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Yuan J, Zhang X, Zhang X, Sun Y, Liu C, Li S, Yu Y, Zhang C, Jin S, Wang M, Xiang J, Li F. An ancient whole-genome duplication in barnacles contributes to their diversification and intertidal sessile life adaptation. J Adv Res 2024; 62:91-103. [PMID: 37734567 PMCID: PMC11331182 DOI: 10.1016/j.jare.2023.09.015] [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: 01/26/2023] [Revised: 09/01/2023] [Accepted: 09/18/2023] [Indexed: 09/23/2023] Open
Abstract
INTRODUCTION Whole-genome duplication (WGD) is one of the most sudden and dramatic events rarely reported in invertebrates, but its occurrence can lead to physiological, morphological, and behavioral diversification. WGD has also never been reported in barnacles, which is one of the most unique groups of crustaceans with extremely speciallized morphology (calcareous shells) and habits (intertidal sessile lifestyle). OBJECTIVES To investigate whether WGD has occurred in barnacles and examine its potential role in driving the adaptive evolution and diversification of barnacles. METHODS Based on a newly sequenced and assembled chromosome-level barnacle genome, a novel WGD event has been identified in barnacles through a comprehensive analysis of interchromosomal synteny, the Hox gene cluster, and synonymous substitution distribution. RESULTS We provide ample evidences for WGD in the barnacle genomes. Comparative genomic analysis indicates that this WGD event predates the divergence of Thoracicalcarea, occurring more than 247 million years ago. The retained ohnologs from the WGD are primarily enriched in various pathways related to environmental information processing, shedding light on the adaptive evolution and diversification of intertidal sessile lifestyle. In addition, transcriptomic analyses show that most of these ohnologs were differentially expressed following the ebb of tide. And the cytochrome P450 ohnologs with differential expression patterns are subject to subfunctionalization and/or neofunctionalization for intertidal adaptation. Besides WGD, parallel evolution underlying intertidal adaptation has also occurred in barnacles. CONCLUSION This study revealed an ancient WGD event in the barnacle genomes, which is potentially associated with the origin and diversification of thoracican barnacles, and may have contributed to the adaptive evolution of their intertidal sessile lifestyle.
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Affiliation(s)
- Jianbo Yuan
- CAS and Shandong Province Key Laboratory of Experimental Marine Biology, Center for Ocean Mega-Science, Institute of Oceanology, Chinese Academy of Sciences, Qingdao 266071, China; Laboratory for Marine Biology and Biotechnology, Qingdao National Laboratory for Marine Science and Technology, Qingdao 266237, China
| | - Xiaojun Zhang
- CAS and Shandong Province Key Laboratory of Experimental Marine Biology, Center for Ocean Mega-Science, Institute of Oceanology, Chinese Academy of Sciences, Qingdao 266071, China; Laboratory for Marine Biology and Biotechnology, Qingdao National Laboratory for Marine Science and Technology, Qingdao 266237, China
| | - Xiaoxi Zhang
- CAS and Shandong Province Key Laboratory of Experimental Marine Biology, Center for Ocean Mega-Science, Institute of Oceanology, Chinese Academy of Sciences, Qingdao 266071, China
| | - Yamin Sun
- Research Center for Functional Genomics and Biochip, Tianjin 300457, China
| | - Chengzhang Liu
- CAS and Shandong Province Key Laboratory of Experimental Marine Biology, Center for Ocean Mega-Science, Institute of Oceanology, Chinese Academy of Sciences, Qingdao 266071, China; Laboratory for Marine Biology and Biotechnology, Qingdao National Laboratory for Marine Science and Technology, Qingdao 266237, China
| | - Shihao Li
- CAS and Shandong Province Key Laboratory of Experimental Marine Biology, Center for Ocean Mega-Science, Institute of Oceanology, Chinese Academy of Sciences, Qingdao 266071, China; Laboratory for Marine Biology and Biotechnology, Qingdao National Laboratory for Marine Science and Technology, Qingdao 266237, China
| | - Yang Yu
- CAS and Shandong Province Key Laboratory of Experimental Marine Biology, Center for Ocean Mega-Science, Institute of Oceanology, Chinese Academy of Sciences, Qingdao 266071, China; Laboratory for Marine Biology and Biotechnology, Qingdao National Laboratory for Marine Science and Technology, Qingdao 266237, China
| | - Chengsong Zhang
- CAS and Shandong Province Key Laboratory of Experimental Marine Biology, Center for Ocean Mega-Science, Institute of Oceanology, Chinese Academy of Sciences, Qingdao 266071, China; Laboratory for Marine Biology and Biotechnology, Qingdao National Laboratory for Marine Science and Technology, Qingdao 266237, China
| | - Songjun Jin
- CAS and Shandong Province Key Laboratory of Experimental Marine Biology, Center for Ocean Mega-Science, Institute of Oceanology, Chinese Academy of Sciences, Qingdao 266071, China; Laboratory for Marine Biology and Biotechnology, Qingdao National Laboratory for Marine Science and Technology, Qingdao 266237, China
| | - Min Wang
- TEDA Institute of Biological Sciences and Biotechnology, Nankai University, Tianjin 300457, China; Key Laboratory of Molecular Microbiology and Technology, Ministry of Education, Nankai University, Tianjin 300071, China.
| | - Jianhai Xiang
- CAS and Shandong Province Key Laboratory of Experimental Marine Biology, Center for Ocean Mega-Science, Institute of Oceanology, Chinese Academy of Sciences, Qingdao 266071, China; Laboratory for Marine Biology and Biotechnology, Qingdao National Laboratory for Marine Science and Technology, Qingdao 266237, China.
| | - Fuhua Li
- CAS and Shandong Province Key Laboratory of Experimental Marine Biology, Center for Ocean Mega-Science, Institute of Oceanology, Chinese Academy of Sciences, Qingdao 266071, China; Laboratory for Marine Biology and Biotechnology, Qingdao National Laboratory for Marine Science and Technology, Qingdao 266237, China.
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Johns JW, Min Y, Ballerini ES, Kramer EM, Hodges SA. Loss of staminodes in Aquilegia jonesii reveals a fading stamen-staminode boundary. EvoDevo 2024; 15:6. [PMID: 38796457 PMCID: PMC11127400 DOI: 10.1186/s13227-024-00225-3] [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: 03/19/2024] [Accepted: 05/09/2024] [Indexed: 05/28/2024] Open
Abstract
The modification of fertile stamens into sterile staminodes has occurred independently many times in the flowering plant lineage. In the genus Aquilegia (columbine) and its closest relatives, the two stamen whorls closest to the carpels have been converted to staminodes. In Aquilegia, the only genetic analyses of staminode development have been reverse genetic approaches revealing that B-class floral identity genes are involved. A. jonesii, the only species of columbine where staminodes have reverted to fertile stamens, allows us to explore the genetic architecture of staminode development using a forward genetic approach. We performed QTL analysis using an outcrossed F2 population between A. jonesii and a horticultural variety that makes fully developed staminodes, A. coerulea 'Origami'. Our results reveal a polygenic basis for staminode loss where the two staminode whorls are under some level of independent control. We also discovered that staminode loss in A. jonesii is not complete, in which staminode-like traits sometimes occur in the inner fertile stamens, potentially representing a fading boundary of gene expression. The QTLs identified in this study provide a map to guide future reverse genetic and functional studies examining the genetic basis and evolutionary significance of this trait.
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Affiliation(s)
- Jason W Johns
- Department of Ecology, Evolution, and Marine Biology, University of California Santa Barbara, Santa Barbara, CA, 93106, USA.
| | - Ya Min
- Department of Ecology and Evolutionary Biology, University of Connecticut, 75 N. Eagleville Rd., Unit 3043, Storrs, CT, 06269, USA
| | - Evangeline S Ballerini
- Department of Biological Sciences, California State University Sacramento, 6000 J. St., Sacramento, 95819, CA, USA
| | - Elena M Kramer
- Department of Organismic and Evolutionary Biology, Harvard University, 16 Divinity Ave., Cambridge, 02138, MA, USA
| | - Scott A Hodges
- Department of Ecology, Evolution, and Marine Biology, University of California Santa Barbara, Santa Barbara, CA, 93106, USA.
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Blaxter M, Lawniczak M. The genome sequence of the crab hacker barnacle, Sacculina carcini (Thompson, 1836). Wellcome Open Res 2023. [DOI: 10.12688/wellcomeopenres.18936.1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/22/2023] Open
Abstract
We present a genome assembly from an individual female Sacculina carcini (crab hacker barnacle; Arthropoda; Crustacea; Thecostraca; Sacculinidae). The genome sequence is 264 megabases in span. Most of the assembly is scaffolded into 28 chromosomal pseudomolecules plus 10 unlocalised. The mitochondrial genome was not identified.
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Martin S, Lesny P, Glenner H, Hecht J, Vilcinskas A, Bartolomaeus T, Podsiadlowski L. Genomic Adaptations to an Endoparasitic Lifestyle in the Morphologically Atypical Crustacean Sacculina carcini (Cirripedia: Rhizocephala). Genome Biol Evol 2022; 14:6758533. [PMID: 36221914 PMCID: PMC9582164 DOI: 10.1093/gbe/evac149] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2021] [Revised: 09/16/2022] [Accepted: 09/26/2022] [Indexed: 01/24/2023] Open
Abstract
The endoparasitic crustacean Sacculina carcini (Cirripedia: Rhizocephala) has a much simpler morphology than conventional filter-feeding barnacles, reflecting its parasitic lifestyle. To investigate the molecular basis of its refined developmental program, we produced a draft genome sequence for comparison with the genomes of nonparasitic barnacles and characterized the transcriptomes of internal and external tissues. The comparison of clusters of orthologous genes revealed the depletion of multiple gene families but also several unanticipated expansions compared to non-parasitic crustaceans. Transcriptomic analyses comparing interna and externa tissues revealed an unexpected variation of gene expression between rootlets sampled around host midgut and thoracic ganglia. Genes associated with lipid uptake were strongly expressed by the internal tissues. We identified candidate genes probably involved in host manipulation (suppression of ecdysis and gonad development) including those encoding crustacean neurohormones and the juvenile hormone binding protein. The evolution of Rhizocephala therefore appears to have involved a rapid turnover of genes (losses and expansions) as well as the fine tuning of gene expression.
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Affiliation(s)
- Sebastian Martin
- Centre for Molecular Biodiversity Research (zmb), Zoological Research Museum Alexander Koenig (ZFMK), LIB, Bonn, Germany,Department of Comparative Ultrastructure and Evolution of Invertebrates, Institute for Evolutionary Biology & Animal Ecology, University Bonn, Bonn, Germany
| | - Peter Lesny
- Department of Comparative Ultrastructure and Evolution of Invertebrates, Institute for Evolutionary Biology & Animal Ecology, University Bonn, Bonn, Germany
| | - Henrik Glenner
- Department of Biol. Sciences, University Bergen, Bergen, Norway,Centre for Macroecology, Evolution and Climate, Copenhagen, Denmark
| | - Jochen Hecht
- Genomics Unit, Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Barcelona, Spain
| | - Andreas Vilcinskas
- Department of Insect Biotechnology, Justus-Liebig-University of Giessen, Giessen, Germany,Department of Bioressources, Fraunhofer Institute for Molecular Biology and Applied Ecology, Giessen, Germany
| | - Thomas Bartolomaeus
- Department of Comparative Ultrastructure and Evolution of Invertebrates, Institute for Evolutionary Biology & Animal Ecology, University Bonn, Bonn, Germany
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Cabin Z, Derieg NJ, Garton A, Ngo T, Quezada A, Gasseholm C, Simon M, Hodges SA. Non-pollinator selection for a floral homeotic mutant conferring loss of nectar reward in Aquilegia coerulea. Curr Biol 2022; 32:1332-1341.e5. [PMID: 35176226 DOI: 10.1016/j.cub.2022.01.066] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2021] [Revised: 11/12/2021] [Accepted: 01/21/2022] [Indexed: 12/12/2022]
Abstract
Here, we describe a polymorphic population of Aquilegia coerulea with a naturally occurring floral homeotic mutant, A. coerulea var. daileyae, where the characteristic petals with nectar spurs are replaced with a second set of sepals. Although it would be expected that this loss of pollinator reward would be disadvantageous to the mutant, we find that it has reached relatively high frequency (∼25%) and is under strong, positive selection across multiple seasons (s = 0.17-0.3) primarily due to reduced floral herbivory. We identify the underlying locus (APETALA3-3) and multiple causal loss-of-function mutations indicating an ongoing soft sweep. Elevated linkage disequilibrium around the two most common causal alleles indicates that positive selection has been occurring for many generations. Lastly, genotypic frequencies at AqAP3-3 indicate a degree of positive assortative mating by morphology. Together, these data provide both a compelling example that large-scale discontinuous morphological changes differentiating taxa can occur due to single mutations and a particularly clear example of linking genotype, phenotype, and fitness.
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Affiliation(s)
- Zachary Cabin
- Department of Ecology, Evolution, and Marine Biology, University of California, Santa Barbara, Santa Barbara, CA 93106, USA.
| | - Nathan J Derieg
- Department of Ecology, Evolution, and Marine Biology, University of California, Santa Barbara, Santa Barbara, CA 93106, USA
| | - Alexandra Garton
- Department of Ecology, Evolution, and Marine Biology, University of California, Santa Barbara, Santa Barbara, CA 93106, USA
| | - Timothy Ngo
- Department of Ecology, Evolution, and Marine Biology, University of California, Santa Barbara, Santa Barbara, CA 93106, USA
| | - Ashley Quezada
- Department of Ecology, Evolution, and Marine Biology, University of California, Santa Barbara, Santa Barbara, CA 93106, USA
| | - Constantine Gasseholm
- Department of Ecology, Evolution, and Marine Biology, University of California, Santa Barbara, Santa Barbara, CA 93106, USA
| | - Mark Simon
- Department of Ecology, Evolution, and Marine Biology, University of California, Santa Barbara, Santa Barbara, CA 93106, USA
| | - Scott A Hodges
- Department of Ecology, Evolution, and Marine Biology, University of California, Santa Barbara, Santa Barbara, CA 93106, USA.
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Persons WS, Currie PJ. Feather evolution exemplifies sexually selected bridges across the adaptive landscape. Evolution 2019; 73:1686-1694. [PMID: 31359437 DOI: 10.1111/evo.13795] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2019] [Accepted: 06/17/2019] [Indexed: 11/26/2022]
Abstract
Over the last two decades, paleontologists have pieced together the early evolutionary history of feathers. Simple hair-like feathers served as insulating pelage, but the first feathers with complex branching structures and a plainer form evolved for the purpose of sexual display. The evolution of these complex display feathers was essential to the later evolution of flight. Feathers illustrate how sexual selection can generate complex novel phenotypes, which are then available for natural selection to modify and direct toward novel functions. In the longstanding metaphor of the adaptive landscape, sexual selection is a means by which lineages resting on one adaptive peak may gradually bridge a gap to another peak, without the landscape itself being first altered by environmental changes.
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Affiliation(s)
- W Scott Persons
- Mace Brown Museum of Natural History, College of Charleston, Charleston, South Carolina, 29424
| | - Philip J Currie
- Department of Biological Sciences, University of Alberta, Edmonton, Alberta, T6G 2E9, Canada
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Posterior Hox gene reduction in an arthropod: Ultrabithorax and Abdominal-B are expressed in a single segment in the mite Archegozetes longisetosus. EvoDevo 2013; 4:23. [PMID: 23991696 PMCID: PMC3766265 DOI: 10.1186/2041-9139-4-23] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2013] [Accepted: 07/15/2013] [Indexed: 01/18/2023] Open
Abstract
Background Hox genes encode transcription factors that have an ancestral role in all bilaterian animals in specifying regions along the antero-posterior axis. In arthropods (insects, crustaceans, myriapods and chelicerates), Hox genes function to specify segmental identity, and changes in Hox gene expression domains in different segments have been causal to the evolution of novel arthropod morphologies. Despite this, the roles of Hox genes in arthropods that have secondarily lost or reduced their segmental composition have been relatively unexplored. Recent data suggest that acariform mites have a reduced segmental component of their posterior body tagma, the opisthosoma, in that only two segments are patterned during embryogenesis. This is in contrast to the observation that in many extinct and extant chelicerates (that is, horseshoe crabs, scorpions, spiders and harvestmen) the opisthosoma is comprised of ten or more segments. To explore the role of Hox genes in this reduced body region, we followed the expression of the posterior-patterning Hox genes Ultrabithorax (Ubx) and Abdominal-B (Abd-B), as well as the segment polarity genes patched (ptc) and engrailed (en), in the oribatid mite Archegozetes longisetosus. Results We find that the expression patterns of ptc are in agreement with previous reports of a reduced mite opisthosoma. In comparison to the ptc and en expression patterns, we find that Ubx and Abd-B are expressed in a single segment in A. longisetosus, the second opisthosomal segment. Abd-B is initially expressed more posteriorly than Ubx, that is, into the unsegmented telson; however, this domain clears in subsequent stages where it remains in the second opisthosomal segment. Conclusions Our findings suggest that Ubx and Abd-B are expressed in a single segment in the opisthosoma. This is a novel observation, in that these genes are expressed in several segments in all studied arthropods. These data imply that a reduction in opisthosomal segmentation may be tied to a dramatically reduced Hox gene input in the opisthosoma.
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Holland PWH. Evolution of homeobox genes. WILEY INTERDISCIPLINARY REVIEWS-DEVELOPMENTAL BIOLOGY 2012; 2:31-45. [DOI: 10.1002/wdev.78] [Citation(s) in RCA: 179] [Impact Index Per Article: 14.9] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
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Niehrs C. On growth and form: a Cartesian coordinate system of Wnt and BMP signaling specifies bilaterian body axes. Development 2010; 137:845-57. [DOI: 10.1242/dev.039651] [Citation(s) in RCA: 197] [Impact Index Per Article: 14.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
The regulation of body axis specification in the common ancestor of bilaterians remains controversial. BMP signaling appears to be an ancient program for patterning the secondary, or dorsoventral, body axis, but any such program for the primary, or anteroposterior, body axis is debated. Recent work in invertebrates indicates that posterior Wnt/β-catenin signaling is such a mechanism and that it evolutionarily predates the cnidarian-bilaterian split. Here, I argue that a Cartesian coordinate system of positional information set up by gradients of perpendicular Wnt and BMP signaling is conserved in bilaterians, orchestrates body axis patterning and contributes to both the relative invariance and diversity of body forms.
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Affiliation(s)
- Christof Niehrs
- Division of Molecular Embryology, DKFZ-ZMBH Alliance, Deutsches Krebsforschungszentrum, Im Neuenheimer Feld 280, D-69120 Heidelberg, Germany
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Theissen G. Saltational evolution: hopeful monsters are here to stay. Theory Biosci 2009; 128:43-51. [PMID: 19224263 DOI: 10.1007/s12064-009-0058-z] [Citation(s) in RCA: 56] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2009] [Accepted: 01/27/2009] [Indexed: 10/21/2022]
Abstract
Since 150 years it is hypothesized now that evolution always proceeds in a countless number of very small steps (Darwin in On the origin of species by means of natural selection or the preservation of favoured races in the struggle of life, Murray, London, 1859), a view termed "gradualism". Few contemporary biologists will doubt that gradualism reflects the most frequent mode of evolution, but whether it is the only one remains controversial. It has been suggested that in some cases profound ("saltational") changes may have occurred within one or a few generations of organisms. Organisms with a profound mutant phenotype that have the potential to establish a new evolutionary lineage have been termed "hopeful monsters". Recently I have reviewed the concept of hopeful monsters in this journal mainly from a historical perspective, and provided some evidence for their past and present existence. Here I provide a brief update on data and discussions supporting the view that hopeful monsters and saltational evolution are valuable biological concepts. I suggest that far from being mutually exclusive scenarios, both gradual and saltational evolution are required to explain the complexity and diversity of life on earth. In my view, gradual changes represent the usual mode of evolution, but are unlikely to be able to explain all key innovations and changes in body plans. Saltational changes involving hopeful monsters are probably very exceptional events, but since they have the potential to establish profound novelties sometimes facilitating adaptive radiations, they are of quite some importance, even if they would occur in any evolutionary lineage less than once in a million years. From that point of view saltational changes are not more bizarre scenarios of evolutionary change than whole genome duplications, endosymbiosis or impacts of meteorites. In conclusion I argue that the complete dismissal of saltational evolution is a major historical error of evolutionary biology tracing back to Darwin that needs to be rectified.
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Affiliation(s)
- Günter Theissen
- Department of Genetics, Friedrich Schiller University Jena, Jena, Germany.
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