The genetic basis of novel trait gain in walking fish
Posted on: 14 February 2024
Preprint posted on 14 October 2023
Article now published in Current Biology at http://dx.doi.org/10.1016/j.cub.2024.08.042
Ever wondered how a species can create new body parts? Walking fish hold the answer!
Selected by Roberto Rodríguez-Morales
Categories: developmental biology, evolutionary biology, genetics
Background
A central question in evolutionary biology is how organisms change across evolutionary timescales. Broadly speaking, evolutionary changes come in one of two ways. Species can “lose traits”, a term referred to as regressive evolution, or “gain new traits”, a term referred to as constructive evolution. Most studies in this field have uncovered the genetic and environmental underpinnings of regressive evolution, including those underlying eye and pigmentation loss in blind cavefish (Gross, 2012), loss of bristles in flies (Suscena, 2000), and loss of legs in snakes (Leal, 2016). These studies identified discrete genetic loci encoding critical developmental regulators, including cis-regulatory element mutations, that underlie trait loss. However, whether constructive evolution uses similar genetic mechanisms to produce new traits, particularly in vertebrates, remains poorly understood.
The authors of this preprint established a new marine fish model for studying the genetics underlying constructive evolution: the sea robin. These fish are particularly suitable for the study of constructive evolution as they have remarkable evolutionary novelties. These include winglike pectoral fins and six prominent detached “legs” that provide sensory information and the ability to walk, dig, and find food on the ocean floor (Fig. 1a). These new “leg-like” structures are accompanied by increases in muscle, sensory and motor systems which include the formation of novel enlarged lobes in the central nervous system.
In this study, the authors use two sea robin species, Prionotus carolinus and Prionotus evolans, that have differences in pectoral fin size, pigmentation pattern and leg size to uncover the genetic underpinnings of evolutionary novelty in vertebrates.
Figure 1. Sea robin leg development. Novel leg-like structures in sea robins (A, black arrowheads) develop from the bottom three ray fins (B, white arrowheads) of the pectoral fin. Scale bar: 1 mm. (B) Schematic representing tissues collected for RNA-seq before and after leg separation. (D) PCA showing clustering of gene expression profiles of legs with pelvic fins before and after separation. (E) Volcano plot showing upregulated gene expression, including tbx3a, in the future legs compared with the top portion of the pectoral fin before leg separation.
Key findings:
Developmental mechanisms of leg development
Sea robin “legs” form from the three ventral-most pectoral fin rays that separate from the pectoral fin during development (Yuschak, 1984 and 1985). In this preprint, the authors molecularly characterized sea robin leg development by sequencing the genome of P. carolinus and performing tissue-specific RNA sequencing (RNA-seq) before and after the leg rays separate from the pectoral fin. They observed expression of several well-known developmental transcription factors in the separating leg rays, including members of the hox gene family. However, the most upregulated gene in leg rays was the T-box transcription factor tbx3a, which is associated to skeletal alterations of posterior forelimb development in humans.
Functional testing of leg developmental genes
Next, the authors established CRISPR/Cas9 genome editing in sea robins to test the functional relevance of candidate genes derived from their genomics experiment. Using the CRISPR/Cas9 injected fish (or “crispants”), they found that mutating hox genes resulted in a reduced number of legs in sea robins, while mutating tbx3a resulted in variable phenotypes, with the most common being smaller legs. The authors point out that humans heterozygous for TBX3 mutations also exhibit variable forelimb associated phenotypes.
Functional and molecular changes in tbx3a targeted fish
To determine if tbx3a is a genetic driver of leg specification, the authors performed RNA-seq on tbx3a crispants and control siblings before and after leg separation. They found a number of pectoral fin marker genes upregulated in tbx3a crispant leg rays before separation, indicating that these become more “fin-like” in the absence of tbx3a expression.
Next, they examined the novel dorsal accessory spinal lobes of sea robins which are organized in a one-to-one relationship with legs. They found significant reductions in the size of these lobes in tbx3a crispants compared to their control siblings, which were potentially related to their reduced ability to sense and find buried mussels. These results highlight the role of tbx3a in sea robin leg development, behavior and neural function.
Cis- and trans-regulatory control of species-specific differences
Leveraging phenotypic differences between P. carolinus and P. evolans, the authors fully assembled a genome for P. evolans to uncover the genetic underpinnings of trait variation between the two species. Next, using in vitro fertilization, the authors created an F1 hybrid generation between the two species to identify allele-specific expression, specifically the contribution of cis– and trans-acting changes to species-specific phenotypes. A large fraction of the genes differentially expressed between both species showed allele-specific expression in the hybrids, suggesting most of the expression differences between the two species are through cis-regulatory mechanisms. However, the authors provide evidence for trans-regulatory control of tbx3a in the formation of novel epithelial papillae that enhance digging and sensory capabilities in P. carolinus, suggesting that trans-regulation can also be a driver of evolutionary change.
What I like about the preprint/Why this work is important:
Unconventional and non-model organisms most often hold the answers to many exciting questions in evolutionary biology. While some of these have helped uncover the mechanisms underlying trait loss, we still know very little about how novel traits emerge. This preprint from the Kingsley and Bellono labs dives into this question by examining the genetic underpinnings of leg development in two species of sea robin, P. carolinus and P. evolans. Through transcriptomic analysis and the establishment of CRISPR/Cas9 for gene editing in both species, the authors provide a new model for uncovering the genetic underpinnings of constructive evolution.
Questions for the Authors:
- Do you expect tbx3a phenotypic variability to be reduced if you isolate one allele in a stable mutant line? Is there a limitation to create these types of lines (potentially space limitation)?
- Have you thought about creating F2 hybrids to perform QTL analysis of papillae formation and leg development, which could potentially reveal a number of genetic loci and gene candidates involved in this process? Is creating these F2s feasible?
- Are there any plans to study evolution of new lobes in the CNS associated to legs? How do those develop? Are there any known or suspected molecular pathways involved?
References:
- Gross, J. B., Borowsky, R. & Tabin, C. J. A novel role for Mc1r in the parallel evolution of depigmentation in independent populations of the cavefish Astyanax mexicanus. PLoS Genet. 5, (2009).
- Sucena, E. & Stern, D. L. Divergence of larval morphology between Drosophila sechellia and its sibling species caused by cis-regulatory evolution of ovo/shaven-baby. Proc. Natl. Acad. Sci. U.S.A 97, 4530–4534 (2000).
- Leal, F. & Cohn, M. J. Loss and re-emergence of legs in snakes by modular evolution of sonic hedgehog and HOXD enhancers. Curr. Biol. 26, 2966–2973 (2016).
- Yuschak, P. & Lund, W. A. Eggs, larvae and osteological development of the northern searobin, Prionotus carolinus (Pisces, Triglidae). J. Northwest Atl. Fish. Sci. 5, 1–15 (1984).
- Yuschak, P. Fecundity, eggs, larvae and osteological development of the striped searobin, (Prionotus evolans) (Pisces, Triglidae). J. Northwest Atl. Fish. Sci. 6, 65–85 (1985).
doi: https://doi.org/10.1242/prelights.36519
Read preprint
(No Ratings Yet)Sign up to customise the site to your preferences and to receive alerts
Register hereAlso in the developmental biology category:
Cellular signalling protrusions enable dynamic distant contacts in spinal cord neurogenesis
Ankita Walvekar
Actin-based deformations of the nucleus control multiciliated ependymal cell differentiation
Ryan Harrison
HIF1A contributes to the survival of aneuploid and mosaic pre-implantation embryos
Anchel De Jaime Soguero
Also in the evolutionary biology category:
Enhancer-driven cell type comparison reveals similarities between the mammalian and bird pallium
Rodrigo Senovilla-Ganzo
Modular control of time and space during vertebrate axis segmentation
AND
Natural genetic variation quantitatively regulates heart rate and dimension
Girish Kale, Jennifer Ann Black
Fetal brain response to maternal inflammation requires microglia
Manuel Lessi
Also in the genetics category:
Intracellular diffusion in the cytoplasm increases with cell size in fission yeast
Leeba Ann Chacko, Sameer Thukral
HIF1A contributes to the survival of aneuploid and mosaic pre-implantation embryos
Anchel De Jaime Soguero
Significantly reduced, but balanced, rates of mitochondrial fission and fusion are sufficient to maintain the integrity of yeast mitochondrial DNA
Leeba Ann Chacko
preLists in the developmental biology category:
BSDB/GenSoc Spring Meeting 2024
A list of preprints highlighted at the British Society for Developmental Biology and Genetics Society joint Spring meeting 2024 at Warwick, UK.
| List by | Joyce Yu, Katherine Brown |
GfE/ DSDB meeting 2024
This preList highlights the preprints discussed at the 2024 joint German and Dutch developmental biology societies meeting that took place in March 2024 in Osnabrück, Germany.
| List by | Joyce Yu |
‘In preprints’ from Development 2022-2023
A list of the preprints featured in Development's 'In preprints' articles between 2022-2023
| List by | Alex Eve, Katherine Brown |
preLights peer support – preprints of interest
This is a preprint repository to organise the preprints and preLights covered through the 'preLights peer support' initiative.
| List by | preLights peer support |
The Society for Developmental Biology 82nd Annual Meeting
This preList is made up of the preprints discussed during the Society for Developmental Biology 82nd Annual Meeting that took place in Chicago in July 2023.
| List by | Joyce Yu, Katherine Brown |
CSHL 87th Symposium: Stem Cells
Preprints mentioned by speakers at the #CSHLsymp23
| List by | Alex Eve |
Journal of Cell Science meeting ‘Imaging Cell Dynamics’
This preList highlights the preprints discussed at the JCS meeting 'Imaging Cell Dynamics'. The meeting was held from 14 - 17 May 2023 in Lisbon, Portugal and was organised by Erika Holzbaur, Jennifer Lippincott-Schwartz, Rob Parton and Michael Way.
| List by | Helen Zenner |
9th International Symposium on the Biology of Vertebrate Sex Determination
This preList contains preprints discussed during the 9th International Symposium on the Biology of Vertebrate Sex Determination. This conference was held in Kona, Hawaii from April 17th to 21st 2023.
| List by | Martin Estermann |
Alumni picks – preLights 5th Birthday
This preList contains preprints that were picked and highlighted by preLights Alumni - an initiative that was set up to mark preLights 5th birthday. More entries will follow throughout February and March 2023.
| List by | Sergio Menchero et al. |
CellBio 2022 – An ASCB/EMBO Meeting
This preLists features preprints that were discussed and presented during the CellBio 2022 meeting in Washington, DC in December 2022.
| List by | Nadja Hümpfer et al. |
2nd Conference of the Visegrád Group Society for Developmental Biology
Preprints from the 2nd Conference of the Visegrád Group Society for Developmental Biology (2-5 September, 2021, Szeged, Hungary)
| List by | Nándor Lipták |
Fibroblasts
The advances in fibroblast biology preList explores the recent discoveries and preprints of the fibroblast world. Get ready to immerse yourself with this list created for fibroblasts aficionados and lovers, and beyond. Here, my goal is to include preprints of fibroblast biology, heterogeneity, fate, extracellular matrix, behavior, topography, single-cell atlases, spatial transcriptomics, and their matrix!
| List by | Osvaldo Contreras |
EMBL Synthetic Morphogenesis: From Gene Circuits to Tissue Architecture (2021)
A list of preprints mentioned at the #EESmorphoG virtual meeting in 2021.
| List by | Alex Eve |
EMBL Conference: From functional genomics to systems biology
Preprints presented at the virtual EMBL conference "from functional genomics and systems biology", 16-19 November 2020
| List by | Jesus Victorino |
Single Cell Biology 2020
A list of preprints mentioned at the Wellcome Genome Campus Single Cell Biology 2020 meeting.
| List by | Alex Eve |
Society for Developmental Biology 79th Annual Meeting
Preprints at SDB 2020
| List by | Irepan Salvador-Martinez, Martin Estermann |
FENS 2020
A collection of preprints presented during the virtual meeting of the Federation of European Neuroscience Societies (FENS) in 2020
| List by | Ana Dorrego-Rivas |
Planar Cell Polarity – PCP
This preList contains preprints about the latest findings on Planar Cell Polarity (PCP) in various model organisms at the molecular, cellular and tissue levels.
| List by | Ana Dorrego-Rivas |
Cell Polarity
Recent research from the field of cell polarity is summarized in this list of preprints. It comprises of studies focusing on various forms of cell polarity ranging from epithelial polarity, planar cell polarity to front-to-rear polarity.
| List by | Yamini Ravichandran |
TAGC 2020
Preprints recently presented at the virtual Allied Genetics Conference, April 22-26, 2020. #TAGC20
| List by | Maiko Kitaoka et al. |
3D Gastruloids
A curated list of preprints related to Gastruloids (in vitro models of early development obtained by 3D aggregation of embryonic cells). Updated until July 2021.
| List by | Paul Gerald L. Sanchez and Stefano Vianello |
ASCB EMBO Annual Meeting 2019
A collection of preprints presented at the 2019 ASCB EMBO Meeting in Washington, DC (December 7-11)
| List by | Madhuja Samaddar et al. |
EDBC Alicante 2019
Preprints presented at the European Developmental Biology Congress (EDBC) in Alicante, October 23-26 2019.
| List by | Sergio Menchero et al. |
EMBL Seeing is Believing – Imaging the Molecular Processes of Life
Preprints discussed at the 2019 edition of Seeing is Believing, at EMBL Heidelberg from the 9th-12th October 2019
| List by | Dey Lab |
SDB 78th Annual Meeting 2019
A curation of the preprints presented at the SDB meeting in Boston, July 26-30 2019. The preList will be updated throughout the duration of the meeting.
| List by | Alex Eve |
Lung Disease and Regeneration
This preprint list compiles highlights from the field of lung biology.
| List by | Rob Hynds |
Young Embryologist Network Conference 2019
Preprints presented at the Young Embryologist Network 2019 conference, 13 May, The Francis Crick Institute, London
| List by | Alex Eve |
Pattern formation during development
The aim of this preList is to integrate results about the mechanisms that govern patterning during development, from genes implicated in the processes to theoritical models of pattern formation in nature.
| List by | Alexa Sadier |
BSCB/BSDB Annual Meeting 2019
Preprints presented at the BSCB/BSDB Annual Meeting 2019
| List by | Dey Lab |
Zebrafish immunology
A compilation of cutting-edge research that uses the zebrafish as a model system to elucidate novel immunological mechanisms in health and disease.
| List by | Shikha Nayar |
Also in the evolutionary biology category:
‘In preprints’ from Development 2022-2023
A list of the preprints featured in Development's 'In preprints' articles between 2022-2023
| List by | Alex Eve, Katherine Brown |
preLights peer support – preprints of interest
This is a preprint repository to organise the preprints and preLights covered through the 'preLights peer support' initiative.
| List by | preLights peer support |
EMBO | EMBL Symposium: The organism and its environment
This preList contains preprints discussed during the 'EMBO | EMBL Symposium: The organism and its environment', organised at EMBL Heidelberg, Germany (May 2023).
| List by | Girish Kale |
9th International Symposium on the Biology of Vertebrate Sex Determination
This preList contains preprints discussed during the 9th International Symposium on the Biology of Vertebrate Sex Determination. This conference was held in Kona, Hawaii from April 17th to 21st 2023.
| List by | Martin Estermann |
EMBL Synthetic Morphogenesis: From Gene Circuits to Tissue Architecture (2021)
A list of preprints mentioned at the #EESmorphoG virtual meeting in 2021.
| List by | Alex Eve |
Planar Cell Polarity – PCP
This preList contains preprints about the latest findings on Planar Cell Polarity (PCP) in various model organisms at the molecular, cellular and tissue levels.
| List by | Ana Dorrego-Rivas |
TAGC 2020
Preprints recently presented at the virtual Allied Genetics Conference, April 22-26, 2020. #TAGC20
| List by | Maiko Kitaoka et al. |
ECFG15 – Fungal biology
Preprints presented at 15th European Conference on Fungal Genetics 17-20 February 2020 Rome
| List by | Hiral Shah |
COVID-19 / SARS-CoV-2 preprints
List of important preprints dealing with the ongoing coronavirus outbreak. See http://covidpreprints.com for additional resources and timeline, and https://connect.biorxiv.org/relate/content/181 for full list of bioRxiv and medRxiv preprints on this topic
| List by | Dey Lab, Zhang-He Goh |
1
SDB 78th Annual Meeting 2019
A curation of the preprints presented at the SDB meeting in Boston, July 26-30 2019. The preList will be updated throughout the duration of the meeting.
| List by | Alex Eve |
Pattern formation during development
The aim of this preList is to integrate results about the mechanisms that govern patterning during development, from genes implicated in the processes to theoritical models of pattern formation in nature.
| List by | Alexa Sadier |
Also in the genetics category:
BSDB/GenSoc Spring Meeting 2024
A list of preprints highlighted at the British Society for Developmental Biology and Genetics Society joint Spring meeting 2024 at Warwick, UK.
| List by | Joyce Yu, Katherine Brown |
BSCB-Biochemical Society 2024 Cell Migration meeting
This preList features preprints that were discussed and presented during the BSCB-Biochemical Society 2024 Cell Migration meeting in Birmingham, UK in April 2024. Kindly put together by Sara Morais da Silva, Reviews Editor at Journal of Cell Science.
| List by | Reinier Prosee |
9th International Symposium on the Biology of Vertebrate Sex Determination
This preList contains preprints discussed during the 9th International Symposium on the Biology of Vertebrate Sex Determination. This conference was held in Kona, Hawaii from April 17th to 21st 2023.
| List by | Martin Estermann |
Alumni picks – preLights 5th Birthday
This preList contains preprints that were picked and highlighted by preLights Alumni - an initiative that was set up to mark preLights 5th birthday. More entries will follow throughout February and March 2023.
| List by | Sergio Menchero et al. |
Semmelweis Symposium 2022: 40th anniversary of international medical education at Semmelweis University
This preList contains preprints discussed during the 'Semmelweis Symposium 2022' (7-9 November), organised around the 40th anniversary of international medical education at Semmelweis University covering a wide range of topics.
| List by | Nándor Lipták |
20th “Genetics Workshops in Hungary”, Szeged (25th, September)
In this annual conference, Hungarian geneticists, biochemists and biotechnologists presented their works. Link: http://group.szbk.u-szeged.hu/minikonf/archive/prg2021.pdf
| List by | Nándor Lipták |
2nd Conference of the Visegrád Group Society for Developmental Biology
Preprints from the 2nd Conference of the Visegrád Group Society for Developmental Biology (2-5 September, 2021, Szeged, Hungary)
| List by | Nándor Lipták |
EMBL Conference: From functional genomics to systems biology
Preprints presented at the virtual EMBL conference "from functional genomics and systems biology", 16-19 November 2020
| List by | Jesus Victorino |
TAGC 2020
Preprints recently presented at the virtual Allied Genetics Conference, April 22-26, 2020. #TAGC20
| List by | Maiko Kitaoka et al. |
ECFG15 – Fungal biology
Preprints presented at 15th European Conference on Fungal Genetics 17-20 February 2020 Rome
| List by | Hiral Shah |
Autophagy
Preprints on autophagy and lysosomal degradation and its role in neurodegeneration and disease. Includes molecular mechanisms, upstream signalling and regulation as well as studies on pharmaceutical interventions to upregulate the process.
| List by | Sandra Malmgren Hill |
Zebrafish immunology
A compilation of cutting-edge research that uses the zebrafish as a model system to elucidate novel immunological mechanisms in health and disease.
| List by | Shikha Nayar |