1
|
Satterlee JW, Alonso D, Gramazio P, Jenike KM, He J, Arrones A, Villanueva G, Plazas M, Ramakrishnan S, Benoit M, Gentile I, Hendelman A, Shohat H, Fitzgerald B, Robitaille GM, Green Y, Swartwood K, Passalacqua MJ, Gagnon E, Hilgenhof R, Huggins TD, Eizenga GC, Gur A, Rutten T, Stein N, Yao S, Poncet A, Bellot C, Frary A, Knapp S, Bendahmane M, Särkinen T, Gillis J, Van Eck J, Schatz MC, Eshed Y, Prohens J, Vilanova S, Lippman ZB. Convergent evolution of plant prickles by repeated gene co-option over deep time. Science 2024; 385:eado1663. [PMID: 39088611 DOI: 10.1126/science.ado1663] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2024] [Accepted: 06/06/2024] [Indexed: 08/03/2024]
Abstract
An enduring question in evolutionary biology concerns the degree to which episodes of convergent trait evolution depend on the same genetic programs, particularly over long timescales. In this work, we genetically dissected repeated origins and losses of prickles-sharp epidermal projections-that convergently evolved in numerous plant lineages. Mutations in a cytokinin hormone biosynthetic gene caused at least 16 independent losses of prickles in eggplants and wild relatives in the genus Solanum. Homologs underlie prickle formation across angiosperms that collectively diverged more than 150 million years ago, including rice and roses. By developing new Solanum genetic systems, we leveraged this discovery to eliminate prickles in a wild species and an indigenously foraged berry. Our findings implicate a shared hormone activation genetic program underlying evolutionarily widespread and recurrent instances of plant morphological innovation.
Collapse
Affiliation(s)
- James W Satterlee
- Cold Spring Harbor Laboratory, Cold Spring Harbor, NY, USA
- Howard Hughes Medical Institute, Cold Spring Harbor Laboratory, Cold Spring Harbor, NY, USA
| | - David Alonso
- Instituto de Conservación y Mejora de la Agrodiversidad Valenciana, Universitat Politècnica de València, Valencia, Spain
| | - Pietro Gramazio
- Instituto de Conservación y Mejora de la Agrodiversidad Valenciana, Universitat Politècnica de València, Valencia, Spain
| | - Katharine M Jenike
- Department of Computer Science, Johns Hopkins University, Baltimore, MD, USA
- Department of Genetic Medicine, Johns Hopkins University, Baltimore, MD, USA
| | - Jia He
- Cold Spring Harbor Laboratory, Cold Spring Harbor, NY, USA
- Howard Hughes Medical Institute, Cold Spring Harbor Laboratory, Cold Spring Harbor, NY, USA
| | - Andrea Arrones
- Instituto de Conservación y Mejora de la Agrodiversidad Valenciana, Universitat Politècnica de València, Valencia, Spain
| | - Gloria Villanueva
- Instituto de Conservación y Mejora de la Agrodiversidad Valenciana, Universitat Politècnica de València, Valencia, Spain
| | - Mariola Plazas
- Instituto de Conservación y Mejora de la Agrodiversidad Valenciana, Universitat Politècnica de València, Valencia, Spain
| | - Srividya Ramakrishnan
- Department of Computer Science, Johns Hopkins University, Baltimore, MD, USA
- Department of Genetic Medicine, Johns Hopkins University, Baltimore, MD, USA
| | - Matthias Benoit
- French National Institute for Agriculture, Food, and Environment, Laboratory of Plant-Microbe Interactions, Toulouse, France
| | - Iacopo Gentile
- School of Biological Sciences, Cold Spring Harbor Laboratory, Cold Spring Harbor, NY, USA
| | - Anat Hendelman
- Cold Spring Harbor Laboratory, Cold Spring Harbor, NY, USA
- Howard Hughes Medical Institute, Cold Spring Harbor Laboratory, Cold Spring Harbor, NY, USA
| | - Hagai Shohat
- Cold Spring Harbor Laboratory, Cold Spring Harbor, NY, USA
| | - Blaine Fitzgerald
- Cold Spring Harbor Laboratory, Cold Spring Harbor, NY, USA
- Howard Hughes Medical Institute, Cold Spring Harbor Laboratory, Cold Spring Harbor, NY, USA
| | - Gina M Robitaille
- Cold Spring Harbor Laboratory, Cold Spring Harbor, NY, USA
- Howard Hughes Medical Institute, Cold Spring Harbor Laboratory, Cold Spring Harbor, NY, USA
| | - Yumi Green
- Boyce Thompson Institute, Ithaca, NY, USA
| | | | - Michael J Passalacqua
- School of Biological Sciences, Cold Spring Harbor Laboratory, Cold Spring Harbor, NY, USA
| | - Edeline Gagnon
- Department of Integrative Biology, University of Guelph, Guelph, ON, Canada
- Royal Botanic Garden Edinburgh, Edinburgh, UK
| | | | - Trevis D Huggins
- USDA-ARS, Dale Bumpers National Rice Research Center, Stuttgart, AR, USA
| | - Georgia C Eizenga
- USDA-ARS, Dale Bumpers National Rice Research Center, Stuttgart, AR, USA
| | - Amit Gur
- Cucurbits Section, Department of Vegetable Sciences, Agricultural Research Organization, Newe Ya'ar Research Center, Ramat Yishay, Israel
| | - Twan Rutten
- Leibniz Institute of Plant Genetics and Crop Plant Research, Gatersleben, Germany
| | - Nils Stein
- Leibniz Institute of Plant Genetics and Crop Plant Research, Gatersleben, Germany
- Crop Plant Genetics, Martin Luther University of Halle-Wittenberg, Halle (Saale), Germany
| | - Shengrui Yao
- Department of Plant and Environmental Sciences, New Mexico State University, Las Cruces, NM, USA
- Sustainable Agriculture Sciences Center, New Mexico State University, Alcalde, NM, USA
| | - Adrien Poncet
- Laboratoire Reproduction et Developpement des Plantes, INRAE, CNRS, Universite Lyon, Ecole Normale Superieure de Lyon, Lyon, France
| | - Clement Bellot
- Laboratoire Reproduction et Developpement des Plantes, INRAE, CNRS, Universite Lyon, Ecole Normale Superieure de Lyon, Lyon, France
| | - Amy Frary
- Department of Biological Sciences, Mount Holyoke College, South Hadley, MA, USA
| | | | - Mohammed Bendahmane
- Laboratoire Reproduction et Developpement des Plantes, INRAE, CNRS, Universite Lyon, Ecole Normale Superieure de Lyon, Lyon, France
| | | | - Jesse Gillis
- Cold Spring Harbor Laboratory, Cold Spring Harbor, NY, USA
- Physiology Department and Donnelly Centre for Cellular and Biomolecular Research, University of Toronto, Toronto, ON, Canada
| | - Joyce Van Eck
- Boyce Thompson Institute, Ithaca, NY, USA
- Plant Breeding and Genetics Section, Cornell University, Ithaca, NY, USA
| | - Michael C Schatz
- Department of Computer Science, Johns Hopkins University, Baltimore, MD, USA
- Department of Genetic Medicine, Johns Hopkins University, Baltimore, MD, USA
| | - Yuval Eshed
- Department of Plant and Environmental Sciences, The Weizmann Institute of Science, Rehovot, Israel
| | - Jaime Prohens
- Instituto de Conservación y Mejora de la Agrodiversidad Valenciana, Universitat Politècnica de València, Valencia, Spain
| | - Santiago Vilanova
- Instituto de Conservación y Mejora de la Agrodiversidad Valenciana, Universitat Politècnica de València, Valencia, Spain
| | - Zachary B Lippman
- Cold Spring Harbor Laboratory, Cold Spring Harbor, NY, USA
- Howard Hughes Medical Institute, Cold Spring Harbor Laboratory, Cold Spring Harbor, NY, USA
- School of Biological Sciences, Cold Spring Harbor Laboratory, Cold Spring Harbor, NY, USA
| |
Collapse
|
2
|
Inui N, Miura T. Comparisons of developmental processes of air-breathing organs among terrestrial isopods (Crustacea, Oniscidea): implications for their evolutionary origins. EvoDevo 2024; 15:9. [PMID: 39026371 PMCID: PMC11264735 DOI: 10.1186/s13227-024-00229-z] [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: 03/07/2024] [Accepted: 07/15/2024] [Indexed: 07/20/2024] Open
Abstract
BACKGROUND The acquisition of air-breathing organs is one of the key innovations for terrestrialization in animals. Terrestrial isopods, a crustacean lineage, can be interesting models to study the evolution of respiratory organs, as they exhibit varieties of air-breathing structures according to their habitats. However, the evolutionary processes and origins of these structures are unclear, due to the lack of information about their developmental processes. To understand the developmental mechanisms, we compared the developmental processes forming different respiratory structures in three isopod species, i.e., 'uncovered lungs' in Nagurus okinawaensis (Trachelipodidae), 'dorsal respiratory fields' in Alloniscus balssi (Alloniscidae), and pleopods without respiratory structures in Armadilloniscus cf. ellipticus (Detonidae). RESULTS In N. okinawaensis with uncovered lungs, epithelium and cuticle around the proximal hemolymph sinus developed into respiratory structures at post-manca juvenile stages. On the other hand, in Al. balssi with dorsal respiratory fields, the region for the future respiratory structure was already present at manca 1 stage, immediately after hatching, where the lateral protrusion of ventral epithelium occurred, forming the respiratory structure. Furthermore, on pleopods in Ar. cf. ellipticus, only thickened dorsal cuticle and the proximal hemolymph sinus developed during postembryonic development without special morphogenesis. CONCLUSIONS This study shows that the respiratory structures in terrestrial isopods develop primarily by postembryonic epithelial modifications, but the epithelial positions developing into respiratory structures differ between uncovered lungs and dorsal respiratory fields. This suggests that these two types of respiratory structures do not result from simple differences in the degree of development. Future analysis of molecular developmental mechanisms will help determine whether these are the result of heterotopic changes or have different evolutionary origins. Overall, this study provides fundamental information for evolutionary developmental studies of isopod respiratory organs.
Collapse
Affiliation(s)
- Naoto Inui
- Misaki Marine Biological Station, School of Science, The University of Tokyo, Misaki, Miura, Kanagawa, 238-0225, Japan
| | - Toru Miura
- Misaki Marine Biological Station, School of Science, The University of Tokyo, Misaki, Miura, Kanagawa, 238-0225, Japan.
| |
Collapse
|
3
|
Liberali P, Schier AF. The evolution of developmental biology through conceptual and technological revolutions. Cell 2024; 187:3461-3495. [PMID: 38906136 DOI: 10.1016/j.cell.2024.05.053] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2024] [Revised: 05/28/2024] [Accepted: 05/29/2024] [Indexed: 06/23/2024]
Abstract
Developmental biology-the study of the processes by which cells, tissues, and organisms develop and change over time-has entered a new golden age. After the molecular genetics revolution in the 80s and 90s and the diversification of the field in the early 21st century, we have entered a phase when powerful technologies provide new approaches and open unexplored avenues. Progress in the field has been accelerated by advances in genomics, imaging, engineering, and computational biology and by emerging model systems ranging from tardigrades to organoids. We summarize how revolutionary technologies have led to remarkable progress in understanding animal development. We describe how classic questions in gene regulation, pattern formation, morphogenesis, organogenesis, and stem cell biology are being revisited. We discuss the connections of development with evolution, self-organization, metabolism, time, and ecology. We speculate how developmental biology might evolve in an era of synthetic biology, artificial intelligence, and human engineering.
Collapse
Affiliation(s)
- Prisca Liberali
- Friedrich Miescher Institute for Biomedical Research, Basel, Switzerland; University of Basel, Basel, Switzerland.
| | | |
Collapse
|
4
|
Palominos MF, Bharadwaj R, Tralka C, Trang K, Aka D, Alami M, Andrews D, Bartlett BI, Golde C, Liu J, Le-Pedroza M, Perrot R, Seiter B, Sparrow C, Shapira M, Martin CH. The West African lungfish secretes a living cocoon during aestivation with uncertain antimicrobial function. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.07.05.602297. [PMID: 39026789 PMCID: PMC11257426 DOI: 10.1101/2024.07.05.602297] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/20/2024]
Abstract
One of the most exceptional adaptations to extreme drought is found in the sister group to tetrapods, the lungfishes (Dipnoi), which can aestivate inside a mucus cocoon for multiple years at reduced metabolic rates with complete cessation of ingestion and excretion. However, the function of the cocoon tissue is not fully understood. Here we developed a new more natural laboratory protocol for inducing aestivation in the West African lungfish, Protopterus annectens, and investigated the structure and function of the cocoon. We used electron microscopy and imaging of live tissue-stains to confirm that the inner and outer layers of the paper-thin cocoon are composed primarily of living cells. However, we also repeatedly observed extensive bacterial and fungal growth covering the cocoon and found no evidence of anti-microbial activity in vitro against E. coli for the cocoon tissue in this species. This classroom discovery-based research, performed during a course-based undergraduate research experience course (CURE), provides a robust laboratory protocol for investigating aestivation and calls into the question the function of this bizarre vertebrate adaptation.
Collapse
Affiliation(s)
- M Fernanda Palominos
- Department of Integrative Biology, University of California, Berkeley, CA 94720
- Museum of Vertebrate Zoology, University of California, Berkeley, CA 94720
| | | | - Charles Tralka
- Department of Integrative Biology, University of California, Berkeley, CA 94720
- Museum of Vertebrate Zoology, University of California, Berkeley, CA 94720
| | - Kenneth Trang
- Department of Integrative Biology, University of California, Berkeley, CA 94720
| | - David Aka
- Department of Integrative Biology, University of California, Berkeley, CA 94720
| | - Mariam Alami
- Department of Integrative Biology, University of California, Berkeley, CA 94720
| | - Dominique Andrews
- Department of Integrative Biology, University of California, Berkeley, CA 94720
| | - Ben I Bartlett
- Department of Integrative Biology, University of California, Berkeley, CA 94720
| | - Chloe Golde
- Department of Integrative Biology, University of California, Berkeley, CA 94720
| | - Joseph Liu
- Department of Integrative Biology, University of California, Berkeley, CA 94720
| | - Maya Le-Pedroza
- Department of Integrative Biology, University of California, Berkeley, CA 94720
| | - Robert Perrot
- Department of Integrative Biology, University of California, Berkeley, CA 94720
| | - Blanca Seiter
- Department of Integrative Biology, University of California, Berkeley, CA 94720
| | - Claudia Sparrow
- Department of Integrative Biology, University of California, Berkeley, CA 94720
| | - Michael Shapira
- Department of Integrative Biology, University of California, Berkeley, CA 94720
| | - Christopher H Martin
- Department of Integrative Biology, University of California, Berkeley, CA 94720
- Museum of Vertebrate Zoology, University of California, Berkeley, CA 94720
| |
Collapse
|
5
|
Probst RS, Longino JT, Branstetter MG. Evolutionary déjà vu? A case of convergent evolution in an ant-plant association. Proc Biol Sci 2024; 291:20241214. [PMID: 38981524 DOI: 10.1098/rspb.2024.1214] [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: 10/01/2023] [Accepted: 06/10/2024] [Indexed: 07/11/2024] Open
Abstract
Obligatory ant-plant symbioses often appear to be single evolutionary shifts within particular ant lineages; however, convergence can be revealed once natural history observations are complemented with molecular phylogenetics. Here, we describe a remarkable example of convergent evolution in an ant-plant symbiotic system. Exclusively arboreal, Myrmelachista species can be generalized opportunists nesting in several plant species or obligately symbiotic, live-stem nesters of a narrow set of plant species. Instances of specialization within Myrmelachista are known from northern South America and throughout Middle America. In Middle America, a diverse radiation of specialists occupies understory treelets of lowland rainforests. The morphological and behavioural uniformity of specialists suggests that they form a monophyletic assemblage, diversifying after a single origin of specialization. Using ultraconserved element phylogenomics and ancestral state reconstructions, we show that shifts from opportunistic to obligately symbiotic evolved independently in South and Middle America. Furthermore, our analyses support a remarkable case of convergence within the Middle American radiation, with two independently evolved specialist clades, arising nearly simultaneously from putative opportunistic ancestors during the late Pliocene. This repeated evolution of a complex phenotype suggests similar mechanisms behind trait shifts from opportunists to specialists, generating further questions about the selective forces driving specialization.
Collapse
Affiliation(s)
- Rodolfo S Probst
- Science Research Initiative (SRI), College of Science, University of Utah , Salt Lake City, UT 84112, USA
- School of Biological Sciences, University of Utah , Salt Lake City, UT 84112, USA
| | - John T Longino
- School of Biological Sciences, University of Utah , Salt Lake City, UT 84112, USA
| | - Michael G Branstetter
- U.S. Department of Agriculture, Agricultural Research Service (USDA-ARS), Pollinating Insects Research Unit, Utah State University , Logan, UT 84322, USA
| |
Collapse
|
6
|
Boutillon A, Banavar SP, Campàs O. Conserved physical mechanisms of cell and tissue elongation. Development 2024; 151:dev202687. [PMID: 38767601 PMCID: PMC11190436 DOI: 10.1242/dev.202687] [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: 05/22/2024]
Abstract
Living organisms have the ability to self-shape into complex structures appropriate for their function. The genetic and molecular mechanisms that enable cells to do this have been extensively studied in several model and non-model organisms. In contrast, the physical mechanisms that shape cells and tissues have only recently started to emerge, in part thanks to new quantitative in vivo measurements of the physical quantities guiding morphogenesis. These data, combined with indirect inferences of physical characteristics, are starting to reveal similarities in the physical mechanisms underlying morphogenesis across different organisms. Here, we review how physics contributes to shape cells and tissues in a simple, yet ubiquitous, morphogenetic transformation: elongation. Drawing from observed similarities across species, we propose the existence of conserved physical mechanisms of morphogenesis.
Collapse
Affiliation(s)
- Arthur Boutillon
- Cluster of Excellence Physics of Life, TU Dresden, 01062 Dresden, Germany
| | - Samhita P. Banavar
- Department of Chemical and Biological Engineering, Princeton University, Princeton, NJ 08540, USA
| | - Otger Campàs
- Cluster of Excellence Physics of Life, TU Dresden, 01062 Dresden, Germany
- Max Planck Institute of Molecular Cell Biology and Genetics, 01307 Dresden, Germany
- Center for Systems Biology Dresden, 01307 Dresden, Germany
| |
Collapse
|
7
|
Lau ES, Goodheart JA, Anderson NT, Liu VL, Mukherjee A, Oakley TH. Similar enzymatic functions in distinct bioluminescence systems: evolutionary recruitment of sulfotransferases in ostracod light organs. Biol Lett 2024; 20:20230585. [PMID: 38746983 DOI: 10.1098/rsbl.2023.0585] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2023] [Accepted: 04/18/2024] [Indexed: 05/28/2024] Open
Abstract
Genes from ancient families are sometimes involved in the convergent evolutionary origins of similar traits, even across vast phylogenetic distances. Sulfotransferases are an ancient family of enzymes that transfer sulfate from a donor to a wide variety of substrates, including probable roles in some bioluminescence systems. Here, we demonstrate multiple sulfotransferases, highly expressed in light organs of the bioluminescent ostracod Vargula tsujii, transfer sulfate in vitro to the luciferin substrate, vargulin. We find luciferin sulfotransferases (LSTs) of ostracods are not orthologous to known LSTs of fireflies or sea pansies; animals with distinct and convergently evolved bioluminescence systems compared to ostracods. Therefore, distantly related sulfotransferases were independently recruited at least three times, leading to parallel evolution of luciferin metabolism in three highly diverged organisms. Reuse of homologous genes is surprising in these bioluminescence systems because the other components, including luciferins and luciferases, are completely distinct. Whether convergently evolved traits incorporate ancient genes with similar functions or instead use distinct, often newer, genes may be constrained by how many genetic solutions exist for a particular function. When fewer solutions exist, as in genetic sulfation of small molecules, evolution may be more constrained to use the same genes time and again.
Collapse
Affiliation(s)
- Emily S Lau
- Department of Ecology, Evolution, and Marine Biology, University of California Santa Barbara, Santa Barbara, CA 93106, USA
| | - Jessica A Goodheart
- Department of Ecology, Evolution, and Marine Biology, University of California Santa Barbara, Santa Barbara, CA 93106, USA
- Division of Invertebrate Zoology, American Museum of Natural History, New York, NY 10025, USA
| | - Nolan T Anderson
- Department of Chemical Engineering, University of California Santa Barbara, Santa Barbara, CA 93106, USA
| | - Vannie L Liu
- Department of Chemical Engineering, University of California Santa Barbara, Santa Barbara, CA 93106, USA
| | - Arnab Mukherjee
- Department of Chemical Engineering, University of California Santa Barbara, Santa Barbara, CA 93106, USA
- Department of Biological Engineering, University of California Santa Barbara, Santa Barbara, CA 93106, USA
- Department of Chemistry, University of California Santa Barbara, Santa Barbara, CA 93106, USA
- Neuroscience Research Institute, University of California Santa Barbara, Santa Barbara, CA 93106, USA
| | - Todd H Oakley
- Department of Ecology, Evolution, and Marine Biology, University of California Santa Barbara, Santa Barbara, CA 93106, USA
| |
Collapse
|
8
|
Bishop PJ, Pierce SE. The fossil record of appendicular muscle evolution in Synapsida on the line to mammals: Part I-Forelimb. Anat Rec (Hoboken) 2024; 307:1764-1825. [PMID: 37726984 DOI: 10.1002/ar.25312] [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: 03/17/2023] [Revised: 07/15/2023] [Accepted: 08/08/2023] [Indexed: 09/21/2023]
Abstract
This paper is the first in a two-part series that charts the evolution of appendicular musculature along the mammalian stem lineage, drawing upon the exceptional fossil record of extinct synapsids. Here, attention is focused on muscles of the forelimb. Understanding forelimb muscular anatomy in extinct synapsids, and how this changed on the line to mammals, can provide important perspective for interpreting skeletal and functional evolution in this lineage, and how the diversity of forelimb functions in extant mammals arose. This study surveyed the osteological evidence for muscular attachments in extinct mammalian and nonmammalian synapsids, two extinct amniote outgroups, and a large selection of extant mammals, saurians, and salamanders. Observations were integrated into an explicit phylogenetic framework, comprising 73 character-state complexes covering all muscles crossing the shoulder, elbow, and wrist joints. These were coded for 33 operational taxonomic units spanning >330 Ma of tetrapod evolution, and ancestral state reconstruction was used to evaluate the sequence of muscular evolution along the stem lineage from Amniota to Theria. In addition to producing a comprehensive documentation of osteological evidence for muscle attachments in extinct synapsids, this work has clarified homology hypotheses across disparate taxa and helped resolve competing hypotheses of muscular anatomy in extinct species. The evolutionary history of mammalian forelimb musculature was a complex and nonlinear narrative, punctuated by multiple instances of convergence and concentrated phases of anatomical transformation. More broadly, this study highlights the great insight that a fossil-based perspective can provide for understanding the assembly of novel body plans.
Collapse
Affiliation(s)
- Peter J Bishop
- Museum of Comparative Zoology and Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, Massachusetts, USA
- Geosciences Program, Queensland Museum, Brisbane, Queensland, Australia
| | - Stephanie E Pierce
- Museum of Comparative Zoology and Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, Massachusetts, USA
| |
Collapse
|
9
|
Pomaville MB, Sattler SM, Abitua PB. A new dawn for the study of cell type evolution. Development 2024; 151:dev200884. [PMID: 38722217 PMCID: PMC11128286 DOI: 10.1242/dev.200884] [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: 05/28/2024]
Abstract
Animal evolution is influenced by the emergence of new cell types, yet our understanding of this process remains elusive. This prompts the need for a broader exploration across diverse research organisms, facilitated by recent breakthroughs, such as gene editing tools and single-cell genomics. Essential to our understanding of cell type evolution is the accurate identification of homologous cells. We delve into the significance of considering developmental ontogeny and potential pitfalls when drawing conclusions about cell type homology. Additionally, we highlight recent discoveries in the study of cell type evolution through the application of single-cell transcriptomics and pinpoint areas ripe for further exploration.
Collapse
Affiliation(s)
| | | | - Philip B. Abitua
- Genome Sciences, University of Washington, Seattle, WA 98105, USA
| |
Collapse
|
10
|
Ertl HA, Bayala EX, Siddiq MA, Wittkopp PJ. Divergence of Grainy head affects chromatin accessibility, gene expression, and embryonic viability in Drosophila melanogaster. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.04.07.588430. [PMID: 38645200 PMCID: PMC11030446 DOI: 10.1101/2024.04.07.588430] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/23/2024]
Abstract
Pioneer factors are critical for gene regulation and development because they bind chromatin and make DNA more accessible for binding by other transcription factors. The pioneer factor Grainy head (Grh) is present across metazoans and has been shown to retain a role in epithelium development in fruit flies, nematodes, and mice despite extensive divergence in both amino acid sequence and length. Here, we investigate the evolution of Grh function by comparing the effects of the fly ( Drosophila melanogaster ) and worm ( Caenorhabditis elegans ) Grh orthologs on chromatin accessibility, gene expression, embryonic development, and viability in transgenic D. melanogaster . We found that the Caenorhabditis elegans ortholog rescued cuticle development but not full embryonic viability in Drosophila melanogaster grh null mutants. At the molecular level, the C. elegans ortholog only partially rescued chromatin accessibility and gene expression. Divergence in the disordered N-terminus of the Grh protein contributes to these differences in embryonic viability and molecular phenotypes. These data show how pioneer factors can diverge in sequence and function at the molecular level while retaining conserved developmental functions at the organismal level. SUMMARY STATEMENT Despite divergence in a disordered region that affects function at both molecular and organismal levels, the Caenorhabditis elegans Grainy head (Grh) protein rescued cuticle morphology in D. melanogaster embryos.
Collapse
|
11
|
Hintermann A, Bolt CC, Hawkins MB, Valentin G, Lopez-Delisle L, Gitto S, Gómez PB, Mascrez B, Mansour TA, Nakamura T, Harris MP, Shubin NH, Duboule D. EVOLUTIONARY CO-OPTION OF AN ANCESTRAL CLOACAL REGULATORY LANDSCAPE DURING THE EMERGENCE OF DIGITS AND GENITALS. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.03.24.586442. [PMID: 38585989 PMCID: PMC10996561 DOI: 10.1101/2024.03.24.586442] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/09/2024]
Abstract
The transition from fins to limbs has been a rich source of discussion for more than a century. One open and important issue is understanding how the mechanisms that pattern digits arose during vertebrate evolution. In this context, the analysis of Hox gene expression and functions to infer evolutionary scenarios has been a productive approach to explain the changes in organ formation, particularly in limbs. In tetrapods, the transcription of Hoxd genes in developing digits depends on a well-characterized set of enhancers forming a large regulatory landscape1,2. This control system has a syntenic counterpart in zebrafish, even though they lack bona fide digits, suggestive of deep homology3 between distal fin and limb developmental mechanisms. We tested the global function of this landscape to assess ancestry and source of limb and fin variation. In contrast to results in mice, we show here that the deletion of the homologous control region in zebrafish has a limited effect on the transcription of hoxd genes during fin development. However, it fully abrogates hoxd expression within the developing cloaca, an ancestral structure related to the mammalian urogenital sinus. We show that similar to the limb, Hoxd gene function in the urogenital sinus of the mouse also depends on enhancers located in this same genomic domain. Thus, we conclude that the current regulation underlying Hoxd gene expression in distal limbs was co-opted in tetrapods from a preexisting cloacal program. The orthologous chromatin domain in fishes may illustrate a rudimentary or partial step in this evolutionary co-option.
Collapse
Affiliation(s)
- Aurélie Hintermann
- Department of Genetics and Evolution, University of Geneva, 30 quai Ernest Ansermet, 1211, Geneva, Switzerland
| | - Christopher Chase Bolt
- School of Life Sciences, Ecole Polytechnique Fédérale de Lausanne EPFL, 1015 Lausanne, Switzerland
| | - M. Brent Hawkins
- Department of Genetics, Harvard Medical School, Boston, Massachusetts, USA, Department of Orthopedic Research, Boston Children’s Hospital, Boston, Massachusetts, USA
| | - Guillaume Valentin
- School of Life Sciences, Ecole Polytechnique Fédérale de Lausanne EPFL, 1015 Lausanne, Switzerland
| | - Lucille Lopez-Delisle
- School of Life Sciences, Ecole Polytechnique Fédérale de Lausanne EPFL, 1015 Lausanne, Switzerland
| | - Sandra Gitto
- Department of Genetics and Evolution, University of Geneva, 30 quai Ernest Ansermet, 1211, Geneva, Switzerland
| | - Paula Barrera Gómez
- School of Life Sciences, Ecole Polytechnique Fédérale de Lausanne EPFL, 1015 Lausanne, Switzerland
| | - Bénédicte Mascrez
- Department of Genetics and Evolution, University of Geneva, 30 quai Ernest Ansermet, 1211, Geneva, Switzerland
| | | | - Tetsuya Nakamura
- Department of Genetics, Rutgers University, New Brunswick, NJ, USA
| | - Matthew P. Harris
- Department of Genetics, Harvard Medical School, Boston, Massachusetts, USA, Department of Orthopedic Research, Boston Children’s Hospital, Boston, Massachusetts, USA
| | - Neil H. Shubin
- Department of Organismal Biology and Anatomy, The University of Chicago, Chicago, IL, USA
| | - Denis Duboule
- Department of Genetics and Evolution, University of Geneva, 30 quai Ernest Ansermet, 1211, Geneva, Switzerland
- School of Life Sciences, Ecole Polytechnique Fédérale de Lausanne EPFL, 1015 Lausanne, Switzerland
- Center for Interdisciplinary Research in Biology CIRB, Collège de France, CNRS, INSERM, Université PSL, Paris, France
| |
Collapse
|
12
|
Ridgway AM, Hood EJ, Jimenez JF, Nunes MDS, McGregor AP. Sox21b underlies the rapid diversification of a novel male genital structure between Drosophila species. Curr Biol 2024; 34:1114-1121.e7. [PMID: 38309269 DOI: 10.1016/j.cub.2024.01.022] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2023] [Revised: 12/02/2023] [Accepted: 01/08/2024] [Indexed: 02/05/2024]
Abstract
The emergence and diversification of morphological novelties is a major feature of animal evolution.1,2,3,4,5,6,7,8,9 However, relatively little is known about the genetic basis of the evolution of novel structures and the mechanisms underlying their diversification. The epandrial posterior lobes of male genitalia are a novelty of particular Drosophila species.10,11,12,13 The lobes grasp the female ovipositor and insert between her abdominal tergites and, therefore, are important for copulation and species recognition.10,11,12,14,15,16,17 The posterior lobes likely evolved from co-option of a Hox-regulated gene network from the posterior spiracles10 and have since diversified in morphology in the D. simulans clade, in particular, over the last 240,000 years, driven by sexual selection.18,19,20,21 The genetic basis of this diversification is polygenic but, to the best of our knowledge, none of the causative genes have been identified.22,23,24,25,26,27,28,29,30 Identifying the genes underlying the diversification of these secondary sexual structures is essential to understanding the evolutionary impact on copulation and species recognition. Here, we show that Sox21b negatively regulates posterior lobe size. This is consistent with expanded Sox21b expression in D. mauritiana, which develops smaller posterior lobes than D. simulans. We tested this by generating reciprocal hemizygotes and confirmed that changes in Sox21b underlie posterior lobe evolution between these species. Furthermore, we found that posterior lobe size differences caused by the species-specific allele of Sox21b significantly affect copulation duration. Taken together, our study reveals the genetic basis for the sexual-selection-driven diversification of a novel morphological structure and its functional impact on copulatory behavior.
Collapse
Affiliation(s)
- Amber M Ridgway
- Department of Biological and Medical Sciences, Oxford Brookes University, Oxford OX3 0BP, UK
| | - Emily J Hood
- Department of Biological and Medical Sciences, Oxford Brookes University, Oxford OX3 0BP, UK
| | | | - Maria D S Nunes
- Department of Biological and Medical Sciences, Oxford Brookes University, Oxford OX3 0BP, UK.
| | | |
Collapse
|
13
|
Kariyayama H, Gogoleva N, Harada K, Yokoyama H, Ono H, Suzuki DG, Yamazaki Y, Wada H. Development of the vertebra and fin skeleton in the lamprey and its implications for the homology of vertebrate vertebrae. Dev Dyn 2024; 253:283-295. [PMID: 37732630 DOI: 10.1002/dvdy.657] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2023] [Revised: 08/17/2023] [Accepted: 08/22/2023] [Indexed: 09/22/2023] Open
Abstract
BACKGROUND Although vertebrae are the defining character of vertebrates, they are found only in rudimentary form in extant agnathans. In addition, the vertebrae of agnathans possess several unique features, such as elastin-like molecules as the main matrix component and late (post-metamorphosis) differentiation of lamprey vertebrae. In this study, by tracing the developmental process of vertebrae in lamprey, we examined the homology of vertebrae between lampreys and gnathostomes. RESULTS We found that the lamprey somite is first subdivided mediolaterally, with myotome cells differentiating medially and non-myotome cells emerging laterally. Subsequently, collagen-positive non-myotome cells surround the myotome. This pattern of somitogenesis is rather similar to that in amphioxi and sheds doubt on the presence of a sclerotome, in terms of mesenchyme cells induced by a signal from the notochord, in lamprey. Further tracing of non-myotome cell development revealed that fin cartilage develops in ammocoete larvae approximately 35 mm in body length. The development of the fin cartilage occurs much earlier than that of the vertebra whose development proceeds during metamorphosis. CONCLUSION We propose that the homology of vertebrae between agnathans and gnathostomes should be discussed carefully, because the developmental process of the lamprey vertebra is different from that of gnathostomes.
Collapse
Affiliation(s)
- Hirofumi Kariyayama
- Graduate School of Life and Environmental Sciences, University of Tsukuba, Tsukuba, Ibaraki, Japan
| | - Natalia Gogoleva
- Graduate School of Life and Environmental Sciences, University of Tsukuba, Tsukuba, Ibaraki, Japan
| | - Keishi Harada
- Graduate School of Life and Environmental Sciences, University of Tsukuba, Tsukuba, Ibaraki, Japan
| | - Hiromasa Yokoyama
- Graduate School of Life and Environmental Sciences, University of Tsukuba, Tsukuba, Ibaraki, Japan
| | - Hiroki Ono
- Graduate School of Life and Environmental Sciences, University of Tsukuba, Tsukuba, Ibaraki, Japan
| | - Daichi G Suzuki
- Institute of Life and Environmental Sciences, University of Tsukuba, Tsukuba, Ibaraki, Japan
| | - Yuji Yamazaki
- Faculty of Science, Department of Biology, University of Toyama, Toyama, Japan
| | - Hiroshi Wada
- Institute of Life and Environmental Sciences, University of Tsukuba, Tsukuba, Ibaraki, Japan
| |
Collapse
|
14
|
Sullivan LF, Barker MS, Felix PC, Vuong RQ, White BH. Neuromodulation and the toolkit for behavioural evolution: can ecdysis shed light on an old problem? FEBS J 2024; 291:1049-1079. [PMID: 36223183 PMCID: PMC10166064 DOI: 10.1111/febs.16650] [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: 06/21/2022] [Revised: 09/06/2022] [Accepted: 10/12/2022] [Indexed: 05/10/2023]
Abstract
The geneticist Thomas Dobzhansky famously declared: 'Nothing in biology makes sense except in the light of evolution'. A key evolutionary adaptation of Metazoa is directed movement, which has been elaborated into a spectacularly varied number of behaviours in animal clades. The mechanisms by which animal behaviours have evolved, however, remain unresolved. This is due, in part, to the indirect control of behaviour by the genome, which provides the components for both building and operating the brain circuits that generate behaviour. These brain circuits are adapted to respond flexibly to environmental contingencies and physiological needs and can change as a function of experience. The resulting plasticity of behavioural expression makes it difficult to characterize homologous elements of behaviour and to track their evolution. Here, we evaluate progress in identifying the genetic substrates of behavioural evolution and suggest that examining adaptive changes in neuromodulatory signalling may be a particularly productive focus for future studies. We propose that the behavioural sequences used by ecdysozoans to moult are an attractive model for studying the role of neuromodulation in behavioural evolution.
Collapse
Affiliation(s)
- Luis F Sullivan
- Section on Neural Function, Laboratory of Molecular Biology, National Institute of Mental Health, Bethesda, MD, USA
| | - Matthew S Barker
- Section on Neural Function, Laboratory of Molecular Biology, National Institute of Mental Health, Bethesda, MD, USA
| | - Princess C Felix
- Section on Neural Function, Laboratory of Molecular Biology, National Institute of Mental Health, Bethesda, MD, USA
| | - Richard Q Vuong
- Section on Neural Function, Laboratory of Molecular Biology, National Institute of Mental Health, Bethesda, MD, USA
| | - Benjamin H White
- Section on Neural Function, Laboratory of Molecular Biology, National Institute of Mental Health, Bethesda, MD, USA
| |
Collapse
|
15
|
Eastment RV, Wong BBM, McGee MD. Convergent genomic signatures associated with vertebrate viviparity. BMC Biol 2024; 22:34. [PMID: 38331819 PMCID: PMC10854053 DOI: 10.1186/s12915-024-01837-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2023] [Accepted: 01/30/2024] [Indexed: 02/10/2024] Open
Abstract
BACKGROUND Viviparity-live birth-is a complex and innovative mode of reproduction that has evolved repeatedly across the vertebrate Tree of Life. Viviparous species exhibit remarkable levels of reproductive diversity, both in the amount of care provided by the parent during gestation, and the ways in which that care is delivered. The genetic basis of viviparity has garnered increasing interest over recent years; however, such studies are often undertaken on small evolutionary timelines, and thus are not able to address changes occurring on a broader scale. Using whole genome data, we investigated the molecular basis of this innovation across the diversity of vertebrates to answer a long held question in evolutionary biology: is the evolution of convergent traits driven by convergent genomic changes? RESULTS We reveal convergent changes in protein family sizes, protein-coding regions, introns, and untranslated regions (UTRs) in a number of distantly related viviparous lineages. Specifically, we identify 15 protein families showing evidence of contraction or expansion associated with viviparity. We additionally identify elevated substitution rates in both coding and noncoding sequences in several viviparous lineages. However, we did not find any convergent changes-be it at the nucleotide or protein level-common to all viviparous lineages. CONCLUSIONS Our results highlight the value of macroevolutionary comparative genomics in determining the genomic basis of complex evolutionary transitions. While we identify a number of convergent genomic changes that may be associated with the evolution of viviparity in vertebrates, there does not appear to be a convergent molecular signature shared by all viviparous vertebrates. Ultimately, our findings indicate that a complex trait such as viviparity likely evolves with changes occurring in multiple different pathways.
Collapse
Affiliation(s)
- Rhiannon V Eastment
- School of Biological Sciences, Monash University, Melbourne, 3800, Australia.
| | - Bob B M Wong
- School of Biological Sciences, Monash University, Melbourne, 3800, Australia
| | - Matthew D McGee
- School of Biological Sciences, Monash University, Melbourne, 3800, Australia
| |
Collapse
|
16
|
Longtine C, Eliason CM, Mishkind D, Lee C, Chiappone M, Goller F, Love J, Kingsley EP, Clarke JA, Tabin CJ. Homology and the evolution of vocal folds in the novel avian voice box. Curr Biol 2024; 34:461-472.e7. [PMID: 38183987 DOI: 10.1016/j.cub.2023.12.013] [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: 06/14/2023] [Revised: 08/29/2023] [Accepted: 12/06/2023] [Indexed: 01/08/2024]
Abstract
The origin of novel traits, those that are not direct modifications of a pre-existing ancestral structure, remains a fundamental problem in evolutionary biology. For example, little is known about the evolutionary and developmental origins of the novel avian vocal organ, the syrinx. Located at the tracheobronchial junction, the syrinx is responsible for avian vocalization, but it is unclear whether avian vocal folds are homologous to the laryngeal vocal folds in other tetrapods or convergently evolved. Here, we identify a core developmental program involved in avian vocal fold formation and infer the morphology of the syrinx of the ancestor of modern birds. We find that this ancestral syrinx had paired sound sources induced by a conserved developmental pathway and show that shifts in these signals correlate with syringeal diversification. We show that, despite being derived from different developmental tissues, vocal folds in the syrinx and larynx have similar tissue composition and are established through a strikingly similar developmental program, indicating that co-option of an ancestral developmental program facilitated the origin of vocal folds in the avian syrinx.
Collapse
Affiliation(s)
- Charlie Longtine
- Department of Genetics, Harvard Medical School, Boston, MA 02115, USA
| | - Chad M Eliason
- The Jackson School of Geosciences and Department of Integrative Biology, The University of Texas at Austin, Austin, TX 78712, USA
| | - Darcy Mishkind
- Department of Genetics, Harvard Medical School, Boston, MA 02115, USA
| | - ChangHee Lee
- Department of Genetics, Harvard Medical School, Boston, MA 02115, USA
| | - Michael Chiappone
- The Jackson School of Geosciences and Department of Integrative Biology, The University of Texas at Austin, Austin, TX 78712, USA
| | - Franz Goller
- School of Biological Sciences, University of Utah, Salt Lake City, UT 84112, USA; Department of Zoophysiology, University of Münster, 48149 Münster, Germany
| | - Jay Love
- School of Biological Sciences, University of Utah, Salt Lake City, UT 84112, USA
| | - Evan P Kingsley
- Department of Genetics, Harvard Medical School, Boston, MA 02115, USA.
| | - Julia A Clarke
- The Jackson School of Geosciences and Department of Integrative Biology, The University of Texas at Austin, Austin, TX 78712, USA.
| | - Clifford J Tabin
- Department of Genetics, Harvard Medical School, Boston, MA 02115, USA.
| |
Collapse
|
17
|
Zhang Y, Fu Y, Xian W, Li X, Feng Y, Bu F, Shi Y, Chen S, van Velzen R, Battenberg K, Berry AM, Salgado MG, Liu H, Yi T, Fournier P, Alloisio N, Pujic P, Boubakri H, Schranz ME, Delaux PM, Wong GKS, Hocher V, Svistoonoff S, Gherbi H, Wang E, Kohlen W, Wall LG, Parniske M, Pawlowski K, Normand P, Doyle JJ, Cheng S. Comparative phylogenomics and phylotranscriptomics provide insights into the genetic complexity of nitrogen-fixing root-nodule symbiosis. PLANT COMMUNICATIONS 2024; 5:100671. [PMID: 37553834 PMCID: PMC10811378 DOI: 10.1016/j.xplc.2023.100671] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/25/2023] [Revised: 07/10/2023] [Accepted: 08/03/2023] [Indexed: 08/10/2023]
Abstract
Plant root-nodule symbiosis (RNS) with mutualistic nitrogen-fixing bacteria is restricted to a single clade of angiosperms, the Nitrogen-Fixing Nodulation Clade (NFNC), and is best understood in the legume family. Nodulating species share many commonalities, explained either by divergence from a common ancestor over 100 million years ago or by convergence following independent origins over that same time period. Regardless, comparative analyses of diverse nodulation syndromes can provide insights into constraints on nodulation-what must be acquired or cannot be lost for a functional symbiosis-and the latitude for variation in the symbiosis. However, much remains to be learned about nodulation, especially outside of legumes. Here, we employed a large-scale phylogenomic analysis across 88 species, complemented by 151 RNA-seq libraries, to elucidate the evolution of RNS. Our phylogenomic analyses further emphasize the uniqueness of the transcription factor NIN as a master regulator of nodulation and identify key mutations that affect its function across the NFNC. Comparative transcriptomic assessment revealed nodule-specific upregulated genes across diverse nodulating plants, while also identifying nodule-specific and nitrogen-response genes. Approximately 70% of symbiosis-related genes are highly conserved in the four representative species, whereas defense-related and host-range restriction genes tend to be lineage specific. Our study also identified over 900 000 conserved non-coding elements (CNEs), over 300 000 of which are unique to sampled NFNC species. NFNC-specific CNEs are enriched with the active H3K9ac mark and are correlated with accessible chromatin regions, thus representing a pool of candidate regulatory elements for genes involved in RNS. Collectively, our results provide novel insights into the evolution of nodulation and lay a foundation for engineering of RNS traits in agriculturally important crops.
Collapse
Affiliation(s)
- Yu Zhang
- Shenzhen Branch, Guangdong Laboratory for Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen 518124, China
| | - Yuan Fu
- Shenzhen Branch, Guangdong Laboratory for Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen 518124, China; State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, Beijing 100093, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Wenfei Xian
- Shenzhen Branch, Guangdong Laboratory for Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen 518124, China
| | - Xiuli Li
- Shenzhen Branch, Guangdong Laboratory for Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen 518124, China
| | - Yong Feng
- Shenzhen Branch, Guangdong Laboratory for Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen 518124, China
| | - Fengjiao Bu
- Shenzhen Branch, Guangdong Laboratory for Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen 518124, China
| | - Yan Shi
- Shenzhen Branch, Guangdong Laboratory for Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen 518124, China
| | - Shiyu Chen
- Shenzhen Branch, Guangdong Laboratory for Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen 518124, China
| | - Robin van Velzen
- Biosystematics Group, Department of Plant Sciences, Wageningen University, 6708PB Wageningen, the Netherlands
| | - Kai Battenberg
- Department of Plant Sciences, University of California, Davis, Davis, CA 95616, USA
| | - Alison M Berry
- Department of Plant Sciences, University of California, Davis, Davis, CA 95616, USA
| | - Marco G Salgado
- Department of Ecology, Environment and Plant Sciences, Stockholm University, 106 91 Stockholm, Sweden
| | - Hui Liu
- Germplasm Bank of Wild Species, Kunming Institute of Botany, Chinese Academy of Sciences, Lanhei Road, Kunming 650201, China
| | - Tingshuang Yi
- Germplasm Bank of Wild Species, Kunming Institute of Botany, Chinese Academy of Sciences, Lanhei Road, Kunming 650201, China
| | - Pascale Fournier
- Université de Lyon, Université Lyon 1, CNRS, UMR5557, Ecologie Microbienne, INRA, UMR 1418, 43 bd du 11 novembre 1918, 69622 Villeurbanne, France
| | - Nicole Alloisio
- Université de Lyon, Université Lyon 1, CNRS, UMR5557, Ecologie Microbienne, INRA, UMR 1418, 43 bd du 11 novembre 1918, 69622 Villeurbanne, France
| | - Petar Pujic
- Université de Lyon, Université Lyon 1, CNRS, UMR5557, Ecologie Microbienne, INRA, UMR 1418, 43 bd du 11 novembre 1918, 69622 Villeurbanne, France
| | - Hasna Boubakri
- Université de Lyon, Université Lyon 1, CNRS, UMR5557, Ecologie Microbienne, INRA, UMR 1418, 43 bd du 11 novembre 1918, 69622 Villeurbanne, France
| | - M Eric Schranz
- Biosystematics Group, Department of Plant Sciences, Wageningen University, 6708PB Wageningen, the Netherlands
| | - Pierre-Marc Delaux
- Laboratoire de Recherche en Sciences Végétales (LRSV), Université de Toulouse, CNRS, UPS, 24 chemin de Borde Rouge, Auzeville, BP42617, 31326 Castanet Tolosan, France
| | - Gane Ka-Shu Wong
- Department of Biological Sciences, University of Alberta, Edmonton, AB T6G 2E9, Canada
| | - Valerie Hocher
- French National Research Institute for Sustainable Development (IRD), UMR LSTM (IRD/CIRAD/INRAe/Montpellier University/Supagro)- Campus International Baillarguet, TA A-82/J, 34398 Montpellier Cedex 5, France
| | - Sergio Svistoonoff
- French National Research Institute for Sustainable Development (IRD), UMR LSTM (IRD/CIRAD/INRAe/Montpellier University/Supagro)- Campus International Baillarguet, TA A-82/J, 34398 Montpellier Cedex 5, France
| | - Hassen Gherbi
- French National Research Institute for Sustainable Development (IRD), UMR LSTM (IRD/CIRAD/INRAe/Montpellier University/Supagro)- Campus International Baillarguet, TA A-82/J, 34398 Montpellier Cedex 5, France
| | - Ertao Wang
- National Key Laboratory of Plant Molecular Genetics, CAS Center for Excellence in Molecular Plant Sciences, Institute of Plant Physiology and Ecology, SIBS, Chinese Academy of Sciences, Shanghai, China
| | - Wouter Kohlen
- Laboratory of Molecular Biology, Department of Plant Sciences, Wageningen University, 6708PB Wageningen, the Netherlands
| | - Luis G Wall
- Laboratory of Biochemistry, Microbiology and Soil Biological Interactions, Department of Science and Technology, National University of Quilmes, CONICET, Bernal, Argentina
| | - Martin Parniske
- Faculty of Biology, Genetics, LMU Munich, Großhaderner Strasse 2-4, 82152 Martinsried, Germany
| | - Katharina Pawlowski
- Department of Ecology, Environment and Plant Sciences, Stockholm University, 106 91 Stockholm, Sweden
| | - Philippe Normand
- Université de Lyon, Université Lyon 1, CNRS, UMR5557, Ecologie Microbienne, INRA, UMR 1418, 43 bd du 11 novembre 1918, 69622 Villeurbanne, France
| | - Jeffrey J Doyle
- School of Integrative Plant Science, Sections of Plant Biology and Plant Breeding & Genetics, Cornell University, Ithaca, NY 14853, USA.
| | - Shifeng Cheng
- Shenzhen Branch, Guangdong Laboratory for Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen 518124, China.
| |
Collapse
|
18
|
Stahlman WD, Leising KJ. The behavioral origins of phylogenic responses and ontogenic habits. J Exp Anal Behav 2024; 121:27-37. [PMID: 38010287 DOI: 10.1002/jeab.892] [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: 06/15/2023] [Accepted: 11/09/2023] [Indexed: 11/29/2023]
Abstract
An examination of innate behavior and its possible origins suggests parallels with the formation of habitual behavior. Inflexible but adaptive responses-innate reflexive behavior, Pavlovian conditioned responses, and operant habits-may have evolved from variable behavior in phylogeny and ontogeny. This form of "plasticity-first" scientific narrative was unpopular post-Darwin but has recently gained credibility in evolutionary biology. The present article seeks to identify originating events and contingencies contributing to such inflexible but adaptive behavior at both phylogenic and ontogenic levels of selection. In ontogeny, the development of inflexible performance (i.e., habit) from variable operant behavior is reminiscent of the genetic accommodation of initially variable phylogenic traits. The effects characteristic of habit (e.g., unresponsiveness to reinforcer devaluation) are explicable as the result of a conflict between behaviors at distinct levels of selection. The present interpretation validates the practice of seeking hard analogies between evolutionary biology and operant behavior. Finding such parallels implies the validity of a claim that organismal behavior, both innate and learned, is a product of selection by consequences. A complete and coherent account of organismal behavior may ultimately focus on functional selective histories in much the same way evolutionary biology does with its subject matter.
Collapse
Affiliation(s)
- W David Stahlman
- University of Mary Washington-Department of Psychological Science, Fredericksburg, VA, USA
| | | |
Collapse
|
19
|
Rasys AM, Wegerski A, Trainor PA, Hufnagel RB, Menke DB, Lauderdale JD. Dynamic changes in ocular shape during human development and its implications for retina fovea formation. Bioessays 2024; 46:e2300054. [PMID: 38037292 DOI: 10.1002/bies.202300054] [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: 03/27/2023] [Revised: 10/10/2023] [Accepted: 10/24/2023] [Indexed: 12/02/2023]
Abstract
The human fovea is known for its distinctive pit-like appearance, which results from the displacement of retinal layers superficial to the photoreceptors cells. The photoreceptors are found at high density within the foveal region but not the surrounding retina. Efforts to elucidate the mechanisms responsible for these unique features have ruled out cell death as an explanation for pit formation and changes in cell proliferation as the cause of increased photoreceptor density. These findings have led to speculation that mechanical forces acting within and on the retina during development underly the formation of foveal architecture. Here we review eye morphogenesis and retinal remodeling in human embryonic development. Our meta-analysis of the literature suggests that fovea formation is a protracted process involving dynamic changes in ocular shape that start early and continue throughout most of human embryonic development. From these observations, we propose a new model for fovea development.
Collapse
Affiliation(s)
- Ashley M Rasys
- Department of Cellular Biology, The University of Georgia, Athens, Georgia, USA
| | - Andrew Wegerski
- Ophthalmic Genetics and Visual Function Branch, National Eye Institute, National Institutes of Health, Bethesda, Maryland, USA
| | - Paul A Trainor
- Stowers Institute for Medical Research, Kansas City, Missouri, USA
- Department of Anatomy & Cell Biology, The University of Kansas School of Medicine, Kansas City, Kansas, USA
| | - Robert B Hufnagel
- Ophthalmic Genetics and Visual Function Branch, National Eye Institute, National Institutes of Health, Bethesda, Maryland, USA
| | - Douglas B Menke
- Department of Genetics, The University of Georgia, Athens, Georgia, USA
| | - James D Lauderdale
- Department of Cellular Biology, The University of Georgia, Athens, Georgia, USA
- Neuroscience Division of the Biomedical and Health Sciences Institute, The University of Georgia, Athens, Georgia, USA
| |
Collapse
|
20
|
Loffet EA, Durel JF, Nerurkar NL. Evo-Devo Mechanobiology: The Missing Link. Integr Comp Biol 2023; 63:1455-1473. [PMID: 37193661 DOI: 10.1093/icb/icad033] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2023] [Revised: 05/11/2023] [Accepted: 05/12/2023] [Indexed: 05/18/2023] Open
Abstract
While the modern framework of evolutionary development (evo-devo) has been decidedly genetic, historic analyses have also considered the importance of mechanics in the evolution of form. With the aid of recent technological advancements in both quantifying and perturbing changes in the molecular and mechanical effectors of organismal shape, how molecular and genetic cues regulate the biophysical aspects of morphogenesis is becoming increasingly well studied. As a result, this is an opportune time to consider how the tissue-scale mechanics that underlie morphogenesis are acted upon through evolution to establish morphological diversity. Such a focus will enable a field of evo-devo mechanobiology that will serve to better elucidate the opaque relations between genes and forms by articulating intermediary physical mechanisms. Here, we review how the evolution of shape is measured and related to genetics, how recent strides have been made in the dissection of developmental tissue mechanics, and how we expect these areas to coalesce in evo-devo studies in the future.
Collapse
Affiliation(s)
- Elise A Loffet
- Department of Biomedical Engineering, Columbia University, 351 Engineering Terrace, 1210 Amsterdam Avenue, New York, NY 10027, USA
| | - John F Durel
- Department of Biomedical Engineering, Columbia University, 351 Engineering Terrace, 1210 Amsterdam Avenue, New York, NY 10027, USA
| | - Nandan L Nerurkar
- Department of Biomedical Engineering, Columbia University, 351 Engineering Terrace, 1210 Amsterdam Avenue, New York, NY 10027, USA
| |
Collapse
|
21
|
Assis LCS. Pollination syndromes and the origins of floral traits. ANNALS OF BOTANY 2023; 132:1055-1072. [PMID: 37814841 PMCID: PMC10809047 DOI: 10.1093/aob/mcad147] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/29/2023] [Accepted: 09/27/2023] [Indexed: 10/11/2023]
Abstract
BACKGROUND A general view in the study of pollination syndromes is that floral traits usually represent convergent floral adaptations to specific functional pollinator groups. However, the definition of convergence is elusive and contradictory in the literature. Is convergence the independent evolution of either the same trait or similar traits with the same function? A review of the concept of convergence in developmental biology and phylogenetic systematics may shed new light in studies of pollination syndromes. SCOPE The aims of this article are (1) to explore the notion of convergence and other concepts (analogy, homoplasy and parallelism) within the theory and practice of developmental evolution and phylogenetic systematics; (2) to modify the definitions of syndromes in order to embrace the concepts of analogy and convergence; (3) to revisit the bat pollination syndrome in the context of angiosperm phylogeny, with focus on the showy 'petaloid' organs associated with the syndrome; (4) to revisit the genetic-developmental basis of flower colour; (5) to raise evolutionary hypotheses of floral evolution associated with the bat pollination syndrome; and (6) to highlight some of the current frontiers of research on the origin and evolution of flowers and its impact on pollination syndrome studies in the 21st century. CONCLUSIONS The inclusion of the concepts of analogy and convergence within the concept of syndromes will constitute a new agenda of inquiry that integrates floral biology, phylogenetic systematics and developmental biology. Phyllostomid and pteropodid bat pollination syndrome traits in eudicots and monocots represent cases of analogous and convergent evolution. Pollination syndromes are a multivariate concept intrinsically related to the understanding of flower organogenesis and evolution. The formulation of hypotheses of pollination syndromes must consider the phylogenetic levels of universality for both plant and animal taxa, flower development, genetics, homology and evolution, and a clear definition of evolutionary concepts, including analogy, convergence, homoplasy and parallelism.
Collapse
Affiliation(s)
- Leandro C S Assis
- Departamento de Botânica, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Belo Horizonte, Minas Gerais 31270-901, Brazil
| |
Collapse
|
22
|
Engel MS. Grand challenges in insect systematics. FRONTIERS IN INSECT SCIENCE 2023; 3:1327005. [PMID: 38469463 PMCID: PMC10926366 DOI: 10.3389/finsc.2023.1327005] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/24/2023] [Accepted: 11/13/2023] [Indexed: 03/13/2024]
Affiliation(s)
- Michael S. Engel
- Division of Invertebrate Zoology, American Museum of Natural History, New York, NY, United States
- Institut de Systématique, Évolution, Biodiversité (ISYEB), Muséum National d’Histoire Naturelle, Centre National de la Recherche Scientifique, Sorbonne Université, École Pratique des Hautes Études, Université des Antilles, Paris, France
- Museum at Prairiefire, Overland Park, KS, United States
| |
Collapse
|
23
|
Brazeau MD, Castiello M, El Fassi El Fehri A, Hamilton L, Ivanov AO, Johanson Z, Friedman M. Fossil evidence for a pharyngeal origin of the vertebrate pectoral girdle. Nature 2023; 623:550-554. [PMID: 37914937 PMCID: PMC10651482 DOI: 10.1038/s41586-023-06702-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2023] [Accepted: 10/02/2023] [Indexed: 11/03/2023]
Abstract
The origin of vertebrate paired appendages is one of the most investigated and debated examples of evolutionary novelty1-7. Paired appendages are widely considered as key innovations that enabled new opportunities for controlled swimming and gill ventilation and were prerequisites for the eventual transition from water to land. The past 150 years of debate8-10 has been shaped by two contentious theories4,5: the ventrolateral fin-fold hypothesis9,10 and the archipterygium hypothesis8. The latter proposes that fins and girdles evolved from an ancestral gill arch. Although studies in animal development have revived interest in this idea11-13, it is apparently unsupported by fossil evidence. Here we present palaeontological support for a pharyngeal basis for the vertebrate shoulder girdle. We use computed tomography scanning to reveal details of the braincase of Kolymaspis sibirica14, an Early Devonian placoderm fish from Siberia, that suggests a pharyngeal component of the shoulder. We combine these findings with refreshed comparative anatomy of placoderms and jawless outgroups to place the origin of the shoulder girdle on the sixth branchial arch. These findings provide a novel framework for understanding the origin of the pectoral girdle. Our evidence clarifies the location of the presumptive head-trunk interface in jawless fishes and explains the constraint on branchial arch number in gnathostomes15. The results revive a key aspect of the archipterygium hypothesis and help reconcile it with the ventrolateral fin-fold model.
Collapse
Affiliation(s)
- Martin D Brazeau
- Department of Life Sciences, Imperial College London, Ascot, UK.
- The Natural History Museum, London, UK.
| | - Marco Castiello
- Department of Life Sciences, Imperial College London, Ascot, UK
- London Academy of Excellence, London, United Kingdom
| | - Amin El Fassi El Fehri
- Department of Life Sciences, Imperial College London, Ascot, UK
- Paläontologisches Institut und Museum, Universität Zürich, Zurich, Switzerland
| | - Louis Hamilton
- Department of Life Sciences, Imperial College London, Ascot, UK
| | - Alexander O Ivanov
- Department of Sedimentary Geology, Institute of Earth Sciences, St Petersburg State University, St Petersburg, Russia
- Institute of Geology and Petroleum Technologies, Kazan Federal University, Kazan, Russia
| | | | - Matt Friedman
- The Natural History Museum, London, UK
- Museum of Paleontology, University of Michigan, Ann Arbor, MI, USA
- Department of Earth and Environmental Sciences, University of Michigan, Ann Arbor, MI, USA
| |
Collapse
|
24
|
Goekoop R, de Kleijn R. Hierarchical network structure as the source of hierarchical dynamics (power-law frequency spectra) in living and non-living systems: How state-trait continua (body plans, personalities) emerge from first principles in biophysics. Neurosci Biobehav Rev 2023; 154:105402. [PMID: 37741517 DOI: 10.1016/j.neubiorev.2023.105402] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2023] [Revised: 09/19/2023] [Accepted: 09/20/2023] [Indexed: 09/25/2023]
Abstract
Living systems are hierarchical control systems that display a small world network structure. In such structures, many smaller clusters are nested within fewer larger ones, producing a fractal-like structure with a 'power-law' cluster size distribution (a mereology). Just like their structure, the dynamics of living systems shows fractal-like qualities: the timeseries of inner message passing and overt behavior contain high frequencies or 'states' (treble) that are nested within lower frequencies or 'traits' (bass), producing a power-law frequency spectrum that is known as a 'state-trait continuum' in the behavioral sciences. Here, we argue that the power-law dynamics of living systems results from their power-law network structure: organisms 'vertically encode' the deep spatiotemporal structure of their (anticipated) environments, to the effect that many small clusters near the base of the hierarchy produce high frequency signal changes and fewer larger clusters at its top produce ultra-low frequencies. Such ultra-low frequencies exert a tonic regulatory pressure that produces morphological as well as behavioral traits (i.e., body plans and personalities). Nested-modular structure causes higher frequencies to be embedded within lower frequencies, producing a power-law state-trait continuum. At the heart of such dynamics lies the need for efficient energy dissipation through networks of coupled oscillators, which also governs the dynamics of non-living systems (e.q., earthquakes, stock market fluctuations). Since hierarchical structure produces hierarchical dynamics, the development and collapse of hierarchical structure (e.g., during maturation and disease) should leave specific traces in system dynamics (shifts in lower frequencies, i.e. morphological and behavioral traits) that may serve as early warning signs to system failure. The applications of this idea range from (bio)physics and phylogenesis to ontogenesis and clinical medicine.
Collapse
Affiliation(s)
- R Goekoop
- Free University Amsterdam, Department of Behavioral and Movement Sciences, Parnassia Academy, Parnassia Group, PsyQ, Department of Anxiety Disorders, Early Detection and Intervention Team (EDIT), Lijnbaan 4, 2512VA The Hague, the Netherlands.
| | - R de Kleijn
- Faculty of Social and Behavioral Sciences, Department of Cognitive Psychology, Pieter de la Courtgebouw, Postbus 9555, 2300 RB Leiden, the Netherlands
| |
Collapse
|
25
|
Flores-Arguedas H, Antolin-Camarena O, Saavedra S, Angulo MT. Assembly archetypes in ecological communities. J R Soc Interface 2023; 20:20230349. [PMID: 38016640 PMCID: PMC10684342 DOI: 10.1098/rsif.2023.0349] [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: 06/20/2023] [Accepted: 11/03/2023] [Indexed: 11/30/2023] Open
Abstract
An instrumental discovery in comparative and developmental biology is the existence of assembly archetypes that synthesize the vast diversity of organisms' body plans-from legs and wings to human arms-into simple, interpretable and general design principles. Here, we combine a novel mathematical formalism based on category theory with experimental data to show that similar 'assembly archetypes' exist at the larger organization scale of ecological communities when assembling a species pool across diverse environmental contexts, particularly when species interactions are highly structured. We applied our formalism to clinical data discovering two assembly archetypes that differentiate between healthy and unhealthy human gut microbiota. The concept of assembly archetypes and the methods to synthesize them can pave the way to discovering the general assembly principles of the ecological communities we observe in nature.
Collapse
Affiliation(s)
- Hugo Flores-Arguedas
- Institute of Mathematics, Universidad Nacional Autónoma de México, Juriquilla, Queretaro, Mexico
| | - Omar Antolin-Camarena
- Institute of Mathematics, Universidad Nacional Autónoma de México, Ciudad Universitaria, Mexico City, Mexico
| | - Serguei Saavedra
- Department of Civil and Environmental Engineering, MIT, 77 Massachusetts Avenue, Cambridge, MA 02139, USA
- Santa Fe Institute, 1399 Hyde Park Road, Santa Fe, NM 87501, USA
| | - Marco Tulio Angulo
- Institute of Mathematics, Universidad Nacional Autónoma de México, Juriquilla, Queretaro, Mexico
| |
Collapse
|
26
|
Witzmann F, Fröbisch N. Morphology and ontogeny of carpus and tarsus in stereospondylomorph temnospondyls. PeerJ 2023; 11:e16182. [PMID: 37904842 PMCID: PMC10613440 DOI: 10.7717/peerj.16182] [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: 03/13/2023] [Accepted: 09/05/2023] [Indexed: 11/01/2023] Open
Abstract
Skeletal development is well known in temnospondyls, the most diverse group of Paleozoic and Mesozoic amphibians. However, the elements of carpus and tarsus (i.e., the mesopodium) were always the last bones to ossify relative to the other limb bones and with regard to the rest of the skeleton, and are preserved only in rare cases. Thus, in contrast to the other parts of the limb skeleton, little is known about the ontogeny and sequence of ossification of the temnospondyl carpus and tarsus. We intended to close this gap by studying the ontogenies of a number of Permo/Carboniferous stereospondylomorphs, the only temnospondyls with preserved growth series in which the successive ossification of carpals and tarsals can be traced. Studying the degree of mesopodial ossification within the same species show that it is not necessarily correlated with body size. This indicates that individual age rather than size determined the degree of mesopodial ossification in stereospondylomorphs and that the largest individuals are not necessarily the oldest ones. In the stereospondylomorph tarsus, the distal tarsals show preaxial development in accordance with most early tetrapods and salamanders. However, the more proximal mesopodials exhibit postaxial dominance, i.e., the preaxial column (tibiale, centrale 1) consistently started to ossify after the central column (centralia 2-4, intermedium) and the postaxial column (fibulare). Likewise, we observed preaxial development of the distal carpals in the stereospondylomorph carpus, as in most early tetrapods for which a statement can be made. However, in contrast to the tarsus, the more proximal carpals were formed by preaxial development, i.e., the preaxial column (radiale, centrale 1) ossified after the central column (centralia 2-4, intermedium) and before the postaxial column (ulnare). This pattern is unique among known early tetrapods and occurs only in certain extant salamanders. Furthermore, ossification proceeded from distal to proximal in the central column of the stereospondylomorph carpus, whereas the ossification advanced from proximal to distal in the central column of the tarsus. Despite these differences, a general ossification pattern that started from proximolateral (intermedium or centrale 4) to mediodistal (distal tarsal and carpal 1) roughly in a diagonal line is common to all stereospondylomorph mesopodials investigated. This pattern might basically reflect the alignment of stress within the mesopodium during locomotion. Our observations might point to a greater variability in the development of the mesopodium in stereospondylomorphs and probably other early tetrapods than in most extant tetrapods, possibly mirroring a similar variation as seen in the early phases of skeletogenesis in salamander carpus and tarsus.
Collapse
Affiliation(s)
- Florian Witzmann
- Museum für Naturkunde Berlin, Leibniz Institute for Evolution and Biodiversity Science, Berlin, Germany
| | - Nadia Fröbisch
- Museum für Naturkunde Berlin, Leibniz Institute for Evolution and Biodiversity Science, Berlin, Germany
- Department of Biology, Humboldt Universität Berlin, Berlin, Germany
| |
Collapse
|
27
|
Sidorov D. Trans-Japan Sea land-bridge disjunction: A case of vicariance in the subterranean genus Nipponasellus (Crustacea, Isopoda, Asellidae) in a large-scale biogeographical context. Zootaxa 2023; 5357:342-374. [PMID: 38220641 DOI: 10.11646/zootaxa.5357.3.2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2023] [Indexed: 01/16/2024]
Abstract
This study examines nineteen phreatobiological hand pump samples collected in 20092010 in three separate areas of salmon river basins in the southern part of Primorye, in the Far East of Russia. For the first time, faunal groundwater patterns were assessed for the rivers of Eastern Manchuria, the Ussury River Basin and the rivers of the south-western slope of Sikhote Alin. A total of 164 species (including 32 stygobionts) belonging to the phyla Annelida, Mollusca and Arthropoda are first records of groundwater animals, and two of the stygobionts are described below as new species for Science. Nipponasellus sudzukhensis spec. nov. and N. matsumotoi spec. nov. are described and illustrated, and their taxonomic affinities with congeners are discussed. The morphology of male pleopod 2 of the genus Nipponasellus is re-examined using scanning electron microscopy (SEM), which revealed fine details of the pleopodal structures. The two new continental species of Nipponasellus were characterised by a distinct cannula completely immersed in ctenoid cuticular scales and the absence of a labial spur. Informal macrogroups were proposed based on the structure of the appendix masculina and an analysis of family distribution. The results of cladistic analyses revealed relationships between the proposed groups, but phylogenetic relationships within the Caecidotea-Proasellus group remain challenging. Common diagnostic characters of Nipponasellus showed that the group occupies an independent position close to the Caecidotea-Proasellus group rather than the Asellus-pattern sensu Magniez. Revised diagnosis for the genus Nipponasellus is given, including the two new species and the five previously described ones. The species diversity of East Asian stygobiotic asellid isopods is briefly reviewed to infer a biogeographic distribution pattern that emphasises the strict endemicity of members of the genus Nipponasellus. The intracontinental separation between continental Far East Asia and the Japanese archipelago highlights the biogeographic importance of the land-bridge in the Oligocene and raises questions about hypotheses explaining the (disjunct) distribution in East Asia, together with the circumstances preceding an ancient colonisation of the region.
Collapse
Affiliation(s)
- Dmitry Sidorov
- Department of Invertebrate Zoology; Federal Scientific Center of East Asia Terrestrial Biodiversity; Vladivostok 690022; RF.
| |
Collapse
|
28
|
Abstract
Animal tissues are made up of multiple cell types that are increasingly well-characterized, yet our understanding of the core principles that govern tissue organization is still incomplete. This is in part because many observable tissue characteristics, such as cellular composition and spatial patterns, are emergent properties, and as such, they cannot be explained through the knowledge of individual cells alone. Here we propose a complex systems theory perspective to address this fundamental gap in our understanding of tissue biology. We introduce the concept of cell categories, which is based on cell relations rather than cell identity. Based on these notions we then discuss common principles of tissue modularity, introducing compositional, structural, and functional tissue modules. Cell diversity and cell relations provide a basis for a new perspective on the underlying principles of tissue organization in health and disease.
Collapse
Affiliation(s)
- Miri Adler
- Tananbaum Center for Theoretical and Analytical Human Biology, Yale University School of Medicine, New Haven, Connecticut, USA;
- Department of Immunobiology, Yale University School of Medicine, New Haven, Connecticut, USA
| | - Arun R Chavan
- Department of Immunobiology, Yale University School of Medicine, New Haven, Connecticut, USA
| | - Ruslan Medzhitov
- Tananbaum Center for Theoretical and Analytical Human Biology, Yale University School of Medicine, New Haven, Connecticut, USA;
- Department of Immunobiology, Yale University School of Medicine, New Haven, Connecticut, USA
- Howard Hughes Medical Institute, Yale University School of Medicine, New Haven, Connecticut, USA
| |
Collapse
|
29
|
Ballego-Campos I, Bonifácio SKV, Assis LCS. A unified view of homology. Cladistics 2023; 39:398-417. [PMID: 37097257 DOI: 10.1111/cla.12541] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2022] [Revised: 03/29/2023] [Accepted: 04/05/2023] [Indexed: 04/26/2023] Open
Abstract
As it spread through time and into distinct areas of science-from comparative anatomy to evolutionary biology, cladistics, developmental and molecular biology-the homology concept has changed considerably, presenting various meanings. Despite many attempts at developing a comprehensive understanding of the concept, this context-sensitive notion of homology has been a subject of an ongoing debate. Inspired by that and following Kevin de Queiroz and Richard Mayden's view on species concept and delimitation, we presented in this article an attempt to systematize and advance the understanding of the homology problem. Our main goals were: (i) to present a comprehensive checklist of 'concepts of homology'; (ii) to identify which are really concepts with ontological definitions (theoretically rooted in structural correspondence and common ancestry), and which are, in fact, not concepts, but epistemological (empirical and methodological) criteria of homology delimitation; (iii) to provide a synonymy of the concepts and criteria of homology delimitation; (iv) to present a hierarchy of homology concepts within Hennig's hologenetic system; and (v) to endorse the adoption of a unified view of homology by treating homology as a correspondence of spatio-temporal properties (genetic, epigenetic, developmental and positional) at the level of the individual, species or monophyletic group. We found 59 'concepts of homology' in the literature, from which 34 were categorically treated as concepts, 17 as criteria of homology delimitation, Four were excluded from our treatment, and Müller's five concepts were rather treated as approaches to homology. Homology concepts and criteria were synonymized based on structural correspondence, replicability, common ancestry, genetic and epigenetic developmental causes, position and optimization. Regarding the synonymy, we conclusively recognized 21 different concepts of homology, and five empirical and four methodological criteria. Hierarchical ontological aspects of homology were systematized under Hennig's hologenetic system, based on the existence of ontogenetic, tokogenetic and phylogenetic levels of homology. The delimitation of tokogenetic and phylogenetic homologies depends on optimization criteria. The unified view of homology is discussed in the context of the ancestral angiosperm flower.
Collapse
Affiliation(s)
- Igor Ballego-Campos
- Departamento de Botânica, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Belo Horizonte, 31270-901, MG, Brazil
| | - Stéphani K V Bonifácio
- Departamento de Botânica, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Belo Horizonte, 31270-901, MG, Brazil
| | - Leandro C S Assis
- Departamento de Botânica, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Belo Horizonte, 31270-901, MG, Brazil
| |
Collapse
|
30
|
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.
Collapse
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
| |
Collapse
|
31
|
Bowsher J, Jockusch EL, Nagy L. Editorial. Semin Cell Dev Biol 2023; 145:1-2. [PMID: 36702721 DOI: 10.1016/j.semcdb.2022.12.005] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023]
Affiliation(s)
- Julia Bowsher
- Department of Biological Sciences, North Dakota State University, Fargo, North Dakota, USA
| | - Elizabeth L Jockusch
- Department of Ecology & Evolutionary Biology, University of Connecticut, Storrs, Connecticut, USA
| | - Lisa Nagy
- Molecular and Cellular Biology, University of Arizona, Tucson, Arizona USA.
| |
Collapse
|
32
|
Robbins AE, Horst SG, Lewis VM, Stewart S, Stankunas K. The Fraser complex interconnects tissue layers to support basal epidermis and osteoblast integrated morphogenesis underlying fin skeletal patterning. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.07.08.548238. [PMID: 37461516 PMCID: PMC10350090 DOI: 10.1101/2023.07.08.548238] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/24/2024]
Abstract
Fraser Syndrome is a rare, multisystemic autosomal recessive disorder characterized by disrupted epithelial-mesenchymal associations upon loss of Fraser Complex genes. Disease manifestation and affected organs are highly variable. Digit malformations such as syndactyly are common but of unclear developmental origins. We explored if zebrafish fraser extracellular matrix complex subunit 1 (fras1) mutants model Fraser Syndrome-associated appendicular skeleton patterning defects. Approximately 10% of fras1 mutants survive to adulthood, displaying striking and varied fin abnormalities, including endochondral bone fusions, ectopic cartilage, and disrupted caudal fin symmetry. The fins of surviving fras1 mutants frequently have fewer and unbranched bony rays. fras1 mutant fins regenerate to their original size but with exacerbated ray branching and fin symmetry defects. Single cell RNA-Seq analysis, in situ hybridizations, and antibody staining show specific Fraser complex expression in the basal epidermis during regenerative outgrowth. Fras1 and Fraser Complex component Frem2 accumulate along the basal side of distal-most basal epidermal cells. Greatly reduced and mislocalized Frem2 accompanies loss of Fras1 in fras1 mutants. The Sonic hedgehog signaling between distal basal epidermis and adjacent mesenchymal pre-osteoblasts that promotes ray branching persists upon Fraser Complex loss. However, fras1 mutant regenerating fins exhibit extensive sub-epidermal blistering associated with a disorganized basal epidermis and adjacent pre-osteoblasts. We propose Fraser Complex-supported tissue layer adhesion enables robust integrated tissue morphogenesis involving the basal epidermis and osteoblasts. Further, we establish zebrafish fin development and regeneration as an accessible model to explore mechanisms of Fraser Syndrome-associated digit defects and Fraser Complex function at epithelial-mesenchymal interfaces.
Collapse
|
33
|
Roston RA, Boessenecker RW, Geisler JH. Evolution and development of the cetacean skull roof: a case study in novelty and homology. Philos Trans R Soc Lond B Biol Sci 2023; 378:20220086. [PMID: 37183892 PMCID: PMC10184229 DOI: 10.1098/rstb.2022.0086] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2022] [Accepted: 11/15/2022] [Indexed: 05/16/2023] Open
Abstract
Skulls of living whales and dolphins (cetaceans) are telescoped-bones of the skull roof are overlapped by expanded facial bones and/or anteriorly extended occipital bones. Evolution of the underlying skull roof (calvarium), which lies between the telescoped regions, is relatively unstudied. We explore the evolution and development of the calvarium of toothed whales (odontocetes) by integrating fetal data with Oligocene odontocete fossils from North America, including eight neonatal and juvenile skulls of Olympicetus†. We identified two potential synapomorphies of crown Cetacea: contact of interparietals with frontals, and a single anterior median interparietal (AMI) element. Within Odontoceti, loss of contact between the parietals diagnoses the clade including Delphinida, Ziphiidae and Platanistidae (=Synrhina). Delphinida is characterized by a greatly enlarged interparietal. New fetal series of delphinoids reveal a consistent developmental pattern with three elements: the AMI and bilateral posterior interparietals (PIs). The PIs most resemble the medial interparietal elements of terrestrial artiodactyls, suggesting that the AMI of cetaceans could be a unique ossification. More broadly, the paucity of conserved anatomical relationships of the interparietals, as well as the fact that the elements often do not coalesce into a single bone, demonstrates that assessing homology of the interparietals across mammals remains challenging. This article is part of the theme issue 'The mammalian skull: development, structure and function'.
Collapse
Affiliation(s)
- R. A. Roston
- Department of Oral Health Sciences, School of Dentistry, University of Washington, Seattle, WA 98195, USA
- Center for Developmental Biology and Regenerative Medicine, Seattle Children's Research Institute, Seattle, WA 98101, USA
| | - R. W. Boessenecker
- Department of Geology and Environmental Geosciences, College of Charleston, Charleston, SC 29424, USA
- University of California Museum of Paleontology, University of California, Berkeley, CA 94720, USA
| | - J. H. Geisler
- Department of Anatomy, College of Osteopathic Medicine, New York Institute of Technology, Old Westbury, NY 11568, USA
- Department of Paleobiology, National Museum of Natural History, Washington, DC 20560, USA
| |
Collapse
|
34
|
Aprison EZ, Dzitoyeva S, Ruvinsky I. Serotonergic signaling plays a deeply conserved role in improving oocyte quality. Dev Biol 2023; 499:24-30. [PMID: 37121310 PMCID: PMC10247452 DOI: 10.1016/j.ydbio.2023.04.008] [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: 03/23/2023] [Revised: 04/21/2023] [Accepted: 04/27/2023] [Indexed: 05/02/2023]
Abstract
Declining germline quality is a major cause of reproductive senescence. Potential remedies could be found by studying regulatory pathways that promote germline quality. Several lines of evidence, including a C. elegans male pheromone ascr#10 that counteracts the effects of germline aging in hermaphrodites, suggest that the nervous system plays an important role in regulating germline quality. Inspired by the fact that serotonin mediates ascr#10 signaling, here we show that serotonin reuptake inhibitors recapitulate the effects of ascr#10 on the germline and promote healthy oocyte aging in C. elegans. Surprisingly, we found that pharmacological increase of serotonin signaling stimulates several developmental processes in D. melanogaster, including improved oocyte quality, although underlying mechanisms appear to be different between worms and flies. Our results reveal a plausibly conserved role for serotonin in maintaining germline quality and identify a class of therapeutic interventions using available compounds that could efficiently forestall reproductive aging.
Collapse
Affiliation(s)
- Erin Z Aprison
- Department of Molecular Biosciences, Northwestern University, Evanston, IL, 60208, USA
| | - Svetlana Dzitoyeva
- Department of Molecular Biosciences, Northwestern University, Evanston, IL, 60208, USA
| | - Ilya Ruvinsky
- Department of Molecular Biosciences, Northwestern University, Evanston, IL, 60208, USA.
| |
Collapse
|
35
|
Schuster HC, Hirth F. Phylogenetic tracing of midbrain-specific regulatory sequences suggests single origin of eubilaterian brains. SCIENCE ADVANCES 2023; 9:eade8259. [PMID: 37224241 PMCID: PMC10208574 DOI: 10.1126/sciadv.ade8259] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/10/2022] [Accepted: 04/18/2023] [Indexed: 05/26/2023]
Abstract
Conserved cis-regulatory elements (CREs) control Engrailed-, Pax2-, and dachshund-related gene expression networks directing the formation and function of corresponding midbrain circuits in arthropods and vertebrates. Polarized outgroup analyses of 31 sequenced metazoan genomes representing all animal clades reveal the emergence of Pax2- and dachshund-related CRE-like sequences in anthozoan Cnidaria. The full complement, including Engrailed-related CRE-like sequences, is only detectable in spiralians, ecdysozoans, and chordates that have a brain; they exhibit comparable genomic locations and extensive nucleotide identities that reveal the presence of a conserved core domain, all of which are absent in non-neural genes and, together, distinguish them from randomly assembled sequences. Their presence concurs with a genetic boundary separating the rostral from caudal nervous systems, demonstrated for the metameric brains of annelids, arthropods, and chordates and the asegmental cycloneuralian and urochordate brain. These findings suggest that gene regulatory networks for midbrain circuit formation evolved within the lineage that led to the common ancestor of protostomes and deuterostomes.
Collapse
Affiliation(s)
- Helen C. Schuster
- Department of Basic and Clinical Neuroscience, Maurice Wohl Clinical Neuroscience Institute, and Institute of Psychiatry, Psychology and Neuroscience, King’s College London, London, UK
| | | |
Collapse
|
36
|
Kocere A, Lalonde RL, Mosimann C, Burger A. Lateral thinking in syndromic congenital cardiovascular disease. Dis Model Mech 2023; 16:dmm049735. [PMID: 37125615 PMCID: PMC10184679 DOI: 10.1242/dmm.049735] [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: 05/02/2023] Open
Abstract
Syndromic birth defects are rare diseases that can present with seemingly pleiotropic comorbidities. Prime examples are rare congenital heart and cardiovascular anomalies that can be accompanied by forelimb defects, kidney disorders and more. Whether such multi-organ defects share a developmental link remains a key question with relevance to the diagnosis, therapeutic intervention and long-term care of affected patients. The heart, endothelial and blood lineages develop together from the lateral plate mesoderm (LPM), which also harbors the progenitor cells for limb connective tissue, kidneys, mesothelia and smooth muscle. This developmental plasticity of the LPM, which founds on multi-lineage progenitor cells and shared transcription factor expression across different descendant lineages, has the potential to explain the seemingly disparate syndromic defects in rare congenital diseases. Combining patient genome-sequencing data with model organism studies has already provided a wealth of insights into complex LPM-associated birth defects, such as heart-hand syndromes. Here, we summarize developmental and known disease-causing mechanisms in early LPM patterning, address how defects in these processes drive multi-organ comorbidities, and outline how several cardiovascular and hematopoietic birth defects with complex comorbidities may be LPM-associated diseases. We also discuss strategies to integrate patient sequencing, data-aggregating resources and model organism studies to mechanistically decode congenital defects, including potentially LPM-associated orphan diseases. Eventually, linking complex congenital phenotypes to a common LPM origin provides a framework to discover developmental mechanisms and to anticipate comorbidities in congenital diseases affecting the cardiovascular system and beyond.
Collapse
Affiliation(s)
- Agnese Kocere
- University of Colorado School of Medicine, Anschutz Medical Campus, Department of Pediatrics, Section of Developmental Biology, Aurora, CO 80045, USA
- Department of Molecular Life Science, University of Zurich, 8057 Zurich, Switzerland
| | - Robert L. Lalonde
- University of Colorado School of Medicine, Anschutz Medical Campus, Department of Pediatrics, Section of Developmental Biology, Aurora, CO 80045, USA
| | - Christian Mosimann
- University of Colorado School of Medicine, Anschutz Medical Campus, Department of Pediatrics, Section of Developmental Biology, Aurora, CO 80045, USA
| | - Alexa Burger
- University of Colorado School of Medicine, Anschutz Medical Campus, Department of Pediatrics, Section of Developmental Biology, Aurora, CO 80045, USA
| |
Collapse
|
37
|
Aspesi D, Bass N, Kavaliers M, Choleris E. The role of androgens and estrogens in social interactions and social cognition. Neuroscience 2023:S0306-4522(23)00151-3. [PMID: 37080448 DOI: 10.1016/j.neuroscience.2023.03.028] [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: 06/13/2022] [Revised: 03/02/2023] [Accepted: 03/28/2023] [Indexed: 04/22/2023]
Abstract
Gonadal hormones are becoming increasingly recognized for their effects on cognition. Estrogens, in particular, have received attention for their effects on learning and memory that rely upon the functioning of various brain regions. However, the impacts of androgens on cognition are relatively under investigated. Testosterone, as well as estrogens, have been shown to play a role in the modulation of different aspects of social cognition. This review explores the impact of testosterone and other androgens on various facets of social cognition including social recognition, social learning, social approach/avoidance, and aggression. We highlight the relevance of considering not only the actions of the most commonly studied steroids (i.e., testosterone, 17β-estradiol, and dihydrotestosterone), but also that of their metabolites and precursors, which interact with a plethora of different receptors and signalling molecules, ultimately modulating behaviour. We point out that it is also essential to investigate the effects of androgens, their precursors and metabolites in females, as prior studies have mostly focused on males. Overall, a comprehensive analysis of the impact of steroids such as androgens on behaviour is fundamental for a full understanding of the neural mechanisms underlying social cognition, including that of humans.
Collapse
Affiliation(s)
- Dario Aspesi
- Department of Psychology and Neuroscience Program, University of Guelph
| | - Noah Bass
- Department of Psychology and Neuroscience Program, University of Guelph
| | - Martin Kavaliers
- Department of Psychology and Neuroscience Program, University of Guelph; Department of Psychology, University of Western Ontario, London, Canada; Graduate Program in Neuroscience, University of Western Ontario, London, Canada
| | - Elena Choleris
- Department of Psychology and Neuroscience Program, University of Guelph.
| |
Collapse
|
38
|
Sumner S, Favreau E, Geist K, Toth AL, Rehan SM. Molecular patterns and processes in evolving sociality: lessons from insects. Philos Trans R Soc Lond B Biol Sci 2023; 378:20220076. [PMID: 36802779 PMCID: PMC9939270 DOI: 10.1098/rstb.2022.0076] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2022] [Accepted: 09/16/2022] [Indexed: 02/21/2023] Open
Abstract
Social insects have provided some of the clearest insights into the origins and evolution of collective behaviour. Over 20 years ago, Maynard Smith and Szathmáry defined the most complex form of insect social behaviour-superorganismality-among the eight major transitions in evolution that explain the emergence of biological complexity. However, the mechanistic processes underlying the transition from solitary life to superorganismal living in insects remain rather elusive. An overlooked question is whether this major transition arose via incremental or step-wise modes of evolution. We suggest that examination of the molecular processes underpinning different levels of social complexity represented across the major transition from solitary to complex sociality can help address this question. We present a framework for using molecular data to assess to what extent the mechanistic processes that take place in the major transition to complex sociality and superorganismality involve nonlinear (implying step-wise evolution) or linear (implying incremental evolution) changes in the underlying molecular mechanisms. We assess the evidence for these two modes using data from social insects and discuss how this framework can be used to test the generality of molecular patterns and processes across other major transitions. This article is part of a discussion meeting issue 'Collective behaviour through time'.
Collapse
Affiliation(s)
- Seirian Sumner
- Centre for Biodiversity and Environmental Research, Department of Genetics, Evolution and Environment, University College London, Gower Street, London WC1E 6BT, UK
| | - Emeline Favreau
- Centre for Biodiversity and Environmental Research, Department of Genetics, Evolution and Environment, University College London, Gower Street, London WC1E 6BT, UK
| | - Katherine Geist
- Department of Ecology, Evolution and Organismal Biology, and Department of Entomology, Iowa State University, Ames, IA 50011, USA
| | - Amy L. Toth
- Department of Ecology, Evolution and Organismal Biology, and Department of Entomology, Iowa State University, Ames, IA 50011, USA
| | - Sandra M. Rehan
- Department of Biology, York University, Toronto, Canada M3J 1P3
| |
Collapse
|
39
|
Fabian P, Crump JG. Reassessing the embryonic origin and potential of craniofacial ectomesenchyme. Semin Cell Dev Biol 2023; 138:45-53. [PMID: 35331627 PMCID: PMC9489819 DOI: 10.1016/j.semcdb.2022.03.018] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2021] [Revised: 02/28/2022] [Accepted: 03/14/2022] [Indexed: 11/27/2022]
Abstract
Of all the cell types arising from the neural crest, ectomesenchyme is likely the most unusual. In contrast to the neuroglial cells generated by neural crest throughout the embryo, consistent with its ectodermal origin, cranial neural crest-derived cells (CNCCs) generate many connective tissue and skeletal cell types in common with mesoderm. Whether this ectoderm-derived mesenchyme (ectomesenchyme) potential reflects a distinct developmental origin from other CNCC lineages, and/or epigenetic reprogramming of the ectoderm, remains debated. Whereas decades of lineage tracing studies have defined the potential of CNCC ectomesenchyme, these are being revisited by modern genetic techniques. Recent work is also shedding light on the extent to which intrinsic and extrinsic cues determine ectomesenchyme potential, and whether maintenance or reacquisition of CNCC multipotency influences craniofacial repair.
Collapse
Affiliation(s)
- Peter Fabian
- Eli and Edythe Broad California Institute for Regenerative Medicine Center for Regenerative Medicine and Stem Cell Research, Department of Stem Cell Biology and Regenerative Medicine, University of Southern California Keck School of Medicine, Los Angeles, CA 90033, USA
| | - J Gage Crump
- Eli and Edythe Broad California Institute for Regenerative Medicine Center for Regenerative Medicine and Stem Cell Research, Department of Stem Cell Biology and Regenerative Medicine, University of Southern California Keck School of Medicine, Los Angeles, CA 90033, USA.
| |
Collapse
|
40
|
Nanglu K, Cole SR, Wright DF, Souto C. Worms and gills, plates and spines: the evolutionary origins and incredible disparity of deuterostomes revealed by fossils, genes, and development. Biol Rev Camb Philos Soc 2023; 98:316-351. [PMID: 36257784 DOI: 10.1111/brv.12908] [Citation(s) in RCA: 9] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2022] [Revised: 09/23/2022] [Accepted: 09/28/2022] [Indexed: 01/12/2023]
Abstract
Deuterostomes are the major division of animal life which includes sea stars, acorn worms, and humans, among a wide variety of ecologically and morphologically disparate taxa. However, their early evolution is poorly understood, due in part to their disparity, which makes identifying commonalities difficult, as well as their relatively poor early fossil record. Here, we review the available morphological, palaeontological, developmental, and molecular data to establish a framework for exploring the origins of this important and enigmatic group. Recent fossil discoveries strongly support a vermiform ancestor to the group Hemichordata, and a fusiform active swimmer as ancestor to Chordata. The diverse and anatomically bewildering variety of forms among the early echinoderms show evidence of both bilateral and radial symmetry. We consider four characteristics most critical for understanding the form and function of the last common ancestor to Deuterostomia: Hox gene expression patterns, larval morphology, the capacity for biomineralization, and the morphology of the pharyngeal region. We posit a deuterostome last common ancestor with a similar antero-posterior gene regulatory system to that found in modern acorn worms and cephalochordates, a simple planktonic larval form, which was later elaborated in the ambulacrarian lineage, the ability to secrete calcium minerals in a limited fashion, and a pharyngeal respiratory region composed of simple pores. This animal was likely to be motile in adult form, as opposed to the sessile origins that have been historically suggested. Recent debates regarding deuterostome monophyly as well as the wide array of deuterostome-affiliated problematica further suggest the possibility that those features were not only present in the last common ancestor of Deuterostomia, but potentially in the ur-bilaterian. The morphology and development of the early deuterostomes, therefore, underpin some of the most significant questions in the study of metazoan evolution.
Collapse
Affiliation(s)
- Karma Nanglu
- Museum of Comparative Zoology and Department of Organismic and Evolutionary Biology, Harvard University, 26 Oxford Street, Cambridge, MA, 02138, USA
| | - Selina R Cole
- Department of Paleobiology, National Museum of Natural History, Smithsonian Institution, 10th & Constitution Avenue NW, Washington, DC, 20560, USA.,Sam Noble Museum, University of Oklahoma, 2401 Chautauqua Avenue, Norman, OK, 73072, USA.,School of Geosciences, University of Oklahoma, 100 E Boyd Street, Norman, OK, 73019, USA
| | - David F Wright
- Department of Paleobiology, National Museum of Natural History, Smithsonian Institution, 10th & Constitution Avenue NW, Washington, DC, 20560, USA.,Sam Noble Museum, University of Oklahoma, 2401 Chautauqua Avenue, Norman, OK, 73072, USA.,School of Geosciences, University of Oklahoma, 100 E Boyd Street, Norman, OK, 73019, USA
| | - Camilla Souto
- Department of Paleobiology, National Museum of Natural History, Smithsonian Institution, 10th & Constitution Avenue NW, Washington, DC, 20560, USA.,School of Natural Sciences & Mathematics, Stockton University, 101 Vera King Farris Dr, Galloway, NJ, 08205, USA
| |
Collapse
|
41
|
He J, Alonge M, Ramakrishnan S, Benoit M, Soyk S, Reem NT, Hendelman A, Van Eck J, Schatz MC, Lippman ZB. Establishing Physalis as a Solanaceae model system enables genetic reevaluation of the inflated calyx syndrome. THE PLANT CELL 2023; 35:351-368. [PMID: 36268892 PMCID: PMC9806562 DOI: 10.1093/plcell/koac305] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/01/2022] [Accepted: 09/22/2022] [Indexed: 06/16/2023]
Abstract
The highly diverse Solanaceae family contains several widely studied models and crop species. Fully exploring, appreciating, and exploiting this diversity requires additional model systems. Particularly promising are orphan fruit crops in the genus Physalis, which occupy a key evolutionary position in the Solanaceae and capture understudied variation in traits such as inflorescence complexity, fruit ripening and metabolites, disease and insect resistance, self-compatibility, and most notable, the striking inflated calyx syndrome (ICS), an evolutionary novelty found across angiosperms where sepals grow exceptionally large to encapsulate fruits in a protective husk. We recently developed transformation and genome editing in Physalis grisea (groundcherry). However, to systematically explore and unlock the potential of this and related Physalis as genetic systems, high-quality genome assemblies are needed. Here, we present chromosome-scale references for P. grisea and its close relative Physalis pruinosa and use these resources to study natural and engineered variations in floral traits. We first rapidly identified a natural structural variant in a bHLH gene that causes petal color variation. Further, and against expectations, we found that CRISPR-Cas9-targeted mutagenesis of 11 MADS-box genes, including purported essential regulators of ICS, had no effect on inflation. In a forward genetics screen, we identified huskless, which lacks ICS due to mutation of an AP2-like gene that causes sepals and petals to merge into a single whorl of mixed identity. These resources and findings elevate Physalis to a new Solanaceae model system and establish a paradigm in the search for factors driving ICS.
Collapse
Affiliation(s)
- Jia He
- Cold Spring Harbor Laboratory, Cold Spring Harbor, New York 11724, USA
- Howard Hughes Medical Institute, Cold Spring Harbor Laboratory, Cold Spring Harbor, New York 11724, USA
| | | | - Srividya Ramakrishnan
- Department of Computer Science, Johns Hopkins University, Baltimore, Maryland 21218, USA
| | | | | | | | - Anat Hendelman
- Cold Spring Harbor Laboratory, Cold Spring Harbor, New York 11724, USA
| | - Joyce Van Eck
- Boyce Thompson Institute, Ithaca, New York 14853, USA
- Plant Breeding and Genetics Section, School of Integrative Plant Science, Cornell University, Ithaca, New York 14853, USA
| | - Michael C Schatz
- Cold Spring Harbor Laboratory, Cold Spring Harbor, New York 11724, USA
- Department of Computer Science, Johns Hopkins University, Baltimore, Maryland 21218, USA
- Department of Biology, Johns Hopkins University, Baltimore, Maryland 21218, USA
| | | |
Collapse
|
42
|
Anthwal N, Tucker AS. Evolution and development of the mammalian jaw joint: Making a novel structure. Evol Dev 2023; 25:3-14. [PMID: 36504442 PMCID: PMC10078425 DOI: 10.1111/ede.12426] [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: 05/29/2022] [Revised: 11/08/2022] [Accepted: 11/22/2022] [Indexed: 12/14/2022]
Abstract
A jaw joint between the squamosal and dentary is a defining feature of mammals and is referred to as the temporomandibular joint (TMJ) in humans. Driven by changes in dentition and jaw musculature, this new joint evolved early in the mammalian ancestral lineage and permitted the transference of the ancestral jaw joint into the middle ear. The fossil record demonstrates the steps in the cynodont lineage that led to the acquisition of the TMJ, including the expansion of the dentary bone, formation of the coronoid process, and initial contact between the dentary and squamosal. From a developmental perspective, the components of the TMJ form through tissue interactions of muscle and skeletal elements, as well as through interaction between the jaw and the cranial base, with the signals involved in these interactions being both biomechanical and biochemical. In this review, we discuss the development of the TMJ in an evolutionary context. We describe the evolution of the TMJ in the fossil record and the development of the TMJ in embryonic development. We address the formation of key elements of the TMJ and how knowledge from developmental biology can inform our understanding of TMJ evolution.
Collapse
Affiliation(s)
- Neal Anthwal
- Centre for Craniofacial and Regenerative Biology, Faculty of Dentisry, Oral and Craniofacial Sciences, London, UK
| | - Abigail S Tucker
- Centre for Craniofacial and Regenerative Biology, Faculty of Dentisry, Oral and Craniofacial Sciences, London, UK
| |
Collapse
|
43
|
Schlosser G. Rebuilding ships while at sea-Character individuality, homology, and evolutionary innovation. J Morphol 2023; 284:e21522. [PMID: 36282954 PMCID: PMC10100095 DOI: 10.1002/jmor.21522] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2022] [Revised: 09/15/2022] [Accepted: 10/15/2022] [Indexed: 11/05/2022]
Abstract
How novel traits originate in evolution is still one of the most perplexing questions in Evolutionary Biology. Building on a previous account of evolutionary innovation, I here propose that evolutionary novelties are those individualized characters that are not homologous to any characters in the ancestor. To clarify this definition, I here provide a detailed analysis of the concepts of "character individuality" and "homology" first, before addressing their role for our understanding of evolutionary innovation. I will argue (1) that functional as well as structural considerations are important for character individualization; and (2) that compositional (structural) and positional homology need to be clearly distinguished to properly describe the evolutionary transformations of hierarchically structured characters. My account will therefore integrate functional and structural perspectives and put forward a new multi-level view of character identity and transformation.
Collapse
Affiliation(s)
- Gerhard Schlosser
- School of Biological and Chemical Sciences, University of Galway, Galway, Ireland
| |
Collapse
|
44
|
DiFrisco J, Love AC, Wagner GP. The hierarchical basis of serial homology and evolutionary novelty. J Morphol 2023; 284:e21531. [PMID: 36317664 DOI: 10.1002/jmor.21531] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2022] [Revised: 10/26/2022] [Accepted: 10/29/2022] [Indexed: 11/05/2022]
Abstract
Given the pervasiveness of gene sharing in evolution and the extent of homology across the tree of life, why is everything not homologous with everything else? The continuity and overlapping genetic contributions to diverse traits across lineages seem to imply that no discrete determination of homology is possible. Although some argue that the widespread overlap in parts and processes should be acknowledged as "partial" homology, this threatens a broad base of presumed comparative morphological knowledge accepted by most biologists. Following a long scientific tradition, we advocate a strategy of "theoretical articulation" that introduces further distinctions to existing concepts to produce increased contrastive resolution among the labels used to represent biological phenomena. We pursue this strategy by drawing on successful patterns of reasoning from serial homology at the level of gene sequences to generate an enriched characterization of serial homology as a hierarchical, phylogenetic concept. Specifically, we propose that the concept of serial homology should be applied primarily to repeated but developmentally individualized body parts, such as cell types, differentiated body segments, or epidermal appendages. For these characters, a phylogenetic history can be reconstructed, similar to families of paralogous genes, endowing the notion of serial homology with a hierarchical, phylogenetic interpretation. On this basis, we propose a five-fold theoretical classification that permits a more fine-grained mapping of diverse trait-types. This facilitates answering the question of why everything is not homologous with everything else, as well as how novelty is possible given that any new character possesses evolutionary precursors. We illustrate the fecundity of our account by reference to debates over insect wing serial homologs and vertebrate paired appendages.
Collapse
Affiliation(s)
| | - Alan C Love
- Department of Philosophy, University of Minnesota, Minneapolis, Minnesota, USA.,Minnesota Center for Philosophy of Sciences, University of Minnesota, Minneapolis, Minnesota, USA
| | - Günter P Wagner
- Department of Ecology and Evolutionary Biology, Yale University, New Haven, Connecticut, USA.,Yale Systems Biology Institute, Yale University, New Haven, Connecticut, USA.,Department of Obstetrics, Gynecology and Reproductive Sciences, Yale Medical School, New Haven, Connecticut, USA.,Department of Obstetrics and Gynecology, Wayne State University, Detroit, Michigan, USA
| |
Collapse
|
45
|
Regionalization, constraints, and the ancestral ossification patterns in the vertebral column of amniotes. Sci Rep 2022; 12:22257. [PMID: 36564413 PMCID: PMC9789111 DOI: 10.1038/s41598-022-24983-z] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2022] [Accepted: 11/23/2022] [Indexed: 12/24/2022] Open
Abstract
The development of the vertebral column has been studied extensively in modern amniotes, yet many aspects of its evolutionary history remain enigmatic. Here we expand the existing data on four major vertebral developmental patterns in amniotes based on exceptionally well-preserved specimens of the early Permian mesosaurid reptile Mesosaurus tenuidens: (i) centrum ossification, (ii) neural arch ossification, (iii) neural arch fusion, and (iv) neurocentral fusion. We retrace the evolutionary history of each pattern and reconstruct the ancestral condition in amniotes. Despite 300 million years of evolutionary history, vertebral development patterns show a surprisingly stability in amniotes since their common ancestor. We propose that this stability may be linked to conservatism in the constraints posed by underlying developmental processes across amniotes. We also point out that birds, mammals, and squamates each show specific trends deviating from the ancestral condition in amniotes, and that they remain rather unchanged within these lineages. The stability of their unique patterns demonstrates a certain homogeneity of vertebral developmental constraints within these lineages, which we suggest might be linked to their specific modes of regionalization. Our research provides a framework for the evolution of axial development in amniotes and a foundation for future studies.
Collapse
|
46
|
Vöcking O, Macias-Muñoz A, Jaeger SJ, Oakley TH. Deep Diversity: Extensive Variation in the Components of Complex Visual Systems across Animals. Cells 2022; 11:cells11243966. [PMID: 36552730 PMCID: PMC9776813 DOI: 10.3390/cells11243966] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2022] [Revised: 11/19/2022] [Accepted: 12/02/2022] [Indexed: 12/13/2022] Open
Abstract
Understanding the molecular underpinnings of the evolution of complex (multi-part) systems is a fundamental topic in biology. One unanswered question is to what the extent do similar or different genes and regulatory interactions underlie similar complex systems across species? Animal eyes and phototransduction (light detection) are outstanding systems to investigate this question because some of the genetics underlying these traits are well characterized in model organisms. However, comparative studies using non-model organisms are also necessary to understand the diversity and evolution of these traits. Here, we compare the characteristics of photoreceptor cells, opsins, and phototransduction cascades in diverse taxa, with a particular focus on cnidarians. In contrast to the common theme of deep homology, whereby similar traits develop mainly using homologous genes, comparisons of visual systems, especially in non-model organisms, are beginning to highlight a "deep diversity" of underlying components, illustrating how variation can underlie similar complex systems across taxa. Although using candidate genes from model organisms across diversity was a good starting point to understand the evolution of complex systems, unbiased genome-wide comparisons and subsequent functional validation will be necessary to uncover unique genes that comprise the complex systems of non-model groups to better understand biodiversity and its evolution.
Collapse
Affiliation(s)
- Oliver Vöcking
- Department of Biology, University of Kentucky, Lexington, KY 40508, USA
| | - Aide Macias-Muñoz
- Department of Ecology, Evolution, and Marine Biology, University of California, Santa Barbara, CA 93106, USA
| | - Stuart J. Jaeger
- Department of Ecology, Evolution, and Marine Biology, University of California, Santa Barbara, CA 93106, USA
| | - Todd H. Oakley
- Department of Ecology, Evolution, and Marine Biology, University of California, Santa Barbara, CA 93106, USA
- Correspondence:
| |
Collapse
|
47
|
Gene expression changes during the evolution of the tetrapod limb. Biol Futur 2022; 73:411-426. [PMID: 36355308 DOI: 10.1007/s42977-022-00136-1] [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: 07/10/2021] [Accepted: 10/26/2022] [Indexed: 11/11/2022]
Abstract
Major changes in the vertebrate anatomy have preceded the conquest of land by the members of this taxon, and continuous changes in limb shape and use have occurred during the later radiation of tetrapods. While the main, conserved mechanisms of limb development have been discerned over the past century using a combination of classical embryological and molecular methods, only recent advances made it possible to identify and study the regulatory changes that have contributed to the evolution of the tetrapod appendage. These advances include the expansion of the model repertoire from traditional genetic model species to non-conventional ones, a proliferation of predictive mathematical models that describe gene interactions, an explosion in genomic data and the development of high-throughput methodologies. These revolutionary innovations make it possible to identify specific mutations that are behind specific transitions in limb evolution. Also, as we continue to apply them to more and more extant species, we can expect to gain a fine-grained view of this evolutionary transition that has been so consequential for our species as well.
Collapse
|
48
|
Forni G, Mikheyev AS, Luchetti A, Mantovani B. Gene transcriptional profiles in gonads of Bacillus taxa (Phasmida) with different cytological mechanisms of automictic parthenogenesis. ZOOLOGICAL LETTERS 2022; 8:14. [PMID: 36435814 PMCID: PMC9701443 DOI: 10.1186/s40851-022-00197-z] [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: 03/21/2022] [Accepted: 10/07/2022] [Indexed: 06/16/2023]
Abstract
The evolution of automixis - i.e., meiotic parthenogenesis - requires several features, including ploidy restoration after meiosis and maintenance of fertility. Characterizing the relative contribution of novel versus pre-existing genes and the similarities in their expression and sequence evolution is fundamental to understand the evolution of reproductive novelties. Here we identify gonads-biased genes in two Bacillus automictic stick-insects and compare their expression profile and sequence evolution with a bisexual congeneric species. The two parthenogens restore ploidy through different cytological mechanisms: in Bacillus atticus, nuclei derived from the first meiotic division fuse to restore a diploid egg nucleus, while in Bacillus rossius, diploidization occurs in some cells of the haploid blastula through anaphase restitution. Parthenogens' gonads transcriptional program is found to be largely assembled from genes that were already present before the establishment of automixis. The three species transcriptional profiles largely reflect their phyletic relationships, yet we identify a shared core of genes with gonad-biased patterns of expression in parthenogens which are either male gonads-biased in the sexual species or are not differentially expressed there. At the sequence level, just a handful of gonads-biased genes were inferred to have undergone instances of positive selection exclusively in the parthenogen species. This work is the first to explore the molecular underpinnings of automixis in a comparative framework: it delineates how reproductive novelties can be sustained by genes whose origin precedes the establishment of the novelty itself and shows that different meiotic mechanisms of reproduction can be associated with a shared molecular ground plan.
Collapse
Affiliation(s)
- Giobbe Forni
- Dip. Scienze Biologiche, Geologiche e Ambientali (BiGeA), University of Bologna, 40126, Bologna, Italy
- Dip. Scienze Agrarie e Ambientali, University of Milano, Milano, Italy
| | - Alexander S Mikheyev
- Australian National University, ACT, Canberra, 2600, Australia
- Okinawa Institute of Science and Technology, 1919-1 Tancha, Onna-son, Okinawa, 904-0495, Japan
| | - Andrea Luchetti
- Dip. Scienze Biologiche, Geologiche e Ambientali (BiGeA), University of Bologna, 40126, Bologna, Italy.
| | - Barbara Mantovani
- Dip. Scienze Biologiche, Geologiche e Ambientali (BiGeA), University of Bologna, 40126, Bologna, Italy
| |
Collapse
|
49
|
Common evolutionary origin of acoustic communication in choanate vertebrates. Nat Commun 2022; 13:6089. [PMID: 36284092 PMCID: PMC9596459 DOI: 10.1038/s41467-022-33741-8] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2022] [Accepted: 09/30/2022] [Indexed: 12/24/2022] Open
Abstract
Acoustic communication, broadly distributed along the vertebrate phylogeny, plays a fundamental role in parental care, mate attraction and various other behaviours. Despite its importance, comparatively less is known about the evolutionary roots of acoustic communication. Phylogenetic comparative analyses can provide insights into the deep time evolutionary origin of acoustic communication, but they are often plagued by missing data from key species. Here we present evidence for 53 species of four major clades (turtles, tuatara, caecilian and lungfish) in the form of vocal recordings and contextual behavioural information accompanying sound production. This and a broad literature-based dataset evidence acoustic abilities in several groups previously considered non-vocal. Critically, phylogenetic analyses encompassing 1800 species of choanate vertebrates reconstructs acoustic communication as a homologous trait, and suggests that it is at least as old as the last common ancestor of all choanate vertebrates, that lived approx. 407 million years before present.
Collapse
|
50
|
Ford KL, Peterson R, Bernt M, Albert JS. Convergence is Only Skin Deep: Craniofacial Evolution in Electric Fishes from South America and Africa (Apteronotidae and Mormyridae). Integr Org Biol 2022; 4:obac022. [PMID: 35976714 PMCID: PMC9375771 DOI: 10.1093/iob/obac022] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2021] [Revised: 03/31/2022] [Accepted: 06/08/2022] [Indexed: 11/29/2022] Open
Abstract
Apteronotidae and Mormyridae are species-rich clades of weakly electric fishes from Neotropical and Afrotropical freshwaters, respectively, known for their high morphological disparity and often regarded as a classic example of convergent evolution. Here, we use CT-imaging and 3D geometric morphometrics to quantify disparity in craniofacial morphologies, and to test the hypothesis of convergent skull-shape evolution in a phylogenetic context. For this study, we examined 391 specimens representing 78 species of Apteronotidae and Mormyridae including 30 of 37 (81%) of all valid genera with the goal to sample most of the craniofacial disparity known in these clades. We found no overlap between Apteronotidae and Mormyridae in the skull-shape morphospace using PCA and a common landmark scheme, and therefore no instances of complete phenotypic convergence. Instead, we found multiple potential instances of incomplete convergence, and at least one parallel shift among electric fish clades. The greatest components of shape variance in both families are the same as observed for most vertebrate clades: heterocephaly (i.e., opposite changes in relative sizes of the snout and braincase regions of the skull), and heterorhynchy (i.e., dorsoventral changes in relative snout flexion and mouth position). Mormyrid species examined here exhibit less craniofacial disparity than do apteronotids, potentially due to constraints associated with a larger brain size, ecological constraints related to food-type availability. Patterns of craniofacial evolution in these two clades depict a complex story of phenotypic divergence and convergence in which certain superficial similarities of external morphology obscure deeper osteological and presumably developmental differences of skull form and function. Among apteronotid and mormyrid electric fishes, craniofacial convergence is only skin deep.
Collapse
Affiliation(s)
- Kassandra L Ford
- Institute of Ecology and Evolution, Universität Bern , Switzerland
- Department of Fish Ecology and Evolution, Eawag Swiss Federal Institute of Aquatic Science and Technology , Switzerland
- Department of Biology, University of Louisiana at Lafayette , USA
| | - Rose Peterson
- Department of Biological Sciences, George Washington University , USA
| | - Maxwell Bernt
- Department of Biology, University of Louisiana at Lafayette , USA
- Department of Ichthyology, American Museum of Natural History , USA
| | - James S Albert
- Department of Biology, University of Louisiana at Lafayette , USA
| |
Collapse
|