1
|
Klementz BC, Brenneis G, Hinne IA, Laumer EM, Neu SM, Hareid GM, Gainett G, Setton EVW, Simian C, Vrech DE, Joyce I, Barnett AA, Patel NH, Harvey MS, Peretti AV, Gulia-Nuss M, Sharma PP. A Novel Expression Domain of extradenticle Underlies the Evolutionary Developmental Origin of the Chelicerate Patella. Mol Biol Evol 2024; 41:msae188. [PMID: 39235104 PMCID: PMC11422720 DOI: 10.1093/molbev/msae188] [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: 05/16/2024] [Revised: 08/02/2024] [Accepted: 08/30/2024] [Indexed: 09/06/2024] Open
Abstract
Neofunctionalization of duplicated gene copies is thought to be an important process underlying the origin of evolutionary novelty and provides an elegant mechanism for the origin of new phenotypic traits. One putative case where a new gene copy has been linked to a novel morphological trait is the origin of the arachnid patella, a taxonomically restricted leg segment. In spiders, the origin of this segment has been linked to the origin of the paralog dachshund-2, suggesting that a new gene facilitated the expression of a new trait. However, various arachnid groups that possess patellae do not have a copy of dachshund-2, disfavoring the direct link between gene origin and trait origin. We investigated the developmental genetic basis for patellar patterning in the harvestman Phalangium opilio, which lacks dachshund-2. Here, we show that the harvestman patella is established by a novel expression domain of the transcription factor extradenticle. Leveraging this definition of patellar identity, we surveyed targeted groups across chelicerate phylogeny to assess when this trait evolved. We show that a patellar homolog is present in Pycnogonida (sea spiders) and various arachnid orders, suggesting a single origin of the patella in the ancestor of Chelicerata. A potential loss of the patella is observed in Ixodida. Our results suggest that the modification of an ancient gene, rather than the neofunctionalization of a new gene copy, underlies the origin of the patella. Broadly, this work underscores the value of comparative data and broad taxonomic sampling when testing hypotheses in evolutionary developmental biology.
Collapse
Affiliation(s)
- Benjamin C Klementz
- Department of Integrative Biology, University of Wisconsin-Madison, Madison, WI, USA
- University of Wisconsin-Madison Zoological Museum, University of Wisconsin-Madison, Madison, WI, USA
| | - Georg Brenneis
- Unit Integrative Zoologie, Department Evolutionsbiologie, Universität Wien, Vienna, Austria
| | - Isaac A Hinne
- Department of Biochemistry and Molecular Biology, University of Nevada, Reno, NV, USA
| | - Ethan M Laumer
- Department of Integrative Biology, University of Wisconsin-Madison, Madison, WI, USA
- University of Wisconsin-Madison Zoological Museum, University of Wisconsin-Madison, Madison, WI, USA
| | - Sophie M Neu
- Department of Integrative Biology, University of Wisconsin-Madison, Madison, WI, USA
- University of Wisconsin-Madison Zoological Museum, University of Wisconsin-Madison, Madison, WI, USA
| | - Grace M Hareid
- Department of Integrative Biology, University of Wisconsin-Madison, Madison, WI, USA
- University of Wisconsin-Madison Zoological Museum, University of Wisconsin-Madison, Madison, WI, USA
| | - Guilherme Gainett
- Department of Integrative Biology, University of Wisconsin-Madison, Madison, WI, USA
- Department of Systems Biology, Harvard Medical School, Boston, MA, USA
- Department of Pathology, Boston Children,'s Hospital, Boston, MA, USA
| | - Emily V W Setton
- Department of Integrative Biology, University of Wisconsin-Madison, Madison, WI, USA
- Department of Ecology and Evolutionary Biology, Cornell University, Ithaca, NY, USA
| | - Catalina Simian
- Laboratorio de Biología Reproductiva y Evolución, Instituto de Diversidad y Ecología Animal (IDEA), Consejo Nacional de Investigaciones Cientifícas Técnicas (CONICET), Universidad Nacional de Córdoba, Córdoba, Argentina
| | - David E Vrech
- Laboratorio de Biología Reproductiva y Evolución, Instituto de Diversidad y Ecología Animal (IDEA), Consejo Nacional de Investigaciones Cientifícas Técnicas (CONICET), Universidad Nacional de Córdoba, Córdoba, Argentina
| | - Isabella Joyce
- Department of Biology, DeSales University, Center Valley, PA, USA
| | - Austen A Barnett
- Department of Biology, DeSales University, Center Valley, PA, USA
| | - Nipam H Patel
- Marine Biological Laboratory, Woods Hole, MA, USA
- Organismal Biology & Anatomy, University of Chicago, Chicago, IL, USA
| | - Mark S Harvey
- Collections & Research, Western Australian Museum, Welshpool, WA, Australia
| | - Alfredo V Peretti
- Laboratorio de Biología Reproductiva y Evolución, Instituto de Diversidad y Ecología Animal (IDEA), Consejo Nacional de Investigaciones Cientifícas Técnicas (CONICET), Universidad Nacional de Córdoba, Córdoba, Argentina
| | - Monika Gulia-Nuss
- Department of Biochemistry and Molecular Biology, University of Nevada, Reno, NV, USA
| | - Prashant P Sharma
- Department of Integrative Biology, University of Wisconsin-Madison, Madison, WI, USA
- University of Wisconsin-Madison Zoological Museum, University of Wisconsin-Madison, Madison, WI, USA
| |
Collapse
|
2
|
Ehemann N, Franchini P, Meyer A, Hulsey CD. Meristic co-evolution and genomic co-localization of lateral line scales and vertebrae in Central American cichlid fishes. Ecol Evol 2024; 14:e70266. [PMID: 39279804 PMCID: PMC11402520 DOI: 10.1002/ece3.70266] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2024] [Revised: 08/12/2024] [Accepted: 08/24/2024] [Indexed: 09/18/2024] Open
Abstract
Meristic traits are often treated as distinct phenotypes that can be used to differentiate and delineate recently diverged species. For instance, the number of lateral line scales and vertebrae, two traits that vary substantially among Neotropical Heroine cichlid species, have been previously suggested to co-evolve. These meristic traits could co-evolve due to shared adaptive, developmental, or genetic factors. If they were found to be genetically or developmentally non-independent, this might require a more general re-evaluation of their role in evolutionary or taxonomic studies. We expanded a previous analysis of correlated evolution of meristic traits (lateral line scales and vertebrae counts) in these fishes to include a range of phylogenetic reconstructions as well as the analyses of 13 Nicaraguan Midas cichlid species (Amphilophus spp.). Additionally, we performed qualitative traits locus (QTL) mapping in a F2 laboratory-reared hybrid population from two ecologically divergent Midas cichlid fish species to discover and evaluate whether genomic co-segregation might explain the observed patterns of meristic co-evolution. Meristic values for these traits were found to morphologically differentiate some species of the Midas cichlid adaptive radiation. Our QTL analysis pinpointed several genomic regions associated with divergence in these traits and highlighted the potential for genomic co-segregation of the lateral line and vertebrae numbers on two chromosomes. Further, our phylogenetic comparative analyses consistently recovered a significant positive evolutionary correlation between the counts of lateral line scale and vertebrae numbers in Neotropical cichlids. Hence, the findings of genomic co-segregation could partially explain the co-evolution of these two meristic traits in these species. Continuing to unravel the genetic architecture governing meristic divergence helps to better understand both trait correlations and the utility of meristic traits in taxonomic diagnoses and how traits in phenotypes might be expected to co-evolve.
Collapse
Affiliation(s)
| | - Paolo Franchini
- Department of BiologyUniversity of KonstanzKonstanzGermany
- Department of Ecological and Biological SciencesTuscia UniversityViterboItaly
| | - Axel Meyer
- Department of BiologyUniversity of KonstanzKonstanzGermany
- Museum of Comparative ZoologyHarvard UniversityCambridgeMassachusettsUSA
- CAS Key Laboratory of Tropical Marine Bio‐Resources and EcologySouth China Sea Institute of Oceanology, Chinese Academy of SciencesGuangzhouChina
| | - C. Darrin Hulsey
- Department of BiologyUniversity of KonstanzKonstanzGermany
- School of Biology and Environmental ScienceUniversity College DublinDublinIreland
| |
Collapse
|
3
|
Adachi U, Koita R, Seto A, Maeno A, Ishizu A, Oikawa S, Tani T, Ishizaka M, Yamada K, Satoh K, Nakazawa H, Furudate H, Kawakami K, Iwanami N, Matsuda M, Kawamura A. Teleost Hox code defines regional identities competent for the formation of dorsal and anal fins. Proc Natl Acad Sci U S A 2024; 121:e2403809121. [PMID: 38861596 PMCID: PMC11194558 DOI: 10.1073/pnas.2403809121] [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: 02/24/2024] [Accepted: 05/07/2024] [Indexed: 06/13/2024] Open
Abstract
The dorsal and anal fins can vary widely in position and length along the anterior-posterior axis in teleost fishes. However, the molecular mechanisms underlying the diversification of these fins remain unknown. Here, we used genetic approaches in zebrafish and medaka, in which the relative positions of the dorsal and anal fins are opposite, to demonstrate the crucial role of hox genes in the patterning of the teleost posterior body, including the dorsal and anal fins. By the CRISPR-Cas9-induced frameshift mutations and positional cloning of spontaneous dorsalfinless medaka, we show that various hox mutants exhibit the absence of dorsal or anal fins, or a stepwise posterior extension of these fins, with vertebral abnormalities. Our results indicate that multiple hox genes, primarily from hoxc-related clusters, encompass the regions responsible for the dorsal and anal fin formation along the anterior-posterior axis. These results further suggest that shifts in the anterior boundaries of hox expression which vary among fish species, lead to diversification in the position and size of the dorsal and anal fins, similar to how modulations in Hox expression can alter the number of anatomically distinct vertebrae in tetrapods. Furthermore, we show that hox genes responsible for dorsal fin formation are different between zebrafish and medaka. Our results suggest that a novel mechanism has occurred during teleost evolution, in which the gene network responsible for fin formation might have switched to the regulation downstream of other hox genes, leading to the remarkable diversity in the dorsal fin position.
Collapse
Affiliation(s)
- Urara Adachi
- Division of Life Science, Graduate School of Science and Engineering, Saitama University, Sakura-ku, Saitama338-8570, Japan
| | - Rina Koita
- Division of Life Science, Graduate School of Science and Engineering, Saitama University, Sakura-ku, Saitama338-8570, Japan
| | - Akira Seto
- Center for Bioscience Research and Education, Utsunomiya University, Utsunomiya321-8505, Japan
| | - Akiteru Maeno
- Cell Architecture Laboratory, National Institute of Genetics, Mishima, Shizuoka411-8540, Japan
| | - Atsuki Ishizu
- Division of Life Science, Graduate School of Science and Engineering, Saitama University, Sakura-ku, Saitama338-8570, Japan
| | - Sae Oikawa
- Division of Life Science, Graduate School of Science and Engineering, Saitama University, Sakura-ku, Saitama338-8570, Japan
| | - Taisei Tani
- Division of Life Science, Graduate School of Science and Engineering, Saitama University, Sakura-ku, Saitama338-8570, Japan
| | - Mizuki Ishizaka
- Division of Life Science, Graduate School of Science and Engineering, Saitama University, Sakura-ku, Saitama338-8570, Japan
| | - Kazuya Yamada
- Division of Life Science, Graduate School of Science and Engineering, Saitama University, Sakura-ku, Saitama338-8570, Japan
| | - Koumi Satoh
- Division of Life Science, Graduate School of Science and Engineering, Saitama University, Sakura-ku, Saitama338-8570, Japan
| | - Hidemichi Nakazawa
- Division of Life Science, Graduate School of Science and Engineering, Saitama University, Sakura-ku, Saitama338-8570, Japan
| | - Hiroyuki Furudate
- Division of Life Science, Graduate School of Science and Engineering, Saitama University, Sakura-ku, Saitama338-8570, Japan
| | - Koichi Kawakami
- Laboratory of Molecular and Developmental Biology, National Institute of Genetics, and Department of Genetics, Graduate University for Advanced Studies (SOKENDAI), Mishima, Shizuoka411-8540, Japan
| | - Norimasa Iwanami
- Center for Bioscience Research and Education, Utsunomiya University, Utsunomiya321-8505, Japan
| | - Masaru Matsuda
- Center for Bioscience Research and Education, Utsunomiya University, Utsunomiya321-8505, Japan
| | - Akinori Kawamura
- Division of Life Science, Graduate School of Science and Engineering, Saitama University, Sakura-ku, Saitama338-8570, Japan
| |
Collapse
|
4
|
Clark B, Hickey A, Marconi A, Fischer B, Elkin J, Mateus R, Santos ME. Developmental plasticity and variability in the formation of egg-spots, a pigmentation ornament in the cichlid Astatotilapia calliptera. Evol Dev 2024; 26:e12475. [PMID: 38555511 DOI: 10.1111/ede.12475] [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: 09/10/2023] [Revised: 03/14/2024] [Accepted: 03/18/2024] [Indexed: 04/02/2024]
Abstract
Vertebrate pigmentation patterns are highly diverse, yet we have a limited understanding of how evolutionary changes to genetic, cellular, and developmental mechanisms generate variation. To address this, we examine the formation of a sexually-selected male ornament exhibiting inter- and intraspecific variation, the egg-spot pattern, consisting of circular yellow-orange markings on the male anal fins of haplochromine cichlid fishes. We focus on Astatotilapia calliptera, the ancestor-type species of the Malawi cichlid adaptive radiation of over 850 species. We identify a key role for iridophores in initializing egg-spot aggregations composed of iridophore-xanthophore associations. Despite adult sexual dimorphism, aggregations initially form in both males and females, with development only diverging between the sexes at later stages. Unexpectedly, we found that the timing of egg-spot initialization is plastic. The earlier individuals are socially isolated, the earlier the aggregations form, with iridophores being the cell type that responds to changes to the social environment. Furthermore, we observe apparent competitive interactions between adjacent egg-spot aggregations, which strongly suggests that egg-spot patterning results mostly from cell-autonomous cellular interactions. Together, these results demonstrate that A. calliptera egg-spot development is an exciting model for investigating pigment pattern formation at the cellular level in a system with developmental plasticity, sexual dimorphism, and intraspecific variation. As A. calliptera represents the ancestral bauplan for egg-spots, these findings provide a baseline for informed comparisons across the incredibly diverse Malawi cichlid radiation.
Collapse
Affiliation(s)
- Bethan Clark
- Department of Zoology, University of Cambridge, Cambridge, UK
| | - Aaron Hickey
- Department of Zoology, University of Cambridge, Cambridge, UK
| | | | - Bettina Fischer
- Department of Genetics, University of Cambridge, Cambridge, UK
| | - Joel Elkin
- Department of Zoology, University of Cambridge, Cambridge, UK
| | - Rita Mateus
- Max Planck Institute for Molecular Cell Biology and Genetics, Dresden, Germany
- Cluster of Excellence Physics of Life, TU Dresden, Dresden, Germany
| | - M Emília Santos
- Department of Zoology, University of Cambridge, Cambridge, UK
| |
Collapse
|
5
|
Kudoh H, Yonei‐Tamura S, Abe G, Iwakiri J, Uesaka M, Makino T, Tamura K. Genomic screening of fish-specific genes in gnathostomes and their functions in fin development. Dev Growth Differ 2024; 66:235-247. [PMID: 38439516 PMCID: PMC11457510 DOI: 10.1111/dgd.12918] [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: 11/28/2023] [Revised: 01/18/2024] [Accepted: 02/01/2024] [Indexed: 03/06/2024]
Abstract
In this study, we comprehensively searched for fish-specific genes in gnathostomes that contribute to development of the fin, a fish-specific trait. Many previous reports suggested that animal group-specific genes are often important for group-specific traits. Clarifying the roles of fish-specific genes in fin development of gnathostomes, for example, can help elucidate the mechanisms underlying the formation of this trait. We first identified 91 fish-specific genes in gnathostomes by comparing the gene repertoire in 16 fish and 35 tetrapod species. RNA-seq analysis narrowed down the 91 candidates to 33 genes that were expressed in the developing pectoral fin. We analyzed the functions of approximately half of the candidate genes by loss-of-function analysis in zebrafish. We found that some of the fish-specific and fin development-related genes, including fgf24 and and1/and2, play roles in fin development. In particular, the newly identified fish-specific gene qkia is expressed in the developing fin muscle and contributes to muscle morphogenesis in the pectoral fin as well as body trunk. These results indicate that the strategy of identifying animal group-specific genes is functional and useful. The methods applied here could be used in future studies to identify trait-associated genes in other animal groups.
Collapse
Affiliation(s)
- Hidehiro Kudoh
- Department of Ecological Developmental Adaptability Life SciencesGraduate School of Life Sciences, Tohoku UniversitySendaiJapan
| | - Sayuri Yonei‐Tamura
- Department of Ecological Developmental Adaptability Life SciencesGraduate School of Life Sciences, Tohoku UniversitySendaiJapan
| | - Gembu Abe
- Department of Ecological Developmental Adaptability Life SciencesGraduate School of Life Sciences, Tohoku UniversitySendaiJapan
- Division of Developmental Biology, Department of Functional MorphologySchool of Life Science, Faculty of Medicine, Tottori UniversityYonagoJapan
| | - Junichi Iwakiri
- Department of Computational Biology and Medical SciencesGraduate School of Frontier Sciences, The University of TokyoChibaJapan
| | - Masahiro Uesaka
- Department of Ecological Developmental Adaptability Life SciencesGraduate School of Life Sciences, Tohoku UniversitySendaiJapan
| | - Takashi Makino
- Department of Molecular and Chemical Life SciencesGraduate School of Life Sciences, Tohoku UniversitySendaiJapan
| | - Koji Tamura
- Department of Ecological Developmental Adaptability Life SciencesGraduate School of Life Sciences, Tohoku UniversitySendaiJapan
| |
Collapse
|
6
|
Gavazzi LM, Nair M, Suydam R, Usip S, Thewissen JGM, Cooper LN. Protein signaling and morphological development of the tail fluke in the embryonic beluga whale (Delphinapterus leucas). Dev Dyn 2024. [PMID: 38494595 DOI: 10.1002/dvdy.704] [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: 04/21/2023] [Revised: 02/20/2024] [Accepted: 02/22/2024] [Indexed: 03/19/2024] Open
Abstract
BACKGROUND During the land-to-sea transition of cetaceans (whales, dolphins, and porpoises), the hindlimbs were lost and replaced by an elaborate tail fluke that evolved 32 Ma. All modern cetaceans utilize flukes for lift-based propulsion, and nothing is known of this organ's molecular origins during embryonic development. This study utilizes immunohistochemistry to identify the spatiotemporal location of protein signals known to drive appendage outgrowth in other vertebrates (e.g., Sonic Hedgehog [SHH], GREMLIN [GREM], wingless-type family member 7a [WNT], and fibroblast growth factors [FGFs]) and to test the hypothesis that signals associated with outgrowth and patterning of the tail fluke are similar to a tetrapod limb. Specifically, this study utilizes an embryo of a beluga whale (Delphinapterus leucas) as a case study. RESULTS Results showed epidermal signals of WNT and FGFs, and mesenchymal/epidermal signals of SHH and GREM. These patterns are most consistent with vertebrate limb development. Overall, these data are most consistent with the hypothesis that outgrowth of tail flukes in cetaceans employs a signaling pattern that suggests genes essential for limb outgrowth and patterning shape this evolutionarily novel appendage. CONCLUSIONS While these data add insights into the molecular signals potentially driving the evolution and development of tail flukes in cetaceans, further exploration of the molecular drivers of fluke development is required.
Collapse
Affiliation(s)
- L M Gavazzi
- School of Biomedical Sciences, Kent State University, Kent, Ohio, USA
- Musculoskeletal Research Focus Area, Department of Anatomy and Neurobiology, Northeast Ohio Medical University, Rootstown, Ohio, USA
| | - M Nair
- Wright State University, Dayton, Ohio, USA
| | - R Suydam
- Department of Wildlife Management, North Slope Borough, Utqiaġvik, Alaska, USA
| | - S Usip
- Musculoskeletal Research Focus Area, Department of Anatomy and Neurobiology, Northeast Ohio Medical University, Rootstown, Ohio, USA
| | - J G M Thewissen
- Musculoskeletal Research Focus Area, Department of Anatomy and Neurobiology, Northeast Ohio Medical University, Rootstown, Ohio, USA
| | - L N Cooper
- Musculoskeletal Research Focus Area, Department of Anatomy and Neurobiology, Northeast Ohio Medical University, Rootstown, Ohio, USA
| |
Collapse
|
7
|
Miyamoto K, Abe G, Tamura K. The dwarf neon rainbowfish Melanotaenia praecox, a small spiny-rayed fish with potential as a new Acanthomorpha model fish: I. Fin ray ontogeny and postembryonic staging. Dev Dyn 2024. [PMID: 38323724 DOI: 10.1002/dvdy.699] [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: 03/22/2023] [Revised: 12/14/2023] [Accepted: 01/13/2024] [Indexed: 02/08/2024] Open
Abstract
BACKGROUND Fish fins with highly variable color patterns and morphologies have many functions. In Actinopterygii, the free parts of fins are supported by "soft rays" and "spiny rays." Spiny rays have various functions and are extremely modified in some species, but they are lacking in popular model fish such as zebrafish and medaka. Additionally, some model fish with spiny rays are difficult to maintain in ordinary laboratory systems. RESULTS Characteristics of the small, spiny-rayed rainbowfish Melanotaenia praecox render it useful as an experimental model species. Neither fish age nor body size correlate well with fin development during postembryonic development in this species. A four-stage developmental classification is proposed that is based on fin ray development. CONCLUSIONS Melanotaenia praecox is an ideal species to rear in laboratories for developmental studies. Our classification allows for postembryonic staging of this species independent of individual age and body size. Development of each fin ray may be synchronized with dorsal fin development. We discuss the differences in mechanisms regulating soft, spiny, and procurrent ray development.
Collapse
Affiliation(s)
- Kazuhide Miyamoto
- Department of Ecological Developmental Adaptability Life Sciences, Graduate School of Life Sciences, Tohoku University, Sendai, Japan
| | - Gembu Abe
- Division of Developmental Biology, Department of Functional Morphology, Faculty of Medicine, School of Life Science, Tottori University, Yonago, Japan
| | - Koji Tamura
- Department of Ecological Developmental Adaptability Life Sciences, Graduate School of Life Sciences, Tohoku University, Sendai, Japan
| |
Collapse
|
8
|
Ehemann NR, Meyer A, Hulsey CD. Morphological description of spontaneous pelvic fin loss in a neotropical cichlid fish. J Morphol 2024; 285:e21663. [PMID: 38100744 DOI: 10.1002/jmor.21663] [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: 10/03/2023] [Revised: 11/29/2023] [Accepted: 12/01/2023] [Indexed: 12/17/2023]
Abstract
Pelvic fins are a characteristic structure of the vertebrate Bauplan. Yet, pelvic fin loss has occurred repeatedly across a wide diversity of other lineages of tetrapods and at least 48 times in teleost fishes. This pelvic finless condition is often associated with other morphological features such as body elongation, loss of additional structures, and bilateral asymmetry. However, despite the remarkable diversity in the several thousand cichlid fish species, none of them are characterized by the complete absence of pelvic fins. Here, we examined the musculoskeletal structure and associated bilateral asymmetry in Midas cichlids (Amphilophus cf. citrinellus) that lost their pelvic fins spontaneously in the laboratory. Due to this apparent mutational loss of the pelvic girdle and fins, the external and internal anatomy are described in a series of "normal" Midas individuals and their pelvic finless sibling tankmates. First, other traits associated with teleost pelvic fin loss, the genetic basis of pelvic fin loss, and the potential for pleiotropic effects of these genes on other traits in teleosts were all reviewed. Using these traits as a guide, we investigated whether other morphological differences were associated with the pelvic girdle/fin loss. The mean values of the masses of muscle of the pectoral fin, fin ray numbers in the unpaired fins, and oral jaw tooth numbers did not differ between the two pelvic fin morphotypes. However, significant differences in meristic values of the paired traits assessed were observed for the same side of the body between morphotypes. Notably, bilateral asymmetry was found exclusively for the posterior lateral line scales. Finally, we found limited evidence of pleiotropic effects, such as lateral line scale numbers and fluctuating asymmetry between the Midas pelvic fin morphotypes. The fast and relatively isolated changes in the Midas cichlids suggest minor but interesting pleiotropic effects could accompany loss of cichlid pelvic fins.
Collapse
Affiliation(s)
| | - Axel Meyer
- Department of Biology, University of Konstanz, Konstanz, Germany
| | | |
Collapse
|
9
|
Clark B, Kuwalekar M, Fischer B, Woltering J, Biran J, Juntti S, Kratochwil CF, Santos ME, Almeida MV. Genome editing in East African cichlids and tilapias: state-of-the-art and future directions. Open Biol 2023; 13:230257. [PMID: 38018094 PMCID: PMC10685126 DOI: 10.1098/rsob.230257] [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: 08/02/2023] [Accepted: 10/27/2023] [Indexed: 11/30/2023] Open
Abstract
African cichlid fishes of the Cichlidae family are a group of teleosts important for aquaculture and research. A thriving research community is particularly interested in the cichlid radiations of the East African Great Lakes. One key goal is to pinpoint genetic variation underlying phenotypic diversification, but the lack of genetic tools has precluded thorough dissection of the genetic basis of relevant traits in cichlids. Genome editing technologies are well established in teleost models like zebrafish and medaka. However, this is not the case for emerging model organisms, such as East African cichlids, where these technologies remain inaccessible to most laboratories, due in part to limited exchange of knowledge and expertise. The Cichlid Science 2022 meeting (Cambridge, UK) hosted for the first time a Genome Editing Workshop, where the community discussed recent advances in genome editing, with an emphasis on CRISPR/Cas9 technologies. Based on the workshop findings and discussions, in this review we define the state-of-the-art of cichlid genome editing, share resources and protocols, and propose new possible avenues to further expand the cichlid genome editing toolkit.
Collapse
Affiliation(s)
- Bethan Clark
- Department of Zoology, University of Cambridge, Cambridge, UK
| | - Muktai Kuwalekar
- Helsinki Institute of Life Science (HiLIFE), University of Helsinki, Helsinki, Uusimaa 00014, Finland
- Faculty of Biological and Environmental Sciences, University of Helsinki, Helsinki, Uusimaa 00014, Finland
| | - Bettina Fischer
- Department of Genetics, University of Cambridge, Cambridge, UK
| | - Joost Woltering
- Zoology and Evolutionary Biology, Department of Biology, University of Konstanz, Konstanz, Baden-Württemberg 78457, Germany
| | - Jakob Biran
- Department of Poultry and Aquaculture, Institute of Animal Sciences, Agricultural Research Organization, Volcani Center, Rishon Lezion, Israel
| | - Scott Juntti
- Department of Biology, University of Maryland, College Park, MD, USA
| | - Claudius F. Kratochwil
- Helsinki Institute of Life Science (HiLIFE), University of Helsinki, Helsinki, Uusimaa 00014, Finland
- Faculty of Biological and Environmental Sciences, University of Helsinki, Helsinki, Uusimaa 00014, Finland
| | | | - Miguel Vasconcelos Almeida
- Department of Biochemistry, University of Cambridge, Cambridge, UK
- Wellcome/CRUK Gurdon Institute, University of Cambridge, Cambridge, UK
| |
Collapse
|
10
|
Zhang S, Li X, Li X, Wang X, Ru S, Tian H. 17β-Trenbolone activates androgen receptor, upregulates transforming growth factor beta/bone morphogenetic protein and Wnt signaling pathways, and induces masculinization of caudal and anal fins in female guppies (Poecilia reticulata). AQUATIC TOXICOLOGY (AMSTERDAM, NETHERLANDS) 2023; 263:106677. [PMID: 37677862 DOI: 10.1016/j.aquatox.2023.106677] [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: 08/27/2022] [Revised: 07/13/2023] [Accepted: 08/30/2023] [Indexed: 09/09/2023]
Abstract
Sexually mature female guppies (Poecilia reticulata) were exposed to environmentally relevant concentrations (20, 200, and 2000 ng/L) of 17β-trenbolone for four weeks. As evidenced by the increased caudal fin index and anal fins developing into gonopodium-like structures, exposed females displayed masculinized secondary sexual characteristics. Differential gene expression and subsequent pathway analysis of mRNA sequencing data revealed that the transcription of transforming growth factor beta/bone morphogenetic protein signaling pathway and Wnt signaling pathway were upregulated following 17β-trenbolone exposure. Enzyme-linked immunosorbent assays showed that the bone morphogenetic protein 7 protein content was elevated after 17β-trenbolone exposure. Finally, real-time PCR revealed that 17β-trenbolone treatment significantly increased androgen receptor mRNA levels, and molecular docking showed potent interaction between 17β-trenbolone and guppy androgen receptor. Furthermore, 17β-trenbolone-induced masculinization of caudal and anal fins in female guppies, concomitant to the upregulated expression of differentially expressed genes involved in the above-mentioned two signaling pathways, was significantly inhibited by flutamide (androgen receptor antagonist). These findings demonstrated that 17β-trenbolone masculinized fins of female guppies by activating the androgen receptor. This study revealed that 17β-trenbolone could upregulate signaling pathways related to fin growth and differentiation, and eventually cause caudal and anal fin masculinization in female guppies.
Collapse
Affiliation(s)
- Suqiu Zhang
- College of Marine Life Sciences, Ocean University of China, Qingdao 266003, Shandong province, China
| | - Xinyu Li
- College of Marine Life Sciences, Ocean University of China, Qingdao 266003, Shandong province, China
| | - Xuefu Li
- College of Marine Life Sciences, Ocean University of China, Qingdao 266003, Shandong province, China; College of Life Science, Langfang Normal University, Langfang 065000, Hebei province, China
| | - Xue Wang
- College of Marine Life Sciences, Ocean University of China, Qingdao 266003, Shandong province, China
| | - Shaoguo Ru
- College of Marine Life Sciences, Ocean University of China, Qingdao 266003, Shandong province, China
| | - Hua Tian
- College of Marine Life Sciences, Ocean University of China, Qingdao 266003, Shandong province, China.
| |
Collapse
|
11
|
Santos ME, Lopes JF, Kratochwil CF. East African cichlid fishes. EvoDevo 2023; 14:1. [PMID: 36604760 PMCID: PMC9814215 DOI: 10.1186/s13227-022-00205-5] [Citation(s) in RCA: 11] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2022] [Accepted: 11/29/2022] [Indexed: 01/06/2023] Open
Abstract
Cichlid fishes are a very diverse and species-rich family of teleost fishes that inhabit lakes and rivers of India, Africa, and South and Central America. Research has largely focused on East African cichlids of the Rift Lakes Tanganyika, Malawi, and Victoria that constitute the biodiversity hotspots of cichlid fishes. Here, we give an overview of the study system, research questions, and methodologies. Research on cichlid fishes spans many disciplines including ecology, evolution, physiology, genetics, development, and behavioral biology. In this review, we focus on a range of organismal traits, including coloration phenotypes, trophic adaptations, appendages like fins and scales, sensory systems, sex, brains, and behaviors. Moreover, we discuss studies on cichlid phylogenies, plasticity, and general evolutionary patterns, ranging from convergence to speciation rates and the proximate and ultimate mechanisms underlying these processes. From a methodological viewpoint, the last decade has brought great advances in cichlid fish research, particularly through the advent of affordable deep sequencing and advances in genetic manipulations. The ability to integrate across traits and research disciplines, ranging from developmental biology to ecology and evolution, makes cichlid fishes a fascinating research system.
Collapse
Affiliation(s)
- M Emília Santos
- Department of Zoology, University of Cambridge, Cambridge, UK.
| | - João F Lopes
- Institute of Biotechnology, HiLIFE, University of Helsinki, Helsinki, Finland
| | | |
Collapse
|
12
|
Wucherpfennig JI, Howes TR, Au JN, Au EH, Roberts Kingman GA, Brady SD, Herbert AL, Reimchen TE, Bell MA, Lowe CB, Dalziel AC, Kingsley DM. Evolution of stickleback spines through independent cis-regulatory changes at HOXDB. Nat Ecol Evol 2022; 6:1537-1552. [PMID: 36050398 PMCID: PMC9525239 DOI: 10.1038/s41559-022-01855-3] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2022] [Accepted: 07/19/2022] [Indexed: 11/10/2022]
Abstract
Understanding the mechanisms leading to new traits or additional features in organisms is a fundamental goal of evolutionary biology. We show that HOXDB regulatory changes have been used repeatedly in different fish genera to alter the length and number of the prominent dorsal spines used to classify stickleback species. In Gasterosteus aculeatus (typically 'three-spine sticklebacks'), a variant HOXDB allele is genetically linked to shortening an existing spine and adding an additional spine. In Apeltes quadracus (typically 'four-spine sticklebacks'), a variant HOXDB allele is associated with lengthening a spine and adding an additional spine in natural populations. The variant alleles alter the same non-coding enhancer region in the HOXDB locus but do so by diverse mechanisms, including single-nucleotide polymorphisms, deletions and transposable element insertions. The independent regulatory changes are linked to anterior expansion or contraction of HOXDB expression. We propose that associated changes in spine lengths and numbers are partial identity transformations in a repeating skeletal series that forms major defensive structures in fish. Our findings support the long-standing hypothesis that natural Hox gene variation underlies key patterning changes in wild populations and illustrate how different mutational mechanisms affecting the same region may produce opposite gene expression changes with similar phenotypic outcomes.
Collapse
Affiliation(s)
- Julia I Wucherpfennig
- Department of Developmental Biology, Stanford University School of Medicine, Stanford, CA, USA
| | - Timothy R Howes
- Department of Chemical and Systems Biology, Stanford University School of Medicine, Stanford, CA, USA
| | - Jessica N Au
- Department of Developmental Biology, Stanford University School of Medicine, Stanford, CA, USA
| | - Eric H Au
- Department of Molecular Genetics and Microbiology, Duke University School of Medicine, Durham, NC, USA
| | | | - Shannon D Brady
- Department of Developmental Biology, Stanford University School of Medicine, Stanford, CA, USA
| | - Amy L Herbert
- Department of Developmental Biology, Stanford University School of Medicine, Stanford, CA, USA
| | - Thomas E Reimchen
- Department of Biology, University of Victoria, Victoria, British Columbia, Canada
| | - Michael A Bell
- University of California Museum of Paleontology, University of California, Berkeley, CA, USA
| | - Craig B Lowe
- Department of Molecular Genetics and Microbiology, Duke University School of Medicine, Durham, NC, USA
| | - Anne C Dalziel
- Department of Biology, Saint Mary's University, Halifax, Nova Scotia, Canada
| | - David M Kingsley
- Department of Developmental Biology, Stanford University School of Medicine, Stanford, CA, USA.
- Howard Hughes Medical Institute, Stanford University School of Medicine, Stanford, CA, USA.
| |
Collapse
|
13
|
Miyamoto K, Kawakami K, Tamura K, Abe G. Developmental independence of median fins from the larval fin fold revises their evolutionary origin. Sci Rep 2022; 12:7521. [PMID: 35525860 PMCID: PMC9079066 DOI: 10.1038/s41598-022-11180-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2022] [Accepted: 04/19/2022] [Indexed: 11/08/2022] Open
Abstract
The median fins of modern fish that show discrete forms (dorsal, anal, and caudal fins) are derived from a continuous fold-like structure, both in ontogeny and phylogeny. The median fin fold (MFF) hypothesis assumes that the median fins evolved by reducing some positions in the continuous fin fold of basal chordates, based on the classical morphological observation of developmental reduction in the larval fin folds of living fish. However, the developmental processes of median fins are still unclear at the cellular and molecular levels. Here, we describe the transition from the larval fin fold into the median fins in zebrafish at the cellular and molecular developmental level. We demonstrate that reduction does not play a role in the emergence of the dorsal fin primordium. Instead, the reduction occurs along with body growth after primordium formation, rather than through actively scrapping the non-fin forming region by inducing cell death. We also report that the emergence of specific mesenchymal cells and their proliferation promote dorsal fin primordium formation. Based on these results, we propose a revised hypothesis for median fin evolution in which the acquisition of de novo developmental mechanisms is a crucial evolutionary component of the discrete forms of median fins.
Collapse
Affiliation(s)
- Kazuhide Miyamoto
- Laboratory of Organ Morphogenesis, Department of Ecological Developmental Adaptability Life Sciences, Graduate School of Life Sciences, Tohoku University, Aobayama Aoba-ku, Sendai, 980-8578, Japan
| | - Koichi Kawakami
- Laboratory of Molecular and Developmental Biology, National Institute of Genetics, Mishima, Shizuoka, 411-8540, Japan
- Department of Genetics, The Graduate University for Advanced Studies, SOKENDAI, Mishima, Shizuoka, 411-8540, Japan
| | - Koji Tamura
- Laboratory of Organ Morphogenesis, Department of Ecological Developmental Adaptability Life Sciences, Graduate School of Life Sciences, Tohoku University, Aobayama Aoba-ku, Sendai, 980-8578, Japan
| | - Gembu Abe
- Laboratory of Organ Morphogenesis, Department of Ecological Developmental Adaptability Life Sciences, Graduate School of Life Sciences, Tohoku University, Aobayama Aoba-ku, Sendai, 980-8578, Japan.
- Division of Developmental Biology, Department of Functional Morphology, School of Life Science, Faculty of Medicine, Tottori University, Nishi-cho 86, Yonago, 683-8503, Japan.
| |
Collapse
|
14
|
Clark B, Elkin J, Marconi A, Turner GF, Smith AM, Joyce D, Miska EA, Juntti SA, Santos ME. Oca2 targeting using CRISPR/Cas9 in the Malawi cichlid Astatotilapia calliptera. ROYAL SOCIETY OPEN SCIENCE 2022; 9:220077. [PMID: 35601449 PMCID: PMC9019512 DOI: 10.1098/rsos.220077] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 01/20/2022] [Accepted: 03/22/2022] [Indexed: 05/03/2023]
Abstract
Identifying genetic loci underlying trait variation provides insights into the mechanisms of diversification, but demonstrating causality and characterizing the role of genetic loci requires testing candidate gene function, often in non-model species. Here we establish CRISPR/Cas9 editing in Astatotilapia calliptera, a generalist cichlid of the remarkably diverse Lake Malawi radiation. By targeting the gene oca2 required for melanin synthesis in other vertebrate species, we show efficient editing and germline transmission. Gene edits include indels in the coding region, probably a result of non-homologous end joining, and a large deletion in the 3' untranslated region due to homology-directed repair. We find that oca2 knock-out A. calliptera lack melanin, which may be useful for developmental imaging in embryos and studying colour pattern formation in adults. As A. calliptera resembles the presumed generalist ancestor of the Lake Malawi cichlids radiation, establishing genome editing in this species will facilitate investigating speciation, adaptation and trait diversification in this textbook radiation.
Collapse
Affiliation(s)
- Bethan Clark
- Department of Zoology, University of Cambridge, UK
| | - Joel Elkin
- Department of Zoology, University of Cambridge, UK
| | | | - George F. Turner
- School of Natural Sciences, Bangor University, Gwynedd LL57 2TH, UK
| | - Alan M. Smith
- Department of Biological and Marine Sciences, University of Hull, UK
| | - Domino Joyce
- Department of Biological and Marine Sciences, University of Hull, UK
| | - Eric A. Miska
- Department of Genetics, University of Cambridge, UK
- Gurdon Institute, University of Cambridge, Cambridge CB2 1QN, UK
- Wellcome Sanger Institute, Wellcome Trust Genome Campus, Cambridge, UK
| | | | | |
Collapse
|