390/ijms222111640] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2021] [Revised: 10/20/2021] [Accepted: 10/25/2021] [Indexed: 12/12/2022] Open
Abstract
The growth of complexity in evolution is a most intriguing phenomenon. Using gene phylostratigraphy, we showed this growth (as reflected in regulatory mechanisms) in the human genome, tracing the path from prokaryotes to hominids. Generally, the different regulatory gene families expanded at different times, yet only up to the Euteleostomi (bony vertebrates). The only exception was the expansion of transcription factors (TF) in placentals; however, we argue that this was not related to increase in general complexity. Surprisingly, although TF originated in the Prokaryota while chromatin appeared only in the Eukaryota, the expansion of epigenetic factors predated the expansion of TF. Signaling receptors, tumor suppressors, oncogenes, and aging- and disease-associated genes (indicating vulnerabilities in terms of complex organization and strongly enrichment in regulatory genes) also expanded only up to the Euteleostomi. The complexity-related gene properties (protein size, number of alternative splicing mRNA, length of untranslated mRNA, number of biological processes per gene, number of disordered regions in a protein, and density of TF–TF interactions) rose in multicellular organisms and declined after the Euteleostomi, and possibly earlier. At the same time, the speed of protein sequence evolution sharply increased in the genes that originated after the Euteleostomi. Thus, several lines of evidence indicate that molecular mechanisms of complexity growth were changing with time, and in the phyletic lineage leading to humans, the most salient shift occurred after the basic vertebrate body plan was fixed with bony skeleton. The obtained results can be useful for evolutionary medicine.
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27
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Bentlage B, Collins AG. Tackling the phylogenetic conundrum of Hydroidolina (Cnidaria: Medusozoa: Hydrozoa) by assessing competing tree topologies with targeted high-throughput sequencing. PeerJ 2021; 9:e12104. [PMID: 34589302 PMCID: PMC8435201 DOI: 10.7717/peerj.12104] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2020] [Accepted: 08/11/2021] [Indexed: 12/28/2022] Open
Abstract
Higher-level relationships of the Hydrozoan subclass Hydroidolina, which encompasses the vast majority of medusozoan cnidarian species diversity, have been elusive to confidently infer. The most widely adopted phylogenetic framework for Hydroidolina based on ribosomal RNA data received low support for several higher level relationships. To address this issue, we developed a set of RNA baits to target more than a hundred loci from the genomes of a broad taxonomic sample of Hydroidolina for high-throughput sequencing. Using these data, we inferred the relationships of Hydroidolina using maximum likelihood and Bayesian approaches. Both inference methods yielded well-supported phylogenetic hypotheses that largely agree with each other. Using maximum likelihood and Baysian hypothesis testing frameworks, we found that several alternate topological hypotheses proposed previously may be rejected in light of the genomic data generated for this study. Both the maximum likelihood and Bayesian topologies inferred herein consistently score well across testing frameworks, suggesting that their consensus represents the most likely phylogenetic hypothesis of Hydroidolina. This phylogenetic framework places Aplanulata as sister lineage to the remainder of Hydroidolina. This is a strong deviation from previous phylogenetic analyses that placed Capitata or Siphonophorae as sister group to the remainder of Hydroidolina. Considering that Aplanulata represents a lineage comprised of species that for the most part possess a life cycle involving a solitary polyp and free-swimming medusa stage, the phylogenetic hypotheses presented herein have potentially large implications for clarifying the evolution of life cycles, coloniality, and the division of labor in Hydrozoa as taxon sampling for phylogenetic analyses becomes more complete.
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Affiliation(s)
| | - Allen G Collins
- National Museum of Natural History & National Systematics Laboratory of NOAA's Fisheries Service, Smithsonian Institution, Washington, DC, USA
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28
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Evans SD, Gehling JG, Erwin DH, Droser ML. Ediacara growing pains: Modular addition and development in Dickinsonia costata. PALEOBIOLOGY 2021; 97:10.1017/pab.2021.31. [PMID: 35001986 PMCID: PMC8740542 DOI: 10.1017/pab.2021.31] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/14/2023]
Abstract
Constraining patterns of growth using directly observable and quantifiable characteristics can reveal a wealth of information regarding the biology of the Ediacara Biota - the oldest macroscopic, complex community forming organisms in the fossil record. However, these rely on individuals captured at an instant in time at various growth stages, and so different interpretations can be derived from the same material. Here we leverage newly discovered and well-preserved Dickinsonia costata Sprigg 1947 from South Australia, combined with hundreds of previously described specimens, to test competing hypotheses for the location of module addition. We find considerable variation in the relationship between the total number of modules and body size that cannot be explained solely by expansion and contraction of individuals. Patterns derived assuming new modules differentiated at the anterior result in numerous examples where the oldest module(s) must decrease in size with overall growth, potentially falsifying this hypothesis. Observed polarity as well as the consistent posterior location of defects and indentations support module formation at this end in D. costata. Regardless, changes in repeated units with growth share similarities with those regulated by morphogen gradients in metazoans today, suggesting that these genetic pathways were operating in Ediacaran animals.
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Affiliation(s)
- Scott D Evans
- Department of Geosciences, Virginia Tech, Blacksburg, VA, 24061, USA
| | - James G Gehling
- South Australia Museum, Adelaide, South Australia 5000, Australia
| | - Douglas H Erwin
- Department of Paleobiology MRC-121, National Museum of Natural History, Washington, DC 20013-7012, USA
| | - Mary L Droser
- Department of Earth and Planetary Sciences, University of California, Riverside, CA 92521, USA
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29
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Lyons TW, Diamond CW, Planavsky NJ, Reinhard CT, Li C. Oxygenation, Life, and the Planetary System during Earth's Middle History: An Overview. ASTROBIOLOGY 2021; 21:906-923. [PMID: 34314605 PMCID: PMC8403206 DOI: 10.1089/ast.2020.2418] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/07/2023]
Abstract
The long history of life on Earth has unfolded as a cause-and-effect relationship with the evolving amount of oxygen (O2) in the oceans and atmosphere. Oxygen deficiency characterized our planet's first 2 billion years, yet evidence for biological O2 production and local enrichments in the surface ocean appear long before the first accumulations of O2 in the atmosphere roughly 2.4 to 2.3 billion years ago. Much has been written about this fundamental transition and the related balance between biological O2 production and sinks coupled to deep Earth processes that could buffer against the accumulation of biogenic O2. However, the relationship between complex life (eukaryotes, including animals) and later oxygenation is less clear. Some data suggest O2 was higher but still mostly low for another billion and a half years before increasing again around 800 million years ago, potentially setting a challenging course for complex life during its initial development and ecological expansion. The apparent rise in O2 around 800 million years ago is coincident with major developments in complex life. Multiple geochemical and paleontological records point to a major biogeochemical transition at that time, but whether rising and still dynamic biospheric oxygen triggered or merely followed from innovations in eukaryotic ecology, including the emergence of animals, is still debated. This paper focuses on the geochemical records of Earth's middle history, roughly 1.8 to 0.5 billion years ago, as a backdrop for exploring possible cause-and-effect relationships with biological evolution and the primary controls that may have set its pace, including solid Earth/tectonic processes, nutrient limitation, and their possible linkages. A richer mechanistic understanding of the interplay between coevolving life and Earth surface environments can provide a template for understanding and remotely searching for sustained habitability and even life on distant exoplanets.
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Affiliation(s)
- Timothy W. Lyons
- Department of Earth and Planetary Sciences, University of California, Riverside, California, USA
- Address correspondence to: Timothy W. Lyons, Department of Earth and Planetary Sciences, University of California, Riverside, CA 92521, USA
| | - Charles W. Diamond
- Department of Earth and Planetary Sciences, University of California, Riverside, California, USA
| | - Noah J. Planavsky
- Department of Earth and Planetary Sciences, Yale University, New Haven, Connecticut, USA
| | - Christopher T. Reinhard
- School of Earth and Atmospheric Sciences, Georgia Institute of Technology, Atlanta, Georgia, USA
| | - Chao Li
- State Key Laboratory of Biogeology and Environmental Geology, China University of Geosciences, Wuhan, China
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Oriola D, Spagnoli FM. Engineering life in synthetic systems. Development 2021; 148:270849. [PMID: 34251450 DOI: 10.1242/dev.199497] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2021] [Accepted: 06/01/2021] [Indexed: 11/20/2022]
Abstract
The second EMBO-EMBL Symposium 'Synthetic Morphogenesis: From Gene Circuits to Tissue Architecture' was held virtually in March 2021, with participants from all over the world joining from the comfort of their sofas to discuss synthetic morphogenesis at large. Leading scientists from a range of disciplines, including developmental biology, physics, chemistry and computer science, covered a gamut of topics from the principles of cell and tissue organization, patterning and gene regulatory networks, to synthetic approaches for exploring evolutionary and developmental biology principles. Here, we describe some of the high points.
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Affiliation(s)
- David Oriola
- EMBL Barcelona, Dr Aiguader 88, 08003 Barcelona, Spain
| | - Francesca M Spagnoli
- Centre for Stem Cells and Regenerative Medicine, King's College London, Guy's Hospital, Floor 28, Tower Wing, Great Maze Pond, London SE1 9RT, UK
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Strother PK, Brasier MD, Wacey D, Timpe L, Saunders M, Wellman CH. A possible billion-year-old holozoan with differentiated multicellularity. Curr Biol 2021; 31:2658-2665.e2. [PMID: 33852871 DOI: 10.1016/j.cub.2021.03.051] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2020] [Revised: 12/07/2020] [Accepted: 03/15/2021] [Indexed: 02/05/2023]
Abstract
Sediments of the Torridonian sequence of the Northwest Scottish Highlands contain a wide array of microfossils, documenting life in a non-marine setting a billion years ago (1 Ga).1-4 Phosphate nodules from the Diabaig Formation at Loch Torridon preserve microorganisms with cellular-level fidelity,5,6 allowing for partial reconstruction of the developmental stages of a new organism, Bicellum brasieri gen. et sp. nov. The mature form of Bicellum consists of a solid, spherical ball of tightly packed cells (a stereoblast) of isodiametric cells enclosed in a monolayer of elongated, sausage-shaped cells. However, two populations of naked stereoblasts show mixed cell shapes, which we infer to indicate incipient development of elongated cells that were migrating to the periphery of the cell mass. These simple morphogenetic movements could be explained by differential cell-cell adhesion.7,8 In fact, the basic morphology of Bicellum is topologically similar to that of experimentally produced cell masses that were shown to spontaneously segregate into two distinct domains based on differential cadherin-based cell adhesion.9 The lack of rigid cell walls in the stereoblast renders an algal affinity for Bicellum unlikely: its overall morphology is more consistent with a holozoan origin. Unicellular holozoans are known today to form multicellular stages within complex life cycles,10-13 so the occurrence of such simple levels of transient multicellularity seen here is consistent with a holozoan affinity. Regardless of precise phylogenetic placement, these fossils demonstrate simple cell differentiation and morphogenic processes that are similar to those seen in some metazoans today.
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Affiliation(s)
- Paul K Strother
- Department of Earth & Environmental Sciences, Weston Observatory of Boston College, 381 Concord Road, Weston, MA 02493, USA.
| | - Martin D Brasier
- Department of Earth Sciences, University of Oxford, South Parks Road, Oxford OX1 3AN, UK
| | - David Wacey
- Centre for Microscopy, Characterisation and Analysis, The University of Western Australia, 35 Stirling Highway, Perth, WA 6009, Australia
| | - Leslie Timpe
- Department of Biology, San Francisco State University, San Francisco, CA 94132, USA
| | - Martin Saunders
- Centre for Microscopy, Characterisation and Analysis, The University of Western Australia, 35 Stirling Highway, Perth, WA 6009, Australia
| | - Charles H Wellman
- Department of Animal & Plant Sciences, University of Sheffield, Alfred Denny Building, Western Bank, Sheffield S10 2TN, UK
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Abstract
The Ediacara Biota preserves the oldest fossil evidence of abundant, complex metazoans. Despite their significance, assigning individual taxa to specific phylogenetic groups has proved problematic. To better understand these forms, we identify developmentally controlled characters in representative taxa from the Ediacaran White Sea assemblage and compare them with the regulatory tools underlying similar traits in modern organisms. This analysis demonstrates that the genetic pathways for multicellularity, axial polarity, musculature, and a nervous system were likely present in some of these early animals. Equally meaningful is the absence of evidence for major differentiation of macroscopic body units, including distinct organs, localized sensory machinery or appendages. Together these traits help to better constrain the phylogenetic position of several key Ediacara taxa and inform our views of early metazoan evolution. An apparent lack of heads with concentrated sensory machinery or ventral nerve cords in such taxa supports the hypothesis that these evolved independently in disparate bilaterian clades.
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Affiliation(s)
- Scott D Evans
- Department of Paleobiology MRC-121, National Museum of Natural History, Washington, DC 20013-7012, USA
| | - Mary L Droser
- Department of Earth and Planetary Sciences, University of California, Riverside, CA 92521, USA
| | - Douglas H Erwin
- Department of Paleobiology MRC-121, National Museum of Natural History, Washington, DC 20013-7012, USA
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Zaquin T, Malik A, Drake JL, Putnam HM, Mass T. Evolution of Protein-Mediated Biomineralization in Scleractinian Corals. Front Genet 2021; 12:618517. [PMID: 33633782 PMCID: PMC7902050 DOI: 10.3389/fgene.2021.618517] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2020] [Accepted: 01/08/2021] [Indexed: 12/19/2022] Open
Abstract
While recent strides have been made in understanding the biological process by which stony corals calcify, much remains to be revealed, including the ubiquity across taxa of specific biomolecules involved. Several proteins associated with this process have been identified through proteomic profiling of the skeletal organic matrix (SOM) extracted from three scleractinian species. However, the evolutionary history of this putative “biomineralization toolkit,” including the appearance of these proteins’ throughout metazoan evolution, remains to be resolved. Here we used a phylogenetic approach to examine the evolution of the known scleractinians’ SOM proteins across the Metazoa. Our analysis reveals an evolutionary process dominated by the co-option of genes that originated before the cnidarian diversification. Each one of the three species appears to express a unique set of the more ancient genes, representing the independent co-option of SOM proteins, as well as a substantial proportion of proteins that evolved independently. In addition, in some instances, the different species expressed multiple orthologous proteins sharing the same evolutionary history. Furthermore, the non-random clustering of multiple SOM proteins within scleractinian-specific branches suggests the conservation of protein function between distinct species for what we posit is part of the scleractinian “core biomineralization toolkit.” This “core set” contains proteins that are likely fundamental to the scleractinian biomineralization mechanism. From this analysis, we infer that the scleractinians’ ability to calcify was achieved primarily through multiple lineage-specific protein expansions, which resulted in a new functional role that was not present in the parent gene.
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Affiliation(s)
- Tal Zaquin
- Department of Marine Biology, The Leon H. Charney School of Marine Sciences, University of Haifa, Haifa, Israel
| | - Assaf Malik
- Department of Marine Biology, The Leon H. Charney School of Marine Sciences, University of Haifa, Haifa, Israel
| | - Jeana L Drake
- Department of Marine Biology, The Leon H. Charney School of Marine Sciences, University of Haifa, Haifa, Israel
| | - Hollie M Putnam
- Department of Biological Sciences, University of Rhode Island, Kingston, RI, United States
| | - Tali Mass
- Department of Marine Biology, The Leon H. Charney School of Marine Sciences, University of Haifa, Haifa, Israel
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McFadden CS, Quattrini AM, Brugler MR, Cowman PF, Dueñas LF, Kitahara MV, Paz-García DA, Reimer JD, Rodríguez E. Phylogenomics, Origin, and Diversification of Anthozoans (Phylum Cnidaria). Syst Biol 2021; 70:635-647. [PMID: 33507310 DOI: 10.1093/sysbio/syaa103] [Citation(s) in RCA: 42] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2020] [Revised: 12/18/2020] [Accepted: 12/21/2020] [Indexed: 01/19/2023] Open
Abstract
Anthozoan cnidarians (corals and sea anemones) include some of the world's most important foundation species, capable of building massive reef complexes that support entire ecosystems. Although previous molecular phylogenetic analyses have revealed widespread homoplasy of the morphological characters traditionally used to define orders and families of anthozoans, analyses using mitochondrial genes or rDNA have failed to resolve many key nodes in the phylogeny. With a fully resolved, time-calibrated phylogeny for 234 species constructed from hundreds of ultraconserved elements and exon loci, we explore the evolutionary origins of the major clades of Anthozoa and some of their salient morphological features. The phylogeny supports reciprocally monophyletic Hexacorallia and Octocorallia, with Ceriantharia as the earliest diverging hexacorals; two reciprocally monophyletic clades of Octocorallia; and monophyly of all hexacoral orders with the exception of the enigmatic sea anemone Relicanthus daphneae. Divergence dating analyses place Anthozoa in the Cryogenian to Tonian periods (648-894 Ma), older than has been suggested by previous studies. Ancestral state reconstructions indicate that the ancestral anthozoan was a solitary polyp that had bilateral symmetry and lacked a skeleton. Colonial growth forms and the ability to precipitate calcium carbonate evolved in the Ediacaran (578 Ma) and Cambrian (503 Ma) respectively; these hallmarks of reef-building species have subsequently arisen multiple times independently in different orders. Anthozoans formed associations with photosymbionts by the Devonian (383 Ma), and photosymbioses have been gained and lost repeatedly in all orders. Together, these results have profound implications for the interpretation of the Precambrian environment and the early evolution of metazoans.[Bilateral symmetry; coloniality; coral; early metazoans; exon capture; Hexacorallia; Octocorallia photosymbiosis; sea anemone; ultraconserved elements.].
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Affiliation(s)
- Catherine S McFadden
- Department of Biology, Harvey Mudd College, 1250 N. Dartmouth Ave., Claremont, CA 91711 USA
| | - Andrea M Quattrini
- Department of Biology, Harvey Mudd College, 1250 N. Dartmouth Ave., Claremont, CA 91711 USA.,Department of Invertebrate Zoology, National Museum of Natural History, Smithsonian Institution, Washington, DC 20560, USA
| | - Mercer R Brugler
- Division of Invertebrate Zoology, American Museum of Natural History, Central Park West at 79th Street, New York, NY 10024, USA.,Biological Sciences Department, NYC College of Technology, City University of New York, 285 Jay Street, Brooklyn, NY 11201, USA.,Department of Natural Sciences, University of South Carolina Beaufort, 801 Carteret Street, Beaufort, SC 29902, USA
| | - Peter F Cowman
- ARC Centre of Excellence for Coral Reef Studies, James Cook University, Townsville, QLD 4811, Australia.,Biodiversity and Geosciences Program, Museum of Tropical Queensland, Queensland Museum, Townsville, QLD 4810, Australia
| | - Luisa F Dueñas
- Departamento de Biología, Facultad de Ciencias, Universidad Nacional de Colombia-Sede Bogotá, Carrera 30 No.45-03 Edificio 421, Bogotá, D.C., Colombia
| | - Marcelo V Kitahara
- Department of Marine Science, Federal University of São Paulo, Santos, SP 11070-100 Brazil.,Centre for Marine Biology, University of São Paulo, São Sebastião, SP 11612-109 Brazil
| | - David A Paz-García
- CONACyT-Centro de Investigaciones Biológicas del Noroeste (CIBNOR). Laboratorio de Necton y Ecología de Arrecifes. Calle IPN 195, Col. Playa Palo de Santa Rita Sur, 23096 La Paz, B.C.S., México
| | - James D Reimer
- Molecular Invertebrate Systematics and Ecology Laboratory, Department of Marine Science, Chemistry, and Biology, Faculty of Science, University of the Ryukyus, 1 Senbaru, Nishihara, Okinawa 903-0213, Japan.,Tropical Biosphere Research Center, University of the Ryukyus, 1 Senbaru, Nishihara, Okinawa 903-0213, Japan
| | - Estefanía Rodríguez
- Division of Invertebrate Zoology, American Museum of Natural History, Central Park West at 79th Street, New York, NY 10024, USA
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Abstract
In this review, we consider transformations of axial symmetry in metazoan evolution and development, the genetic basis, and phenotypic expressions of different axial body plans. In addition to the main symmetry types in metazoan body plans, such as rotation (radial symmetry), reflection (mirror and glide reflection symmetry), and translation (metamerism), many biological objects show scale (fractal) symmetry as well as some symmetry-type combinations. Some genetic mechanisms of axial pattern establishment, creating a coordinate system of a metazoan body plan, bilaterian segmentation, and left–right symmetry/asymmetry, are analysed. Data on the crucial contribution of coupled functions of the Wnt, BMP, Notch, and Hedgehog signaling pathways (all pathways are designated according to the abbreviated or full names of genes or their protein products; for details, see below) and the axial Hox-code in the formation and maintenance of metazoan body plans are necessary for an understanding of the evolutionary diversification and phenotypic expression of various types of axial symmetry. The lost body plans of some extinct Ediacaran and early Cambrian metazoans are also considered in comparison with axial body plans and posterior growth in living animals.
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Erwin DH. A conceptual framework of evolutionary novelty and innovation. Biol Rev Camb Philos Soc 2020; 96:1-15. [PMID: 32869437 DOI: 10.1111/brv.12643] [Citation(s) in RCA: 27] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2020] [Revised: 07/31/2020] [Accepted: 08/12/2020] [Indexed: 12/20/2022]
Abstract
Since 1990 the recognition of deep homologies among metazoan developmental processes and the spread of more mechanistic approaches to developmental biology have led to a resurgence of interest in evolutionary novelty and innovation. Other evolutionary biologists have proposed central roles for behaviour and phenotypic plasticity in generating the conditions for the construction of novel morphologies, or invoked the accessibility of new regions of vast sequence spaces. These approaches contrast with more traditional emphasis on the exploitation of ecological opportunities as the primary source of novelty. This definitional cornucopia reflects differing stress placed on three attributes of novelties: their radical nature, the generation of new taxa, and ecological and evolutionary impact. Such different emphasis has led to conflating four distinct issues: the origin of novel attributes (genes, developmental processes, phenotypic characters), new functions, higher clades and the ecological impact of new structures and functions. Here I distinguish novelty (the origin of new characters, deep character transformations, or new combinations) from innovation, the ecological and evolutionary success of clades. Evidence from the fossil record of macroevolutionary lags between the origin of a novelty and its ecological success demonstrates that novelty may be decoupled from innovation, and only definitions of novelty based on radicality (rather than generativity or consequentiality) can be assessed without reference to the subsequent history of the clade to which a novelty belongs. These considerations suggest a conceptual framework for novelty and innovation, involving: (i) generation of the potential for novelty; (ii) the formation of novel attributes; (iii) refinement of novelties through adaptation; (iv) exploitation of novelties by a clade, which may coincide with a new round of ecological or environmental potentiation; followed by (v) the establishment of innovations through ecological processes. This framework recognizes that there is little empirical support for either the dominance of ecological opportunity, nor abrupt discontinuities (often caricatured as 'hopeful monsters'). This general framework may be extended to aspects of cultural and social innovation.
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Affiliation(s)
- Douglas H Erwin
- Department of Paleobiology, MRC-121 National Museum of Natural History, PO Box 37012, Washington, DC, 20013-7012, U.S.A.,Santa Fe Institute, 1399 Hyde Park Road, Santa Fe, NM, 87501, U.S.A
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Budd GE, Mann RP. Survival and selection biases in early animal evolution and a source of systematic overestimation in molecular clocks. Interface Focus 2020; 10:20190110. [PMID: 32637066 PMCID: PMC7333906 DOI: 10.1098/rsfs.2019.0110] [Citation(s) in RCA: 24] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 05/06/2020] [Indexed: 12/21/2022] Open
Abstract
Important evolutionary events such as the Cambrian Explosion have inspired many attempts at explanation: why do they happen when they do? What shapes them, and why do they eventually come to an end? However, much less attention has been paid to the idea of a 'null hypothesis'-that certain features of such diversifications arise simply through their statistical structure. Such statistical features also appear to influence our perception of the timing of these events. Here, we show in particular that study of unusually large clades leads to systematic overestimates of clade ages from some types of molecular clocks, and that the size of this effect may be enough to account for the puzzling mismatches seen between these molecular clocks and the fossil record. Our analysis of the fossil record of the late Ediacaran to Cambrian suggests that it is likely to be recording a true evolutionary radiation of the bilaterians at this time, and that explanations involving various sorts of cryptic origins for the bilaterians do not seem to be necessary.
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Affiliation(s)
- Graham E. Budd
- Department of Earth Sciences, Palaeobiology, Uppsala University, Villavägen 16, Uppsala 752 36, Sweden
| | - Richard P. Mann
- Department of Statistics, School of Mathematics, University of Leeds, Leeds LS2 9JT, UK
- The Alan Turing Institute, London NW1 2DB, UK
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Hammarlund EU, Amend SR, Pienta KJ. The issues with tissues: the wide range of cell fate separation enables the evolution of multicellularity and cancer. Med Oncol 2020; 37:62. [PMID: 32535731 PMCID: PMC7293661 DOI: 10.1007/s12032-020-01387-5] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2020] [Accepted: 06/03/2020] [Indexed: 12/24/2022]
Abstract
Our understanding of the rises of animal and cancer multicellularity face the same conceptual hurdles: what makes the clade originate and what makes it diversify. Between the events of origination and diversification lies complex tissue organization that gave rise to novel functionality for organisms and, unfortunately, for malignant transformation in cells. Tissue specialization with distinctly separated cell fates allowed novel functionality at organism level, such as for vertebrate animals, but also involved trade-offs at the cellular level that are potentially disruptive. These trade-offs are under-appreciated and here we discuss how the wide separation of cell phenotypes may contribute to cancer evolution by (a) how factors can reverse differentiated cells into a window of phenotypic plasticity, (b) the reversal to phenotypic plasticity coupled with asexual reproduction occurs in a way that the host cannot adapt, and (c) the power of the transformation factor correlates to the power needed to reverse tissue specialization. The role of reversed cell fate separation for cancer evolution is strengthened by how some tissues and organisms maintain high cell proliferation and plasticity without developing tumours at a corresponding rate. This demonstrates a potential proliferation paradox that requires further explanation. These insights from the cancer field, which observes tissue evolution in real time and closer than any other field, allow inferences to be made on evolutionary events in animal history. If a sweet spot of phenotypic and reproductive versatility is key to transformation, factors stimulating cell fate separation may have promoted also animal diversification on Earth.
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Affiliation(s)
- Emma U Hammarlund
- Translational Cancer Research, Department of Laboratory Medicine, Lund University, Lund, Sweden.
- Nordic Center for Earth Evolution, University of Southern Denmark, Odense, DK, Denmark.
| | - Sarah R Amend
- The Brady Urological Institute, Johns Hopkins School of Medicine, Baltimore, MD, 21287, USA
| | - Kenneth J Pienta
- The Brady Urological Institute, Johns Hopkins School of Medicine, Baltimore, MD, 21287, USA
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Mángano MG, Buatois LA. The rise and early evolution of animals: where do we stand from a trace-fossil perspective? Interface Focus 2020; 10:20190103. [PMID: 32642049 DOI: 10.1098/rsfs.2019.0103] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 04/15/2020] [Indexed: 01/10/2023] Open
Abstract
The trace-fossil record provides a wealth of information to track the rise and early evolution of animals. It comprises the activity of both hard- and soft-bodied organisms, is continuous through the Ediacaran (635-539 Ma)- Cambrian (539-485 Ma) transition, yields insights into animal behaviour and their role as ecosystem engineers, and allows for a more refined characterization of palaeoenvironmental context. In order to unravel macroevolutionary signals from the trace-fossil record, a variety of approaches is available, including not only estimation of degree of bioturbation, but also analysis of ichnodiversity and ichnodisparity trajectories, and evaluation of the occupation of infaunal ecospace and styles of ecosystem engineering. Analysis of the trace-fossil record demonstrates the presence of motile benthic bilaterians in the Ediacaran, mostly feeding from biofilms. Although Ediacaran trace fossils are simple and emplaced at or immediately below the sediment surface, an increase in ichnofossil complexity, predation pressure, sediment disturbance and penetration depth is apparent during the terminal Ediacaran. Regardless of this increase, a dramatic rise in trace fossil diversity and disparity took place during the earliest Cambrian, underscoring that the novelty of the Fortunian (539-529 Ma) cannot be underestimated. The Fortunian still shows the persistence of an Ediacaran-style matground ecology, but is fundamentally characterized by the appearance of new trace-fossil architectural plans reflecting novel ways of interacting with the substrate. The appearance of Phanerozoic-style benthic ecosystems attests to an increased length and connectivity of the food web and improved efficiency in organic carbon transfer and nutrient recycling. A profound reorganization of the infaunal ecospace is recorded in both high-energy sand-dominated nearshore areas and low-energy mud-dominated offshore environments, during the early Cambrian, starting approximately during Cambrian Age 2 (529-521 Ma), but continuing during the rest of the early Cambrian. A model comprising four evolutionary phases is proposed to synthetize information from the Ediacaran-Cambrian trace-fossil record. The use of a rich ichnological toolbox; critical, systematic and comprehensive evaluation of the Ediacaran-Cambrian trace-fossil record; and high-resolution integration of the ichnological dataset and sedimentological information show that the advent of biogenic mixing was an important factor in fully marine environments at the dawn of the Phanerozoic.
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Affiliation(s)
- M Gabriela Mángano
- Department of Geological Sciences, University of Saskatchewan, 114 Science Place, Saskatoon, Saskatchewan, Canada S7N 5E2
| | - Luis A Buatois
- Department of Geological Sciences, University of Saskatchewan, 114 Science Place, Saskatoon, Saskatchewan, Canada S7N 5E2
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40
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Murdock DJE. The ‘biomineralization toolkit’ and the origin of animal skeletons. Biol Rev Camb Philos Soc 2020; 95:1372-1392. [DOI: 10.1111/brv.12614] [Citation(s) in RCA: 44] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2020] [Revised: 04/28/2020] [Accepted: 04/30/2020] [Indexed: 12/29/2022]
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