1
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Aryal YP, Neupane S, Kwak HJ, An CH, Sohn WJ, Yamamoto H, Kwon TY, Min BK, Kim JY, Cho SJ. Unraveling the structure, chemical composition, and conserved signaling in leech teeth. Anim Cells Syst (Seoul) 2024; 28:272-282. [PMID: 38741948 PMCID: PMC11089927 DOI: 10.1080/19768354.2024.2350736] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2024] [Accepted: 04/29/2024] [Indexed: 05/16/2024] Open
Abstract
Unlike vertebrates, the number of toothed taxa in invertebrates is very few, with leeches being the only tooth-bearing organisms in the phylum Annelida. Copious studies have been conducted regarding vertebrate teeth; however, studies regarding the structure and function of invertebrate teeth are limited. In this study, the tooth structure of leeches, specifically Hirudo nipponia and Haemadipsa rjukjuana, was revealed, which showed sharp and pointed teeth along the apex of three jaws. Understanding conserved signaling regulations among analogous organs is crucial for uncovering the underlying mechanisms during organogenesis. Therefore, to shed light on the evolutionary perspective of odontogenesis to some extent, we conducted de novo transcriptome analyses using embryonic mouse tooth germs, Hirudo teeth, and Helobdella proboscises to identify conserved signaling molecules involved in tooth development. The selection criteria were particularly based on the presence of tooth-related genes in mice, Hirudo teeth, and Helobdella proboscis, wherein 4113 genes were commonly expressed in all three specimens. Furthermore, the chemical nature of leech teeth was also examined via TEM-EDS to compare the chemical composition with vertebrate teeth. The examination of tissue-specific genetic information and chemical nature between leeches and mice revealed chemical similarities between leech and mice teeth, as well as conserved signaling molecules involved in tooth formation, including Ptpro, Prickle2, and Wnt16. Based on our findings, we propose that leech teeth express signaling molecules conserved in mice and these conserved tooth-specific signaling for dental hard tissue formation in mice would corresponds to the structural formation of the toothed jaw in leeches.
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Affiliation(s)
- Yam Prasad Aryal
- Department of Biological Sciences and Biotechnology, College of Natural Sciences, Chungbuk National University, Cheongju, Korea
| | - Sanjiv Neupane
- Department of Biochemistry and Cell Biology, Stony Brook University, Stony Brook, NY, USA
| | - Hee-Jin Kwak
- Department of Biological Sciences and Biotechnology, College of Natural Sciences, Chungbuk National University, Cheongju, Korea
| | - Chang-Hyeon An
- Department of Oral and Maxillofacial Radiology, School of Dentistry, Kyungpook National University, Daegu, Korea
| | - Wern-Joo Sohn
- Pre-Major of Cosmetics and Pharmaceutics, Daegu Haany University, Gyeongsan, Korea
| | - Hitoshi Yamamoto
- Department of Histology and Developmental Biology, Tokyo Dental College, Tokyo, Japan
| | - Tae-Yub Kwon
- Department of Dental Biomaterials, School of Dentistry, Kyungpook National University, Daegu, Korea
| | - Bong-Ki Min
- Center for Research Facilities, Yeungnam University, Gyeongsan, Korea
| | - Jae-Young Kim
- Department of Biochemistry, School of Dentistry, Kyungpook National University, Daegu, Korea
| | - Sung-Jin Cho
- Department of Biological Sciences and Biotechnology, College of Natural Sciences, Chungbuk National University, Cheongju, Korea
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2
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Hijaze E, Gildor T, Seidel R, Layous M, Winter M, Bertinetti L, Politi Y, Ben-Tabou de-Leon S. ROCK and the actomyosin network control biomineral growth and morphology during sea urchin skeletogenesis. eLife 2024; 12:RP89080. [PMID: 38573316 PMCID: PMC10994658 DOI: 10.7554/elife.89080] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/05/2024] Open
Abstract
Biomineralization had apparently evolved independently in different phyla, using distinct minerals, organic scaffolds, and gene regulatory networks (GRNs). However, diverse eukaryotes from unicellular organisms, through echinoderms to vertebrates, use the actomyosin network during biomineralization. Specifically, the actomyosin remodeling protein, Rho-associated coiled-coil kinase (ROCK) regulates cell differentiation and gene expression in vertebrates' biomineralizing cells, yet, little is known on ROCK's role in invertebrates' biomineralization. Here, we reveal that ROCK controls the formation, growth, and morphology of the calcite spicules in the sea urchin larva. ROCK expression is elevated in the sea urchin skeletogenic cells downstream of the Vascular Endothelial Growth Factor (VEGF) signaling. ROCK inhibition leads to skeletal loss and disrupts skeletogenic gene expression. ROCK inhibition after spicule formation reduces the spicule elongation rate and induces ectopic spicule branching. Similar skeletogenic phenotypes are observed when ROCK is inhibited in a skeletogenic cell culture, indicating that these phenotypes are due to ROCK activity specifically in the skeletogenic cells. Reduced skeletal growth and enhanced branching are also observed under direct perturbations of the actomyosin network. We propose that ROCK and the actomyosin machinery were employed independently, downstream of distinct GRNs, to regulate biomineral growth and morphology in Eukaryotes.
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Affiliation(s)
- Eman Hijaze
- Department of Marine Biology, Leon H. Charney School of Marine Sciences, University of HaifaHaifaIsrael
| | - Tsvia Gildor
- Department of Marine Biology, Leon H. Charney School of Marine Sciences, University of HaifaHaifaIsrael
| | - Ronald Seidel
- B CUBE Center for Molecular Bioengineering, Technische Universität DresdenDresdenGermany
| | - Majed Layous
- Department of Marine Biology, Leon H. Charney School of Marine Sciences, University of HaifaHaifaIsrael
| | - Mark Winter
- Department of Electrical Engineering, Computer Science and Mathematics, Technische Universiteit DelftDelftNetherlands
| | - Luca Bertinetti
- B CUBE Center for Molecular Bioengineering, Technische Universität DresdenDresdenGermany
| | - Yael Politi
- B CUBE Center for Molecular Bioengineering, Technische Universität DresdenDresdenGermany
| | - Smadar Ben-Tabou de-Leon
- Department of Marine Biology, Leon H. Charney School of Marine Sciences, University of HaifaHaifaIsrael
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3
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Jackman WR, Miranda Portillo LS, Cox CK, Ambrosio A, Gibert Y. Blocking endogenous retinoic acid degradation induces oral tooth formation in zebrafish. Proc Natl Acad Sci U S A 2024; 121:e2321162121. [PMID: 38446853 PMCID: PMC10945834 DOI: 10.1073/pnas.2321162121] [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: 12/12/2023] [Accepted: 01/31/2024] [Indexed: 03/08/2024] Open
Abstract
According to Dollo's Law of irreversibility in evolution, a lost structure is usually considered to be unable to reappear in evolution due to the accumulation over time of mutations in the genes required for its formation. Cypriniform fish are a classic model of evolutionary loss because, while they form fully operational teeth in the ventral posterior pharynx, unlike other teleosts, they do not possess oral teeth. Paleontological data show that Cypriniforms, a clade of teleost fish that includes the zebrafish, lost their oral teeth 50 to 100 Mya. In order to attempt to reverse oral tooth loss in zebrafish, we block the degradation of endogenous levels of retinoic acid (RA) using a specific inhibitor of the Cyp26 RA degrading enzymes. We demonstrate the inhibition of endogenous RA degradation is sufficient to restore oral tooth induction as marked by the re-appearance of expression of early dental mesenchyme and epithelium genes such as dlx2b and sp7 in the oral cavity. Furthermore, we show that these exogenously induced oral tooth germs are able to be at least partly calcified. Taken together, our data show that modifications of signaling pathways can have a significant effect on the reemergence of once-lost structures leading to experimentally induced reversibility of evolutionary tooth loss in cypriniforms.
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Affiliation(s)
| | | | - Carol K. Cox
- Department of Cell and Molecular Biology, Cancer Center and Research Institute, University of Mississippi Medical Center, Jackson, MS39216
| | | | - Yann Gibert
- Department of Cell and Molecular Biology, Cancer Center and Research Institute, University of Mississippi Medical Center, Jackson, MS39216
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4
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Huang R, Tang L, Li R, Li Y, Zhan L, Huang X. Tooth pattern, development, and replacement in the yellow catfish, Pelteobagrus fulvidraco. J Morphol 2024; 285:e21657. [PMID: 38100745 DOI: 10.1002/jmor.21657] [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: 07/26/2023] [Revised: 11/06/2023] [Accepted: 11/07/2023] [Indexed: 12/17/2023]
Abstract
Studies of teleost teeth are important for understanding the evolution and mechanisms of tooth development, replacement, and regeneration. Here, we used gross specimens, microcomputed tomography, and histological analysis to characterize tooth structure, development, and resorption patterns in adult Pelteobagrus fulvidraco. The oral and pharyngeal teeth are villiform and conical. Multiple rows of dentition are densely distributed and the tooth germ is derived from the epithelium. P. fulvidraco exhibits a discontinuous and non-permanent dental lamina. Epithelial cells surround the teeth and are separated into distinct tooth units by mesenchymal tissue. Tooth development is completed in the form of independent tooth units. P. fulvidraco does not undergo simultaneous tooth replacement. Based on tooth development and resorption status, five forms of teeth are present in adult P. fulvidraco: developing tooth germs, accompanied by relatively immature tooth germs; mature and well-mineralized tooth accompanied by one tooth germ; teeth that have begun resorption, but not completely fractured; fractured teeth with only residual attachment to the underlying bone; and teeth that are completely resorbed and detached. Seven biological stages of a tooth in P. fulvidraco were also described.
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Affiliation(s)
- Rui Huang
- Department of Stomatology, Beijing Friendship Hospital, Capital Medical University, Beijing, China
- Immunology Research Center for Oral and Systemic Health, Beijing Friendship Hospital, Capital Medical University, Beijing, China
| | - Li Tang
- Department of Stomatology, Beijing Friendship Hospital, Capital Medical University, Beijing, China
- Department of Orthodontics, The Affiliated Hospital of Qingdao University, Qingdao, China
- School of Stomatology, Qingdao University, Qingdao, China
| | - Ruiqi Li
- Department of Stomatology, Beijing Friendship Hospital, Capital Medical University, Beijing, China
- Immunology Research Center for Oral and Systemic Health, Beijing Friendship Hospital, Capital Medical University, Beijing, China
| | - Yongfeng Li
- Department of Stomatology, Beijing Friendship Hospital, Capital Medical University, Beijing, China
- Immunology Research Center for Oral and Systemic Health, Beijing Friendship Hospital, Capital Medical University, Beijing, China
| | - Liping Zhan
- Department of Stomatology, Beijing Friendship Hospital, Capital Medical University, Beijing, China
- Immunology Research Center for Oral and Systemic Health, Beijing Friendship Hospital, Capital Medical University, Beijing, China
| | - Xiaofeng Huang
- Department of Stomatology, Beijing Friendship Hospital, Capital Medical University, Beijing, China
- Immunology Research Center for Oral and Systemic Health, Beijing Friendship Hospital, Capital Medical University, Beijing, China
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5
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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.
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Affiliation(s)
| | - Axel Meyer
- Department of Biology, University of Konstanz, Konstanz, Germany
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6
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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.
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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
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7
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Ma Y, Xiao Y, Xiao Z, Li J. Morphological characteristics of beak-like tooth in spotted knifejaw (Oplegnathus punctatus) and mechanisms of dental development regulation by the Wnt, BMP, FGF and SHH signalling pathways. Int J Biol Macromol 2023; 250:126188. [PMID: 37562479 DOI: 10.1016/j.ijbiomac.2023.126188] [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: 05/03/2023] [Revised: 07/17/2023] [Accepted: 07/30/2023] [Indexed: 08/12/2023]
Abstract
Oplegnathus punctatus is a fish species with beak-like tooth that feeds on algae, oysters, sea urchins, and other organisms attached to rocks. Currently, there are no research reports on the development and regulatory mechanisms of O. punctatus beak-like tooth. This present study firstly elucidated the nesting structure pattern of the beak-like tooth with dental formula (4, 15-16, 10-1) for O. punctatus. Four critical periods during early beak-like tooth development (28dph, 40dph, 50dph, 60dph) were also identified. In addition, 11 key genes (bmp2, bmpr2, smad1, wnt5a, msx, axin2, fgfr1a, fgfr2, pitx2, ptch1, cyp27a1) closely related to the development of beak-like tooth were discovered, with the highest expression levels in the initial stages of functional teeth and replacement teeth development, and expression in the mesenchymal and epithelial tissues of the teeth. Further research found that the cyp27a1 gene, related to vitamin D metabolism and calcium accumulation, was expressed in the maxilla and base of the tooth in O. punctatus. This study provides support for the biological theory of tooth development and healing and provides a reference for the adaptive evolution of tooth healing in special habitats.
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Affiliation(s)
- Yuting Ma
- CAS and Shandong Province Key Laboratory of Experimental Marine Biology, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, China; Laboratory for Marine Biology and Biotechnology, Qingdao National Laboratory for Marine Science and Technology, Qingdao, China; Key Laboratory of Breeding Biotechnology and Sustainable Aquaculture, Chinese Academy of Sciences, Wuhan, China.
| | - Yongshuang Xiao
- CAS and Shandong Province Key Laboratory of Experimental Marine Biology, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, China; Laboratory for Marine Biology and Biotechnology, Qingdao National Laboratory for Marine Science and Technology, Qingdao, China; Key Laboratory of Breeding Biotechnology and Sustainable Aquaculture, Chinese Academy of Sciences, Wuhan, China.
| | - Zhizhong Xiao
- CAS and Shandong Province Key Laboratory of Experimental Marine Biology, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, China; Laboratory for Marine Biology and Biotechnology, Qingdao National Laboratory for Marine Science and Technology, Qingdao, China; Key Laboratory of Breeding Biotechnology and Sustainable Aquaculture, Chinese Academy of Sciences, Wuhan, China.
| | - Jun Li
- CAS and Shandong Province Key Laboratory of Experimental Marine Biology, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, China; Laboratory for Marine Biology and Biotechnology, Qingdao National Laboratory for Marine Science and Technology, Qingdao, China; Key Laboratory of Breeding Biotechnology and Sustainable Aquaculture, Chinese Academy of Sciences, Wuhan, China.
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8
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Litman T, Stein WD. Ancient lineages of the keratin-associated protein (KRTAP) genes and their co-option in the evolution of the hair follicle. BMC Ecol Evol 2023; 23:7. [PMID: 36941546 PMCID: PMC10029157 DOI: 10.1186/s12862-023-02107-z] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2022] [Accepted: 02/23/2023] [Indexed: 03/23/2023] Open
Abstract
BLAST searches against the human genome showed that of the 93 keratin-associated proteins (KRTAPs) of Homo sapiens, 53 can be linked by sequence similarity to an H. sapiens metallothionein and 16 others can be linked similarly to occludin, while the remaining KRTAPs can themselves be linked to one or other of those 69 directly-linked proteins. The metallothionein-linked KRTAPs comprise the high-sulphur and ultrahigh-sulphur KRTAPs and are larger than the occludin-linked set, which includes the tyrosine- and glycine-containing KRTAPs. KRTAPs linked to metallothionein appeared in increasing numbers as evolution advanced from the deuterostomia, where KRTAP-like proteins with strong sequence similarity to their mammalian congeners were found in a sea anemone and a starfish. Those linked to occludins arose only with the later-evolved mollusca, where a KRTAP homologous with its mammalian congener was found in snails. The presence of antecedents of the mammalian KRTAPs in a starfish, a sea anemone, snails, fish, amphibia, reptiles and birds, all of them animals that lack hair, suggests that some KRTAPs may have a physiological role beyond that of determining the characteristics of hair fibres. We suggest that homologues of these KRTAPs found in non-hairy animals were co-opted by placodes, formed by the ectodysplasin pathway, to produce the first hair-producing cells, the trichocytes of the hair follicles.
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Affiliation(s)
- Thomas Litman
- Department of Immunology and Microbiology, University of Copenhagen, Mærsk Tower 07-12-70 Nørre Allé 14, 2200, Copenhagen N, Denmark
| | - Wilfred D Stein
- Silberman Institute of Life Sciences, Hebrew University, 91904, Jerusalem, Israel.
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9
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Mack KL, Square TA, Zhao B, Miller CT, Fraser HB. Evolution of Spatial and Temporal cis-Regulatory Divergence in Sticklebacks. Mol Biol Evol 2023; 40:7048494. [PMID: 36805962 PMCID: PMC10015619 DOI: 10.1093/molbev/msad034] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2022] [Revised: 02/02/2023] [Accepted: 02/08/2023] [Indexed: 02/22/2023] Open
Abstract
Cis-regulatory changes are thought to play a major role in adaptation. Threespine sticklebacks have repeatedly colonized freshwater habitats in the Northern Hemisphere, where they have evolved a suite of phenotypes that distinguish them from marine populations, including changes in physiology, behavior, and morphology. To understand the role of gene regulatory evolution in adaptive divergence, here we investigate cis-regulatory changes in gene expression between marine and freshwater ecotypes through allele-specific expression (ASE) in F1 hybrids. Surveying seven ecologically relevant tissues, including three sampled across two developmental stages, we identified cis-regulatory divergence affecting a third of genes, nearly half of which were tissue-specific. Next, we compared allele-specific expression in dental tissues at two timepoints to characterize cis-regulatory changes during development between marine and freshwater fish. Applying a genome-wide test for selection on cis-regulatory changes, we find evidence for lineage-specific selection on several processes between ecotypes, including the Wnt signaling pathway in dental tissues. Finally, we show that genes with ASE, particularly those that are tissue-specific, are strongly enriched in genomic regions of repeated marine-freshwater divergence, supporting an important role for these cis-regulatory differences in parallel adaptive evolution of sticklebacks to freshwater habitats. Altogether, our results provide insight into the cis-regulatory landscape of divergence between stickleback ecotypes across tissues and during development, and support a fundamental role for tissue-specific cis-regulatory changes in rapid adaptation to new environments.
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Affiliation(s)
- Katya L Mack
- Department of Biology, Stanford University, Stanford, CA
| | - Tyler A Square
- Department of Molecular and Cell Biology, University of California, Berkeley, CA
| | - Bin Zhao
- Department of Biology, Stanford University, Stanford, CA
| | - Craig T Miller
- Department of Molecular and Cell Biology, University of California, Berkeley, CA
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10
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Fiteha YG, Rashed MA, Ali RAM, Magdy M. Characterization and phylogenetic analysis of the complete mitochondrial genome of Mango tilapia (Sarotherodon galilaeus: Cichlidae). Mol Biol Rep 2023; 50:3945-3950. [PMID: 36781609 PMCID: PMC10042889 DOI: 10.1007/s11033-023-08288-6] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2022] [Accepted: 01/17/2023] [Indexed: 02/15/2023]
Abstract
BACKGROUND Sarotherodon galilaeus (Linné, 1758) is a member of the family Cichlidae, which is considered the most important aquaculture freshwater species endemic to Africa and the Middle East. The genetics and molecular biology of this species are rare. This requires more comprehensive mitochondrial genomes-based phylogenetics to enhance understanding of the relationship and delineate this species. METHODS AND RESULTS Here, we assembled the complete mitogenome of S. galilaeus using Illumina high-throughput sequencing technology. The mango tilapia mitogenome was 16,631 bp in length with an AT composition of 53.4% and 46.4% GC content. It encodes 37 genes comprising two ribosomal RNA genes (rRNAs), 22 transfer RNA genes (tRNAs), and 13 protein-coding genes (PCGs) as well as the D-loop known as the control region. The phylogenetic tree was conducted to provide a relationship within the haplotilapiine lineage based on the maximum likelihood method, and the newly sequenced S. galilaeus was clustered with other Sarotherodon species. CONCLUSION Our results provide a new perception of the genetic basis of S. galilaeus species for further research on systematics, evolution, population genetics, and molecular ecology.
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Affiliation(s)
- Yosur G Fiteha
- Genetics Department, Faculty of Agriculture, Ain Shams University, Cairo, Egypt
- Zoology Department, Faculty of Women for Arts, Science and Education, Ain Shams University, Cairo, Egypt
| | - M A Rashed
- Genetics Department, Faculty of Agriculture, Ain Shams University, Cairo, Egypt
| | - R A M Ali
- Zoology Department, Faculty of Women for Arts, Science and Education, Ain Shams University, Cairo, Egypt
| | - M Magdy
- Genetics Department, Faculty of Agriculture, Ain Shams University, Cairo, Egypt.
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11
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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.
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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
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12
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Singh P, Irisarri I, Torres‐Dowdall J, Thallinger GG, Svardal H, Lemmon EM, Lemmon AR, Koblmüller S, Meyer A, Sturmbauer C. Phylogenomics of trophically diverse cichlids disentangles processes driving adaptive radiation and repeated trophic transitions. Ecol Evol 2022; 12:e9077. [PMID: 35866021 PMCID: PMC9288888 DOI: 10.1002/ece3.9077] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2021] [Revised: 05/28/2022] [Accepted: 05/31/2022] [Indexed: 11/12/2022] Open
Abstract
Cichlid fishes of the tribe Tropheini are a striking case of adaptive radiation, exemplifying multiple trophic transitions between herbivory and carnivory occurring in sympatry with other established cichlid lineages. Tropheini evolved highly specialized eco-morphologies to exploit similar trophic niches in different ways repeatedly and rapidly. To better understand the evolutionary history and trophic adaptations of this lineage, we generated a dataset of 532 targeted loci from 21 out of the 22 described Tropheini species. We resolved the Tropheini into seven monophyletic genera and discovered one to be polyphyletic. The polyphyletic genus, Petrochromis, represents three convergent origins of the algae grazing trophic specialization. This repeated evolution of grazing may have been facilitated by adaptive introgression as we found evidence for gene flow among algae grazing genera. We also found evidence of gene flow among algae browsing genera, but gene flow was restricted between herbivorous and carnivorous genera. Furthermore, we observed no evidence supporting a hybrid origin of this radiation. Our molecular evolutionary analyses suggest that opsin genes likely evolved in response to selection pressures associated with trophic ecology in the Tropheini. We found surprisingly little evidence of positive selection in coding regions of jaw-shaping genes in this trophically diverse lineage. This suggests low degrees of freedom for further change in these genes, and possibly a larger role for regulatory variation in driving jaw adaptations. Our study emphasizes Tropheini cichlids as an important model for studying the evolution of trophic specialization and its role in speciation.
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Affiliation(s)
- Pooja Singh
- Institute of BiologyUniversity of GrazGrazAustria
- Lehrstuhl für Zoologie und Evolutionsbiologie, Department of BiologyUniversity of KonstanzConstanceGermany
- Institute of Ecology and EvolutionUniversity of BernBernSwitzerland
| | - Iker Irisarri
- Lehrstuhl für Zoologie und Evolutionsbiologie, Department of BiologyUniversity of KonstanzConstanceGermany
- Leibniz Institute for the Analysis of Biodiversity Change (LIB), Zoological Museum HamburgHamburgGermany
| | - Julián Torres‐Dowdall
- Lehrstuhl für Zoologie und Evolutionsbiologie, Department of BiologyUniversity of KonstanzConstanceGermany
| | - Gerhard G. Thallinger
- Institute of Biomedical InformaticsGraz University of TechnologyGrazAustria
- OMICS Center Graz, BioTechMed GrazGrazAustria
| | - Hannes Svardal
- Department of BiologyUniversity of AntwerpAntwerpBelgium
- Naturalis Biodiversity CenterLeidenThe Netherlands
| | - Emily Moriarty Lemmon
- Department of Biological ScienceFlorida State University, Biomedical Research FacilityTallahasseeFloridaUSA
| | - Alan R. Lemmon
- Department of Biological ScienceFlorida State University, Biomedical Research FacilityTallahasseeFloridaUSA
| | | | - Axel Meyer
- Lehrstuhl für Zoologie und Evolutionsbiologie, Department of BiologyUniversity of KonstanzConstanceGermany
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13
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Font-Porterias N, McNelis MG, Comas D, Hlusko LJ. Evidence of selection in the ectodysplasin pathway among endangered aquatic mammals. Integr Org Biol 2022; 4:obac018. [PMID: 35874492 PMCID: PMC9299678 DOI: 10.1093/iob/obac018] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2022] [Revised: 05/06/2022] [Accepted: 05/21/2022] [Indexed: 11/13/2022] Open
Abstract
Synopsis The ectodysplasin pathway has been a target of evolution repeatedly. Genetic variation in the key genes of this pathway (EDA, EDAR, and EDARADD) results in a rich source of pleiotropic effects across ectodermally-derived structures, including teeth, hair, sweat glands, and mammary glands. In addition, a non-canonical Wnt pathway has a very similar functional role, making variation in the WNT10A gene also of evolutionary significance. The adaptation of mammals to aquatic environments has occurred independently in at least 4 orders, whose species occupy a wide geographic range (from equatorial to polar regions) and exhibit great phenotypic variation in ectodermally-derived structures, including the presence or absence of fur and extreme lactational strategies. The role of the ectodysplasin pathway in the adaptation to aquatic environments has been never explored in mammalian species. In the present study, we analyze the genetic variation in orthologous coding sequences from EDA, EDAR, EDARADD, and WNT10A genes together with ectodermally-derived phenotypic variation from 34 aquatic and non-aquatic mammalian species to assess signals of positive selection, gene-trait coevolution, and genetic convergence. Our study reveals strong evidence of positive selection in a proportion of coding sites in EDA and EDAR genes in 3 endangered aquatic mammals (the Hawaiian monk seal, the Yangtze finless porpoise, and the sea otter). We hypothesize functional implications potentially related to the adaptation to the low-latitude aquatic environment in the Hawaiian monk seal and the freshwater in the Yangtze finless porpoise. The signal in the sea otter is likely the result of an increased genetic drift after an intense bottleneck and reduction of genetic diversity. Besides positive selection, we have not detected robust signals of gene-trait coevolution or convergent amino acid shifts in the ectodysplasin pathway associated with shared phenotypic traits among aquatic mammals. This study provides new evidence of the evolutionary role of the ectodysplasin pathway and encourages further investigation, including functional studies, to fully resolve its relationship with mammalian aquatic adaptation. Spanish La vía de la ectodisplasina ha sido objeto de la evolución repetidamente. La variación genética en los principales genes de esta vía (EDA, EDAR y EDARADD) da como resultado una gran diversidad de efectos pleiotrópicos en las estructuras derivadas del ectodermo, incluidos los dientes, el cabello, las glándulas sudoríparas y las glándulas mamarias. Además, una vía wnt no canónica tiene un papel funcional muy similar, por lo que la variación en el gen WNT10A también tiene importancia evolutiva. La adaptación de los mamíferos a los entornes acuáticos se ha producido de forma independiente en al menos cuatro órdenes, cuyas especies ocupan un amplio rango geográfico (desde regiones ecuatoriales a polares) y presentan una gran variación fenotípica en las estructuras derivadas del ectodermo, incluyendo la presencia o ausencia de pelaje y estrategias de lactancia muy diferentes. El papel de la vía de la ectodisplasina en la adaptación a entornos acuáticos no se ha explorado nunca en especies de mamíferos. En este estudio, analizamos la variación genética en las secuencias codificantes ortólogas de los genes EDA, EDAR, EDARADD y WNT10A junto con la variación fenotípica derivada del ectodermo de 34 especies de mamíferos acuáticos y no acuáticos para evaluar señales de selección positiva, coevolución gen-rasgo y convergencia genética. Nuestro estudio revela señales de selección positiva en regiones de las secuencias codificantes de los genes EDA y EDAR en tres mamíferos acuáticos en peligro de extinción (la foca monje de Hawái, la marsopa lisa y la nutria marina). Estas señales podrían tener implicaciones funcionales potencialmente relacionadas con la adaptación al entorno acuático de baja latitud en la foca monje de Hawái y el agua dulce en la marsopa lisa. La señal en la nutria marina es probablemente el resultado de una mayor deriva genética tras un intenso un cuello de botella y una reducción de la diversidad genética. A parte de selección positiva, no hemos detectado señales sólidas de coevolución gen-rasgo o cambios convergentes de aminoácidos en la vía de la ectodisplasina asociados a rasgos fenotípicos compartidos entre mamíferos acuáticos. Este estudio proporciona nuevas evidencias del papel evolutivo de la vía de la ectodisplasina y quiere promover futuras investigaciones con estudios funcionales para acabar de resolver la relación de esta vía con la adaptación acuática de los mamíferos.
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Affiliation(s)
- Neus Font-Porterias
- Departament de Ciències Experimentals i de la Salut, Universitat Pompeu Fabra, Institut de Biologia Evolutiva (UPF-CSIC) , Barcelona , Spain
| | - Madeline G McNelis
- Department of Integrative Biology, University of California Berkeley , California , USA
| | - David Comas
- Departament de Ciències Experimentals i de la Salut, Universitat Pompeu Fabra, Institut de Biologia Evolutiva (UPF-CSIC) , Barcelona , Spain
| | - Leslea J Hlusko
- Department of Integrative Biology, University of California Berkeley , California , USA
- National Research Center on Human Evolution (CENIEH) , Burgos , Spain
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14
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Ventx Family and Its Functional Similarities with Nanog: Involvement in Embryonic Development and Cancer Progression. Int J Mol Sci 2022; 23:ijms23052741. [PMID: 35269883 PMCID: PMC8911082 DOI: 10.3390/ijms23052741] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2021] [Revised: 02/21/2022] [Accepted: 02/27/2022] [Indexed: 12/27/2022] Open
Abstract
The Ventx family is one of the subfamilies of the ANTP (antennapedia) superfamily and belongs to the NK-like (NKL) subclass. Ventx is a homeobox transcription factor and has a DNA-interacting domain that is evolutionarily conserved throughout vertebrates. It has been extensively studied in Xenopus, zebrafish, and humans. The Ventx family contains transcriptional repressors widely involved in embryonic development and tumorigenesis in vertebrates. Several studies have documented that the Ventx family inhibited dorsal mesodermal formation, neural induction, and head formation in Xenopus and zebrafish. Moreover, Ventx2.2 showed functional similarities to Nanog and Barx1, leading to pluripotency and neural-crest migration in vertebrates. Among them, Ventx protein is an orthologue of the Ventx family in humans. Studies have demonstrated that human Ventx was strongly associated with myeloid-cell differentiation and acute myeloid leukemia. The therapeutic potential of Ventx family inhibition in combating cancer progression in humans is discussed. Additionally, we briefly discuss genome evolution, gene duplication, pseudo-allotetraploidy, and the homeobox family in Xenopus.
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15
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Ronco F, Salzburger W. Tracing evolutionary decoupling of oral and pharyngeal jaws in cichlid fishes. Evol Lett 2021; 5:625-635. [PMID: 34917401 PMCID: PMC8645199 DOI: 10.1002/evl3.257] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2021] [Revised: 08/05/2021] [Accepted: 09/01/2021] [Indexed: 11/08/2022] Open
Abstract
Evolutionary innovations can facilitate diversification if the novel trait enables a lineage to exploit new niches or by expanding character space. The elaborate pharyngeal jaw apparatus of cichlid fishes is often referred to as an evolutionary "key innovation" that has promoted the spectacular adaptive radiations in these fishes. This goes back to the idea that the structural and functional independence of the oral and pharyngeal jaws for food capturing and food processing, respectively, permitted each jaw type to follow independent evolutionary trajectories. This "evolutionary decoupling" is thought to have facilitated novel trait combinations and, hence, ecological specialization, ultimately allowing more species to coexist in sympatry. Here, we test the hypotheses of evolutionary decoupling of the oral and pharyngeal jaws in the massive adaptive radiation of cichlid fishes in African Lake Tanganyika. Based on phylogenetic comparative analyses of oral jaw morphology and lower pharyngeal jaw shape across most of the ∼240 cichlid species occurring in that lake, we show that the two jaws evolved coupled along the main axes of morphological variation, yet most other components of these trait complexes evolved largely independently over the course of the radiation. Further, we find limited correlations between the two jaws in both overall divergence and evolutionary rates. Moreover, we show that the two jaws were evolutionary decoupled at a late stage of the radiation, suggesting that decoupling contributed to micro-niche partitioning and the associated rapidly increasing trophic diversity during this phase.
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Affiliation(s)
- Fabrizia Ronco
- Zoological Institute, Department of Environmental Sciences University of Basel Basel CH-4051 Switzerland
| | - Walter Salzburger
- Zoological Institute, Department of Environmental Sciences University of Basel Basel CH-4051 Switzerland
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16
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Stepaniak MD, Square TA, Miller CT. Evolved Bmp6 enhancer alleles drive spatial shifts in gene expression during tooth development in sticklebacks. Genetics 2021; 219:6374454. [PMID: 34849839 PMCID: PMC8664583 DOI: 10.1093/genetics/iyab151] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2021] [Accepted: 08/31/2021] [Indexed: 11/13/2022] Open
Abstract
Mutations in enhancers have been shown to often underlie natural variation but the evolved differences in enhancer activity can be difficult to identify in vivo. Threespine sticklebacks (Gasterosteus aculeatus) are a robust system for studying enhancer evolution due to abundant natural genetic variation, a diversity of evolved phenotypes between ancestral marine and derived freshwater forms, and the tractability of transgenic techniques. Previous work identified a series of polymorphisms within an intronic enhancer of the Bone morphogenetic protein 6 (Bmp6) gene that are associated with evolved tooth gain, a derived increase in freshwater tooth number that arises late in development. Here, we use a bicistronic reporter construct containing a genetic insulator and a pair of reciprocal two-color transgenic reporter lines to compare enhancer activity of marine and freshwater alleles of this enhancer. In older fish, the two alleles drive partially overlapping expression in both mesenchyme and epithelium of developing teeth, but the freshwater enhancer drives a reduced mesenchymal domain and a larger epithelial domain relative to the marine enhancer. In younger fish, these spatial shifts in enhancer activity are less pronounced. Comparing Bmp6 expression by in situ hybridization in developing teeth of marine and freshwater fish reveals similar evolved spatial shifts in gene expression. Together, these data support a model in which the polymorphisms within this enhancer underlie evolved tooth gain by shifting the spatial expression of Bmp6 during tooth development, and provide a general strategy to identify spatial differences in enhancer activity in vivo.
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Affiliation(s)
- Mark D Stepaniak
- Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA 94720, USA
| | - Tyler A Square
- Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA 94720, USA
| | - Craig T Miller
- Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA 94720, USA
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17
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Pospisilova A, Stundl J, Brejcha J, Metscher BD, Psenicka M, Cerny R, Soukup V. The remarkable dynamics in the establishment, rearrangement, and loss of dentition during the ontogeny of the sterlet sturgeon. Dev Dyn 2021; 251:826-845. [PMID: 34846759 DOI: 10.1002/dvdy.444] [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: 07/23/2021] [Revised: 11/15/2021] [Accepted: 11/22/2021] [Indexed: 11/07/2022] Open
Abstract
BACKGROUND Sturgeons belong to an early-branching lineage often used as a proxy of ancestor-like traits of ray-finned fishes. However, many features of this lineage, such as the transitory presence and the eventual loss of dentition, exemplify specializations that, in fact, provide important information on lineage-specific evolutionary dynamics. RESULTS Here, we introduce a detailed overview of the dentition during the development of the sterlet sturgeon. The dentition is composed of tooth fields at oral, palatal, and anterior pharyngeal regions. Oral fields are single-rowed, non-renewed and are shed early. Palatal and pharyngeal fields are multi-rowed and renewed from the adjacent superficial epithelium without the presence of the successional dental lamina. The early loss of oral fields and subsequent establishment of palatal and pharyngeal fields leads to a translocation of the functional dentition from the front to the rear of the oropharyngeal cavity until the eventual loss of all teeth. CONCLUSIONS Our survey shows the sterlet dentition as a dynamic organ system displaying differential composition at different time points in the lifetime of this fish. These dynamics represent a conspicuous feature of sturgeons, unparalleled among extant vertebrates, and appropriate to scrutinize developmental and evolutionary underpinnings of vertebrate odontogenesis.
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Affiliation(s)
- Anna Pospisilova
- Department of Zoology, Faculty of Science, Charles University, Prague, Czech Republic
| | - Jan Stundl
- Department of Zoology, Faculty of Science, Charles University, Prague, Czech Republic.,Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, California, USA.,Faculty of Fisheries and Protection of Waters, South Bohemian Research Center of Aquaculture and Biodiversity of Hydrocenoses, Research Institute of Fish Culture and Hydrobiology, University of South Bohemia in České Budějovice, Vodňany, Czech Republic
| | - Jindrich Brejcha
- Department of Philosophy and History of Science, Faculty of Science, Charles University, Prague, Czech Republic
| | - Brian D Metscher
- Department of Evolutionary Biology, University of Vienna, Vienna, Austria
| | - Martin Psenicka
- Faculty of Fisheries and Protection of Waters, South Bohemian Research Center of Aquaculture and Biodiversity of Hydrocenoses, Research Institute of Fish Culture and Hydrobiology, University of South Bohemia in České Budějovice, Vodňany, Czech Republic
| | - Robert Cerny
- Department of Zoology, Faculty of Science, Charles University, Prague, Czech Republic
| | - Vladimír Soukup
- Department of Zoology, Faculty of Science, Charles University, Prague, Czech Republic
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18
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Williams KL, Evans KM, Simons AM. Tooth replacement and attachment morphology in the Pacific Leaping Blenny, Alticus arnoldorum (Blenniiformes: Blenniidae: Salariini) with a discussion on tooth function. Anat Rec (Hoboken) 2021; 305:1787-1803. [PMID: 34708582 DOI: 10.1002/ar.24819] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2021] [Revised: 09/08/2021] [Accepted: 09/28/2021] [Indexed: 11/06/2022]
Abstract
Modes of teleost tooth replacement and attachment have historically been described using discrete classification systems that categorize major patterns across taxa. While useful, these discrete classification schemes understate teleost tooth diversity. The "unattached" dentition of salariin combtooth blennies (Blenniiformes: Blenniidae: Salariini) is frequently overlooked due to its perceived complexity, so we examined the Pacific Leaping Blenny, Alticus arnoldorum, to describe this complex morphology. Using a range of methods including histology, SEM, microCT scanning, and clearing and staining, we establish a descriptive model of tooth replacement for A. arnoldorum. We then use our descriptive model of tooth replacement to propose a hypothesis of tooth function in salariin blennies. Our results show that A. arnoldorum exhibits grouped, extraosseous replacement of feeding teeth upon a discontinuous, permanent dental lamina. We also find that tooth replacement occurs within lip tissue that is laterally displaced from the distal margins of the jaw bones, a process previously undocumented in teleost fish. Feeding teeth attach to the dentigerous bone via a primary attachment mode consisting of a continuous collagen band at the posterior base of the teeth, and a secondary attachment mode consisting of epithelial cells. Alticus arnoldorum presents novel modes of tooth replacement and attachment that challenge historical classification modes of teleost dentition. Our descriptive tooth replacement model also provides a reliable framework to propose hypotheses of tooth function that can be applied in future comparative studies on salariin blennies and other long-toothed teleosts to further elucidate the functional role of long-toothed fishes in aquatic ecosystems.
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Affiliation(s)
- Keiffer L Williams
- Department of Biological Sciences, Clemson University, Clemson, South Carolina, USA
| | - Kory M Evans
- Department of BioSciences, Rice University, Houston, Texas, USA
| | - Andrew M Simons
- Department of Fisheries, Wildlife and Conservation Biology, University of Minnesota, Saint Paul, Minnesota, USA.,Bell Museum of Natural History, University of Minnesota, Saint Paul, Minnesota, USA
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19
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Lafuma F, Corfe IJ, Clavel J, Di-Poï N. Multiple evolutionary origins and losses of tooth complexity in squamates. Nat Commun 2021; 12:6001. [PMID: 34650041 PMCID: PMC8516937 DOI: 10.1038/s41467-021-26285-w] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2020] [Accepted: 09/27/2021] [Indexed: 11/21/2022] Open
Abstract
Teeth act as tools for acquiring and processing food, thus holding a prominent role in vertebrate evolution. In mammals, dental-dietary adaptations rely on tooth complexity variations controlled by cusp number and pattern. Complexity increase through cusp addition has dominated the diversification of mammals. However, studies of Mammalia alone cannot reveal patterns of tooth complexity conserved throughout vertebrate evolution. Here, we use morphometric and phylogenetic comparative methods across fossil and extant squamates to show they also repeatedly evolved increasingly complex teeth, but with more flexibility than mammals. Since the Late Jurassic, multiple-cusped teeth evolved over 20 times independently from a single-cusped common ancestor. Squamates frequently lost cusps and evolved varied multiple-cusped morphologies at heterogeneous rates. Tooth complexity evolved in correlation with changes in plant consumption, resulting in several major increases in speciation. Complex teeth played a critical role in vertebrate evolution outside Mammalia, with squamates exemplifying a more labile system of dental-dietary evolution.
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Affiliation(s)
- Fabien Lafuma
- Institute of Biotechnology, Helsinki Institute of Life Science, University of Helsinki, FI-00014, Helsinki, Finland.
| | - Ian J Corfe
- Institute of Biotechnology, Helsinki Institute of Life Science, University of Helsinki, FI-00014, Helsinki, Finland.
- Geological Survey of Finland, FI-02150, Espoo, Finland.
| | - Julien Clavel
- Department of Life Sciences, The Natural History Museum, London, SW7 5BD, UK
- Univ. Lyon, Université Claude Bernard Lyon 1, CNRS, ENTPE, UMR 5023 LEHNA, F-69622, Villeurbanne, France
| | - Nicolas Di-Poï
- Institute of Biotechnology, Helsinki Institute of Life Science, University of Helsinki, FI-00014, Helsinki, Finland.
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20
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Carr EM, Summers AP, Cohen KE. The moment of tooth: rate, fate and pattern of Pacific lingcod dentition revealed by pulse-chase. Proc Biol Sci 2021; 288:20211436. [PMID: 34641728 PMCID: PMC8511758 DOI: 10.1098/rspb.2021.1436] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2021] [Accepted: 09/21/2021] [Indexed: 11/12/2022] Open
Abstract
Tooth replacement rates of polyphyodont cartilaginous and bony fishes are hard to determine because of a lack of obvious patterning and maintaining specimens long enough to observe replacement. Pulse-chase is a fluorescent technique that differentially colours developing mineralized tissue. We present in situ tooth replacement rate and position data for the oral and pharyngeal detentions of Ophiodon elongatus (Pacific lingcod). We assessed over 10 000 teeth, in 20 fish, and found a daily replacement rate of about two teeth (3.6% of the dentition). The average tooth is in the dental battery for 27 days. The replacement was higher in the lower pharyngeal jaw (LPJ). We found no difference between replacement rates of feeding and non-feeding fish, suggesting feeding was not a driver of tooth replacement. Lingcod teeth have both a size and location fate; smaller teeth at one spot will not grow into larger teeth, even if a large tooth nearby is lost. We also found increased rates of replacement at the posterior of the LPJ relative to the anterior. We propose that lingcod teeth do not migrate in the jaw as they develop; their teeth are fated in size and location, erupting in their functional position.
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Affiliation(s)
- E. M. Carr
- Integrative Biology, University of South Florida, Tampa, FL, USA
| | - A. P. Summers
- Friday Harbor Labs, University of Washington, Friday Harbor, WA, USA
| | - K. E. Cohen
- Biology Department, University of Washington, Seattle, WA, USA
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21
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Huysseune A, Cerny R, Witten PE. The conundrum of pharyngeal teeth origin: the role of germ layers, pouches, and gill slits. Biol Rev Camb Philos Soc 2021; 97:414-447. [PMID: 34647411 PMCID: PMC9293187 DOI: 10.1111/brv.12805] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2021] [Revised: 09/27/2021] [Accepted: 09/29/2021] [Indexed: 12/15/2022]
Abstract
There are several competing hypotheses on tooth origins, with discussions eventually settling in favour of an 'outside-in' scenario, in which internal odontodes (teeth) derived from external odontodes (skin denticles) in jawless vertebrates. The evolution of oral teeth from skin denticles can be intuitively understood from their location at the mouth entrance. However, the basal condition for jawed vertebrates is arguably to possess teeth distributed throughout the oropharynx (i.e. oral and pharyngeal teeth). As skin denticle development requires the presence of ectoderm-derived epithelium and of mesenchyme, it remains to be answered how odontode-forming skin epithelium, or its competence, were 'transferred' deep into the endoderm-covered oropharynx. The 'modified outside-in' hypothesis for tooth origins proposed that this transfer was accomplished through displacement of odontogenic epithelium, that is ectoderm, not only through the mouth, but also via any opening (e.g. gill slits) that connects the ectoderm to the epithelial lining of the pharynx (endoderm). This review explores from an evolutionary and from a developmental perspective whether ectoderm plays a role in (pharyngeal) tooth and denticle formation. Historic and recent studies on tooth development show that the odontogenic epithelium (enamel organ) of oral or pharyngeal teeth can be of ectodermal, endodermal, or of mixed ecto-endodermal origin. Comprehensive data are, however, only available for a few taxa. Interestingly, in these taxa, the enamel organ always develops from the basal layer of a stratified epithelium that is at least bilayered. In zebrafish, a miniaturised teleost that only retains pharyngeal teeth, an epithelial surface layer with ectoderm-like characters is required to initiate the formation of an enamel organ from the basal, endodermal epithelium. In urodele amphibians, the bilayered epithelium is endodermal, but the surface layer acquires ectodermal characters, here termed 'epidermalised endoderm'. Furthermore, ectoderm-endoderm contacts at pouch-cleft boundaries (i.e. the prospective gill slits) are important for pharyngeal tooth initiation, even if the influx of ectoderm via these routes is limited. A balance between sonic hedgehog and retinoic acid signalling could operate to assign tooth-initiating competence to the endoderm at the level of any particular pouch. In summary, three characters are identified as being required for pharyngeal tooth formation: (i) pouch-cleft contact, (ii) a stratified epithelium, of which (iii) the apical layer adopts ectodermal features. These characters delimit the area in which teeth can form, yet cannot alone explain the distribution of teeth over the different pharyngeal arches. The review concludes with a hypothetical evolutionary scenario regarding the persisting influence of ectoderm on pharyngeal tooth formation. Studies on basal osteichthyans with less-specialised types of early embryonic development will provide a crucial test for the potential role of ectoderm in pharyngeal tooth formation and for the 'modified outside-in' hypothesis of tooth origins.
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Affiliation(s)
- Ann Huysseune
- Research Group Evolutionary Developmental Biology, Biology Department, Ghent University, K.L. Ledeganckstraat 35, Ghent, B-9000, Belgium
| | - Robert Cerny
- Department of Zoology, Faculty of Science, Charles University, Vinicna 7, Prague, 128 44, Czech Republic
| | - P Eckhard Witten
- Research Group Evolutionary Developmental Biology, Biology Department, Ghent University, K.L. Ledeganckstraat 35, Ghent, B-9000, Belgium
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22
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Conith AJ, Albertson RC. The cichlid oral and pharyngeal jaws are evolutionarily and genetically coupled. Nat Commun 2021; 12:5477. [PMID: 34531386 PMCID: PMC8445992 DOI: 10.1038/s41467-021-25755-5] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2021] [Accepted: 08/30/2021] [Indexed: 02/08/2023] Open
Abstract
Evolutionary constraints may significantly bias phenotypic change, while "breaking" from such constraints can lead to expanded ecological opportunity. Ray-finned fishes have broken functional constraints by developing two jaws (oral-pharyngeal), decoupling prey capture (oral jaw) from processing (pharyngeal jaw). It is hypothesized that the oral and pharyngeal jaws represent independent evolutionary modules and this facilitated diversification in feeding architectures. Here we test this hypothesis in African cichlids. Contrary to our expectation, we find integration between jaws at multiple evolutionary levels. Next, we document integration at the genetic level, and identify a candidate gene, smad7, within a pleiotropic locus for oral and pharyngeal jaw shape that exhibits correlated expression between the two tissues. Collectively, our data show that African cichlid evolutionary success has occurred within the context of a coupled jaw system, an attribute that may be driving adaptive evolution in this iconic group by facilitating rapid shifts between foraging habitats, providing an advantage in a stochastic environment such as the East African Rift-Valley.
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Affiliation(s)
- Andrew J Conith
- Biology Department, University of Massachusetts Amherst, Amherst, MA, 01003, USA.
| | - R Craig Albertson
- Biology Department, University of Massachusetts Amherst, Amherst, MA, 01003, USA.
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Patil C, Sylvester JB, Abdilleh K, Norsworthy MW, Pottin K, Malinsky M, Bloomquist RF, Johnson ZV, McGrath PT, Streelman JT. Genome-enabled discovery of evolutionary divergence in brains and behavior. Sci Rep 2021; 11:13016. [PMID: 34155279 PMCID: PMC8217251 DOI: 10.1038/s41598-021-92385-8] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2021] [Accepted: 06/08/2021] [Indexed: 02/05/2023] Open
Abstract
Lake Malawi cichlid fishes exhibit extensive divergence in form and function built from a relatively small number of genetic changes. We compared the genomes of rock- and sand-dwelling species and asked which genetic variants differed among the groups. We found that 96% of differentiated variants reside in non-coding sequence but these non-coding diverged variants are evolutionarily conserved. Genome regions near differentiated variants are enriched for craniofacial, neural and behavioral categories. Following leads from genome sequence, we used rock- vs. sand-species and their hybrids to (i) delineate the push-pull roles of BMP signaling and irx1b in the specification of forebrain territories during gastrulation and (ii) reveal striking context-dependent brain gene expression during adult social behavior. Our results demonstrate how divergent genome sequences can predict differences in key evolutionary traits. We highlight the promise of evolutionary reverse genetics-the inference of phenotypic divergence from unbiased genome sequencing and then empirical validation in natural populations.
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Affiliation(s)
- Chinar Patil
- School of Biological Sciences and Petit Institute of Bioengineering and Bioscience, Georgia Institute of Technology, Atlanta, GA, USA.
| | - Jonathan B Sylvester
- School of Biological Sciences and Petit Institute of Bioengineering and Bioscience, Georgia Institute of Technology, Atlanta, GA, USA
- Department of Biology, Georgia State University, Atlanta, GA, USA
| | - Kawther Abdilleh
- School of Biological Sciences and Petit Institute of Bioengineering and Bioscience, Georgia Institute of Technology, Atlanta, GA, USA
| | - Michael W Norsworthy
- Catalog Technologies Inc., Boston, MA, USA
- Freedom of Form Foundation, Inc., Cambridge, MA, USA
| | - Karen Pottin
- Laboratoire de Biologie du Dévelopement (IBPS-LBD, UMR7622), CNRS, Institut de Biologie Paris Seine, Sorbonne Université, Paris, France
| | - Milan Malinsky
- Department of Environmental Sciences, Zoological Institute, University of Basel, Basel, Switzerland
- Wellcome Trust Sanger Institute, Cambridge, UK
| | - Ryan F Bloomquist
- School of Biological Sciences and Petit Institute of Bioengineering and Bioscience, Georgia Institute of Technology, Atlanta, GA, USA
- Department of Oral Biology and Diagnostic Sciences, Department of Restorative Sciences, Dental College of Georgia, Augusta University, Augusta, GA, USA
| | - Zachary V Johnson
- School of Biological Sciences and Petit Institute of Bioengineering and Bioscience, Georgia Institute of Technology, Atlanta, GA, USA
| | - Patrick T McGrath
- School of Biological Sciences and Petit Institute of Bioengineering and Bioscience, Georgia Institute of Technology, Atlanta, GA, USA
| | - Jeffrey T Streelman
- School of Biological Sciences and Petit Institute of Bioengineering and Bioscience, Georgia Institute of Technology, Atlanta, GA, USA
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Hulsey CD, Meyer A, Streelman JT. Convergent Evolution of Cichlid Fish Pharyngeal Jaw Dentitions in Mollusk-Crushing Predators: Comparative X-Ray Computed Tomography of Tooth Sizes, Numbers, and Replacement. Integr Comp Biol 2021; 60:656-664. [PMID: 32584994 DOI: 10.1093/icb/icaa089] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
Dental convergence is a hallmark of cichlid fish adaptive radiations. This type of repeated evolution characterizes both the oral jaws of these fishes as well as their pharyngeal jaws that are modified gill arches used to functionally process prey like hard-shelled mollusks. To test several hypotheses regarding the evolution of cichlid crushing pharyngeal dentitions, we used X-ray computed tomography scans to comparatively examine dental evolution in the pharyngeal jaw of a diversity of New World Heroine cichlid lineages. The substantial variation in erupted tooth sizes and numbers as well as replacement teeth found in these fishes showed several general patterns. Larger toothed species tended to have fewer teeth suggesting a potential role of spatial constraints in cichlid dental divergence. Species with larger numbers of erupted pharyngeal teeth also had larger numbers of replacement teeth. Replacement tooth size is almost exactly predicted (r = 0.99) from the size of erupted teeth across all of the species. Mollusk crushing was, therefore, highly associated with not only larger pharyngeal teeth, but also larger replacement teeth. Whether dental divergence arises as a result of environmental induced plasticity or originates via trophic polymorphism as found in the species Herichthys minckleyi, there appear to be general rules that structure interspecific divergence in cichlid pharyngeal erupted and replacement dentitions.
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Affiliation(s)
- C Darrin Hulsey
- Department of Biology, University of Konstanz, Konstanz, Germany
| | - Axel Meyer
- Department of Biology, University of Konstanz, Konstanz, Germany
| | - J Todd Streelman
- School of Biological Sciences, Institute of Technology, Atlanta, GA 30332, USA
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25
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Gorman CE, Hulsey CD. Non-trophic Functional Ecology of Vertebrate Teeth: A Review. Integr Comp Biol 2021; 60:665-675. [PMID: 32573716 DOI: 10.1093/icb/icaa086] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022] Open
Abstract
Teeth are critical to the functional ecology of vertebrate trophic abilities, but are also used for a diversity of other non-trophic tasks. Teeth can play a substantial role in how animals move, manipulate their environment, positively interact with conspecifics, antagonistically interact with other organisms, and sense the environment. We review these non-trophic functions in an attempt to place the utility of human and all other vertebrate dentitions in a more diverse framework that emphasizes an expanded view of the functional importance and ecological diversity of teeth. In light of the extensive understanding of the developmental genetics, trophic functions, and evolutionary history of teeth, comparative studies of vertebrate dentitions will continue to provide unique insights into multi-functionality, many-to-one mapping, and the evolution of novel abilities.
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Affiliation(s)
- Courtney E Gorman
- Department of Biology, University of Konstanz, Konstanz 78457, Germany
| | - C Darrin Hulsey
- Department of Biology, University of Konstanz, Konstanz 78457, Germany
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26
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Karagic N, Meyer A, Hulsey CD. Phenotypic Plasticity in Vertebrate Dentitions. Integr Comp Biol 2021; 60:608-618. [PMID: 32544244 DOI: 10.1093/icb/icaa077] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022] Open
Abstract
Vertebrates interact directly with food items through their dentition, and these interactions with trophic resources could often feedback to influence tooth structure. Although dentitions are often considered to be a fixed phenotype, there is the potential for environmentally induced phenotypic plasticity in teeth to extensively influence their diversity. Here, we review the literature concerning phenotypic plasticity of vertebrate teeth. Even though only a few taxonomically disparate studies have focused on phenotypic plasticity in teeth, there are a number of ways teeth can change their size, shape, or patterns of replacement as a response to the environment. Elucidating the underlying physiological, developmental, and genetic mechanisms that generate phenotypic plasticity can clarify its potential role in the evolution of dental phenotypes.
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Affiliation(s)
- Nidal Karagic
- Department for Zoology and Evolutionary Biology, University of Konstanz, Universitätsstraße 10, Konstanz, 78467, Germany
| | - Axel Meyer
- Department for Zoology and Evolutionary Biology, University of Konstanz, Universitätsstraße 10, Konstanz, 78467, Germany
| | - C Darrin Hulsey
- Department for Zoology and Evolutionary Biology, University of Konstanz, Universitätsstraße 10, Konstanz, 78467, Germany
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27
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Gene coexpression networks reveal molecular interactions underlying cichlid jaw modularity. BMC Ecol Evol 2021; 21:62. [PMID: 33888061 PMCID: PMC8061045 DOI: 10.1186/s12862-021-01787-9] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2020] [Accepted: 04/08/2021] [Indexed: 12/29/2022] Open
Abstract
Background The oral and pharyngeal jaw of cichlid fishes are a classic example of evolutionary modularity as their functional decoupling boosted trophic diversification and contributed to the success of cichlid adaptive radiations. Most studies until now have focused on the functional, morphological, or genetic aspects of cichlid jaw modularity. Here we extend this concept to include transcriptional modularity by sequencing whole transcriptomes of the two jaws and comparing their gene coexpression networks. Results We show that transcriptional decoupling of gene expression underlies the functional decoupling of cichlid oral and pharyngeal jaw apparatus and the two units are evolving independently in recently diverged cichlid species from Lake Tanganyika. Oral and pharyngeal jaw coexpression networks reflect the common origin of the jaw regulatory program as there is high preservation of gene coexpression modules between the two sets of jaws. However, there is substantial rewiring of genetic architecture within those modules. We define a global jaw coexpression network and highlight jaw-specific and species-specific modules within it. Furthermore, we annotate a comprehensive in silico gene regulatory network linking the Wnt and AHR signalling pathways to jaw morphogenesis and response to environmental cues, respectively. Components of these pathways are significantly differentially expressed between the oral and pharyngeal jaw apparatus. Conclusion This study describes the concerted expression of many genes in cichlid oral and pharyngeal jaw apparatus at the onset of the independent life of cichlid fishes. Our findings suggest that – on the basis of an ancestral gill arch network—transcriptional rewiring may have driven the modular evolution of the oral and pharyngeal jaws, highlighting the evolutionary significance of gene network reuse. The gene coexpression and in silico regulatory networks presented here are intended as resource for future studies on the genetics of vertebrate jaw morphogenesis and trophic adaptation. Supplementary Information The online version contains supplementary material available at 10.1186/s12862-021-01787-9.
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Karagic N, Schneider RF, Meyer A, Hulsey CD. A Genomic Cluster Containing Novel and Conserved Genes is Associated with Cichlid Fish Dental Developmental Convergence. Mol Biol Evol 2021; 37:3165-3174. [PMID: 32579214 DOI: 10.1093/molbev/msaa153] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022] Open
Abstract
The two toothed jaws of cichlid fishes provide textbook examples of convergent evolution. Tooth phenotypes such as enlarged molar-like teeth used to process hard-shelled mollusks have evolved numerous times independently during cichlid diversification. Although the ecological benefit of molar-like teeth to crush prey is known, it is unclear whether the same molecular mechanisms underlie these convergent traits. To identify genes involved in the evolution and development of enlarged cichlid teeth, we performed RNA-seq on the serially homologous-toothed oral and pharyngeal jaws as well as the fourth toothless gill arch of Astatoreochromis alluaudi. We identified 27 genes that are highly upregulated on both tooth-bearing jaws compared with the toothless gill arch. Most of these genes have never been reported to play a role in tooth formation. Two of these genes (unk, rpfA) are not found in other vertebrate genomes but are present in all cichlid genomes. They also cluster genomically with two other highly expressed tooth genes (odam, scpp5) that exhibit conserved expression during vertebrate odontogenesis. Unk and rpfA were confirmed via in situ hybridization to be expressed in developing teeth of Astatotilapia burtoni. We then examined expression of the cluster's four genes in six evolutionarily independent and phylogenetically disparate cichlid species pairs each with a large- and a small-toothed species. Odam and unk commonly and scpp5 and rpfA always showed higher expression in larger toothed cichlid jaws. Convergent trophic adaptations across cichlid diversity are associated with the repeated developmental deployment of this genomic cluster containing conserved and novel cichlid-specific genes.
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Affiliation(s)
- Nidal Karagic
- Department for Zoology and Evolutionary Biology, University of Konstanz, Konstanz, Germany
| | - Ralf F Schneider
- Department for Zoology and Evolutionary Biology, University of Konstanz, Konstanz, Germany
| | - Axel Meyer
- Department for Zoology and Evolutionary Biology, University of Konstanz, Konstanz, Germany
| | - C Darrin Hulsey
- Department for Zoology and Evolutionary Biology, University of Konstanz, Konstanz, Germany
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29
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Berio F, Debiais-Thibaud M. Evolutionary developmental genetics of teeth and odontodes in jawed vertebrates: a perspective from the study of elasmobranchs. JOURNAL OF FISH BIOLOGY 2021; 98:906-918. [PMID: 31820456 DOI: 10.1111/jfb.14225] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/03/2019] [Accepted: 12/09/2019] [Indexed: 06/10/2023]
Abstract
Most extant vertebrates display a high variety of tooth and tooth-like organs (odontodes) that vary in shape, position over the body and nature of composing tissues. The development of these structures is known to involve similar genetic cascades and teeth and odontodes are believed to share a common evolutionary history. Gene expression patterns have previously been compared between mammalian and teleost tooth development but we highlight how the comparative framework was not always properly defined to deal with different tooth types or tooth developmental stages. Larger-scale comparative analyses also included cartilaginous fishes: sharks display oral teeth and dermal scales for which the gene expression during development started to be investigated in the small-spotted catshark Scyliorhinus canicula during the past decade. We report several descriptive approaches to analyse the embryonic tooth and caudal scale gene expressions in S. canicula. We compare these expressions wih the ones reported in mouse molars and teleost oral and pharyngeal teeth and highlight contributions and biases that arise from these interspecific comparisons. We finally discuss the evolutionary processes that can explain the observed intra and interspecific similarities and divergences in the genetic cascades involved in tooth and odontode development in jawed vertebrates.
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Affiliation(s)
- Fidji Berio
- Institut des Sciences de l'Evolution de Montpellier, ISEM, Univ Montpellier, CNRS, IRD, EPHE, Montpellier, France
- University of Lyon, Ecole Normale Supérieure de Lyon, Centre National de la Recherche Scientifique, Université Claude Bernard Lyon 1, Institut de Génomique Fonctionnelle de Lyon, UMR5242, 46 Allée d'Italie, Lyon, France
| | - Mélanie Debiais-Thibaud
- Institut des Sciences de l'Evolution de Montpellier, ISEM, Univ Montpellier, CNRS, IRD, EPHE, Montpellier, France
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Square TA, Sundaram S, Mackey EJ, Miller CT. Distinct tooth regeneration systems deploy a conserved battery of genes. EvoDevo 2021; 12:4. [PMID: 33766133 PMCID: PMC7995769 DOI: 10.1186/s13227-021-00172-3] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2020] [Accepted: 01/13/2021] [Indexed: 01/01/2023] Open
Abstract
BACKGROUND Vertebrate teeth exhibit a wide range of regenerative systems. Many species, including most mammals, reptiles, and amphibians, form replacement teeth at a histologically distinct location called the successional dental lamina, while other species do not employ such a system. Notably, a 'lamina-less' tooth replacement condition is found in a paraphyletic array of ray-finned fishes, such as stickleback, trout, cod, medaka, and bichir. Furthermore, the position, renewal potential, and latency times appear to vary drastically across different vertebrate tooth regeneration systems. The progenitor cells underlying tooth regeneration thus present highly divergent arrangements and potentials. Given the spectrum of regeneration systems present in vertebrates, it is unclear if morphologically divergent tooth regeneration systems deploy an overlapping battery of genes in their naïve dental tissues. RESULTS In the present work, we aimed to determine whether or not tooth progenitor epithelia could be composed of a conserved cell type between vertebrate dentitions with divergent regeneration systems. To address this question, we compared the pharyngeal tooth regeneration processes in two ray-finned fishes: zebrafish (Danio rerio) and threespine stickleback (Gasterosteus aculeatus). These two teleost species diverged approximately 250 million years ago and demonstrate some stark differences in dental morphology and regeneration. Here, we find that the naïve successional dental lamina in zebrafish expresses a battery of nine genes (bmpr1aa, bmp6, cd34, gli1, igfbp5a, lgr4, lgr6, nfatc1, and pitx2), while active Wnt signaling and Lef1 expression occur during early morphogenesis stages of tooth development. We also find that, despite the absence of a histologically distinct successional dental lamina in stickleback tooth fields, the same battery of nine genes (Bmpr1a, Bmp6, CD34, Gli1, Igfbp5a, Lgr4, Lgr6, Nfatc1, and Pitx2) are expressed in the basalmost endodermal cell layer, which is the region most closely associated with replacement tooth germs. Like zebrafish, stickleback replacement tooth germs additionally express Lef1 and exhibit active Wnt signaling. Thus, two fish systems that either have an organized successional dental lamina (zebrafish) or lack a morphologically distinct successional dental lamina (sticklebacks) deploy similar genetic programs during tooth regeneration. CONCLUSIONS We propose that the expression domains described here delineate a highly conserved "successional dental epithelium" (SDE). Furthermore, a set of orthologous genes is known to mark hair follicle epithelial stem cells in mice, suggesting that regenerative systems in other epithelial appendages may utilize a related epithelial progenitor cell type, despite the highly derived nature of the resulting functional organs.
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Affiliation(s)
- Tyler A Square
- Department of Molecular & Cell Biology, University of California, Berkeley, USA.
| | - Shivani Sundaram
- Department of Molecular & Cell Biology, University of California, Berkeley, USA
| | - Emma J Mackey
- Department of Molecular & Cell Biology, University of California, Berkeley, USA
| | - Craig T Miller
- Department of Molecular & Cell Biology, University of California, Berkeley, USA.
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Mehta TK, Koch C, Nash W, Knaack SA, Sudhakar P, Olbei M, Bastkowski S, Penso-Dolfin L, Korcsmaros T, Haerty W, Roy S, Di-Palma F. Evolution of regulatory networks associated with traits under selection in cichlids. Genome Biol 2021; 22:25. [PMID: 33419455 PMCID: PMC7791837 DOI: 10.1186/s13059-020-02208-8] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2020] [Accepted: 11/18/2020] [Indexed: 12/15/2022] Open
Abstract
BACKGROUND Seminal studies of vertebrate protein evolution speculated that gene regulatory changes can drive anatomical innovations. However, very little is known about gene regulatory network (GRN) evolution associated with phenotypic effect across ecologically diverse species. Here we use a novel approach for comparative GRN analysis in vertebrate species to study GRN evolution in representative species of the most striking examples of adaptive radiations, the East African cichlids. We previously demonstrated how the explosive phenotypic diversification of East African cichlids can be attributed to diverse molecular mechanisms, including accelerated regulatory sequence evolution and gene expression divergence. RESULTS To investigate these mechanisms across species at a genome-wide scale, we develop a novel computational pipeline that predicts regulators for co-extant and ancestral co-expression modules along a phylogeny, and candidate regulatory regions associated with traits under selection in cichlids. As a case study, we apply our approach to a well-studied adaptive trait-the visual system-for which we report striking cases of network rewiring for visual opsin genes, identify discrete regulatory variants, and investigate their association with cichlid visual system evolution. In regulatory regions of visual opsin genes, in vitro assays confirm that transcription factor binding site mutations disrupt regulatory edges across species and segregate according to lake species phylogeny and ecology, suggesting GRN rewiring in radiating cichlids. CONCLUSIONS Our approach reveals numerous novel potential candidate regulators and regulatory regions across cichlid genomes, including some novel and some previously reported associations to known adaptive evolutionary traits.
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Affiliation(s)
| | - Christopher Koch
- Department of Biostatistics and Medical Informatics, UW Madison, Madison, USA
| | | | - Sara A Knaack
- Wisconsin Institute for Discovery (WID), Madison, USA
| | | | - Marton Olbei
- Earlham Institute (EI), Norwich, UK
- Quadram Institute, Norwich, UK
| | - Sarah Bastkowski
- Earlham Institute (EI), Norwich, UK
- Quadram Institute, Norwich, UK
| | | | - Tamas Korcsmaros
- Earlham Institute (EI), Norwich, UK
- Quadram Institute, Norwich, UK
| | | | - Sushmita Roy
- Department of Biostatistics and Medical Informatics, UW Madison, Madison, USA.
- Wisconsin Institute for Discovery (WID), Madison, USA.
- Department of Computer Sciences, UW Madison, Madison, USA.
| | - Federica Di-Palma
- Earlham Institute (EI), Norwich, UK.
- Norwich Medical School, University of East Anglia, Norwich, UK.
- School of Biological Sciences, University of East Anglia, Norwich, UK.
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Atukorala ADS, Ratnayake RK. Cellular and molecular mechanisms in the development of a cleft lip and/or cleft palate; insights from zebrafish (Danio rerio). Anat Rec (Hoboken) 2020; 304:1650-1660. [PMID: 33099891 DOI: 10.1002/ar.24547] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/29/2020] [Revised: 08/31/2020] [Accepted: 09/09/2020] [Indexed: 12/18/2022]
Abstract
Human cleft lip and/or palate (CLP) are immediately recognizable congenital abnormalities of the face. Lip and palate develop from facial primordia through the coordinated activities of ectodermal epithelium and neural crest cells (NCCs) derived from ectomesenchyme tissue. Subtle changes in the regulatory mechanisms of NCC or ectodermal epithelial cells can result in CLP. Genetic and environmental contributions or a combination of both play a significant role in the progression of CLP. Model organisms provide us with a wealth of information in understanding the pathophysiology and genetic etiology of this complex disease. Small teleost, zebrafish (Danio rerio) is one of the popular model in craniofacial developmental biology. The short generation time and large number of optically transparent, easily manipulated embryos increase the value of zebrafish to identify novel candidate genes and gene regulatory networks underlying craniofacial development. In addition, it is widely used to identify the mechanisms of environmental teratogens and in therapeutic drug screening. Here, we discuss the value of zebrafish as a model to understand epithelial and NCC induced ectomesenchymal cell activities during early palate morphogenesis and robustness of the zebrafish in modern research on identifying the genetic and environmental etiological factors of CLP.
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Affiliation(s)
- Atukorallaya Devi Sewvandini Atukorala
- Rady Faculty of Health Sciences, Department of Oral Biology, Dr. Gerald Niznick College of Dentistry, University of Manitoba, Winnipeg, Manitoba, Canada
| | - Ravindra Kumar Ratnayake
- Rady Faculty of Health Sciences, Department of Oral Biology, Dr. Gerald Niznick College of Dentistry, University of Manitoba, Winnipeg, Manitoba, Canada
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Cadiz L, Jonz MG. A comparative perspective on lung and gill regeneration. ACTA ACUST UNITED AC 2020; 223:223/19/jeb226076. [PMID: 33037099 DOI: 10.1242/jeb.226076] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
The ability to continuously grow and regenerate the gills throughout life is a remarkable property of fish and amphibians. Considering that gill regeneration was first described over one century ago, it is surprising that the underlying mechanisms of cell and tissue replacement in the gills remain poorly understood. By contrast, the mammalian lung is a largely quiescent organ in adults but is capable of facultative regeneration following injury. In the course of the past decade, it has been recognized that lungs contain a population of stem or progenitor cells with an extensive ability to restore tissue; however, despite recent advances in regenerative biology of the lung, the signaling pathways that underlie regeneration are poorly understood. In this Review, we discuss the common evolutionary and embryological origins shared by gills and mammalian lungs. These are evident in homologies in tissue structure, cell populations, cellular function and genetic pathways. An integration of the literature on gill and lung regeneration in vertebrates is presented using a comparative approach in order to outline the challenges that remain in these areas, and to highlight the importance of using aquatic vertebrates as model organisms. The study of gill regeneration in fish and amphibians, which have a high regenerative potential and for which genetic tools are widely available, represents a unique opportunity to uncover common signaling mechanisms that may be important for regeneration of respiratory organs in all vertebrates. This may lead to new advances in tissue repair following lung disease.
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Affiliation(s)
- Laura Cadiz
- Department of Biology, University of Ottawa, 30 Marie Curie Pvt., Ottawa, ON, Canada, K1N 6N5
| | - Michael G Jonz
- Department of Biology, University of Ottawa, 30 Marie Curie Pvt., Ottawa, ON, Canada, K1N 6N5
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Cunha AS, Vertuan Dos Santos L, Schaffer Pugsley Baratto S, Abbasoglu Z, Gerber JT, Paza A, Matsumoto MAN, Scariot R, Stuani MB, Küchler EC. Human permanent tooth sizes are associated with genes encoding oestrogen receptors. J Orthod 2020; 48:24-32. [PMID: 32985343 DOI: 10.1177/1465312520958710] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
OBJECTIVE To evaluate if genetic polymorphisms in the oestrogen receptor 1 (ESR1) and oestrogen receptor 2 (ESR2) genes encoded for oestrogen receptors alpha (ERα) and beta (ERβ) are involved in permanent tooth size. DESIGN Cross-sectional study. SETTING Orthodontic Clinic at School of Dentistry of Ribeirão Preto, University of São Paulo. PARTICIPANTS A total of 108 orthodontic patients. MATERIALS AND METHODS Pre-treatment orthodontic records were evaluated. Dental casts were used to determine the maximum crown measurements of fully erupted permanent teeth in the mesiodistal dimensions. Second and third molars were not included in the analysis. Genomic DNA samples were used for the genotyping of four genetic polymorphisms: ESR1 (rs9340799 and rs2234693) and ESR2 (rs1256049 and rs4986938). The associations between tooth size and sex were evaluated using t test. The associations between tooth size and genotype were analysed with linear regression and adjusted by sex at an alpha of P⩽0.05. RESULTS Female patients presented smaller tooth size than male patients. A statistically significant difference was observed in almost all teeth (P<0.05). The genetic polymorphisms in rs9340799, rs2234693, rs1256049 and rs4986938 were associated with some tooth sizes in both the maxilla and mandible (P<0.05). CONCLUSION This study provides evidence that genetic polymorphisms in ESR1 and ESR2 could be associated with tooth size in permanent teeth.
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Affiliation(s)
- Arthur S Cunha
- Department of Orthodontics, School of Dentistry, State University of Rio de Janeiro, Rio de Janeiro, Brazil
| | - Luiza Vertuan Dos Santos
- Department of Pediatric Dentistry, School of Dentistry of Ribeirão Preto, University of São Paulo, Ribeirão Preto, São Paulo, Brazil
| | | | - Zerrin Abbasoglu
- Department of Pediatric Dentistry, Yeditepe University, Istanbul, Turkey
| | - Jennifer Tsi Gerber
- School of Health and Biological Sciences, Universidade Positivo, Curitiba, Brazil
| | - Aleysson Paza
- School of Dentistry, Univille University, Joinville, Brazil
| | - Mírian Aiko Nakane Matsumoto
- Department of Pediatric Dentistry, School of Dentistry of Ribeirão Preto, University of São Paulo, Ribeirão Preto, São Paulo, Brazil
| | - Rafaela Scariot
- School of Health and Biological Sciences, Universidade Positivo, Curitiba, Brazil
| | - Maria Bernadete Stuani
- Department of Pediatric Dentistry, School of Dentistry of Ribeirão Preto, University of São Paulo, Ribeirão Preto, São Paulo, Brazil
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Samuels BD, Aho R, Brinkley JF, Bugacov A, Feingold E, Fisher S, Gonzalez-Reiche AS, Hacia JG, Hallgrimsson B, Hansen K, Harris MP, Ho TV, Holmes G, Hooper JE, Jabs EW, Jones KL, Kesselman C, Klein OD, Leslie EJ, Li H, Liao EC, Long H, Lu N, Maas RL, Marazita ML, Mohammed J, Prescott S, Schuler R, Selleri L, Spritz RA, Swigut T, van Bakel H, Visel A, Welsh I, Williams C, Williams TJ, Wysocka J, Yuan Y, Chai Y. FaceBase 3: analytical tools and FAIR resources for craniofacial and dental research. Development 2020; 147:dev191213. [PMID: 32958507 PMCID: PMC7522026 DOI: 10.1242/dev.191213] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2020] [Accepted: 08/13/2020] [Indexed: 12/12/2022]
Abstract
The FaceBase Consortium was established by the National Institute of Dental and Craniofacial Research in 2009 as a 'big data' resource for the craniofacial research community. Over the past decade, researchers have deposited hundreds of annotated and curated datasets on both normal and disordered craniofacial development in FaceBase, all freely available to the research community on the FaceBase Hub website. The Hub has developed numerous visualization and analysis tools designed to promote integration of multidisciplinary data while remaining dedicated to the FAIR principles of data management (findability, accessibility, interoperability and reusability) and providing a faceted search infrastructure for locating desired data efficiently. Summaries of the datasets generated by the FaceBase projects from 2014 to 2019 are provided here. FaceBase 3 now welcomes contributions of data on craniofacial and dental development in humans, model organisms and cell lines. Collectively, the FaceBase Consortium, along with other NIH-supported data resources, provide a continuously growing, dynamic and current resource for the scientific community while improving data reproducibility and fulfilling data sharing requirements.
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Affiliation(s)
- Bridget D Samuels
- Center for Craniofacial Molecular Biology, Herman Ostrow School of Dentistry, University of Southern California, Los Angeles, CA 90033, USA
| | - Robert Aho
- Program in Craniofacial Biology, Departments of Orofacial Sciences and of Anatomy, Institute of Human Genetics, University of California San Francisco, San Francisco, CA 94143, USA
| | - James F Brinkley
- Structural Informatics Group, Department of Biological Structure, University of Washington, Seattle, WA 98195, USA
| | - Alejandro Bugacov
- Information Sciences Institute, Viterbi School of Engineering, University of Southern California, Marina del Rey, CA 90292, USA
| | - Eleanor Feingold
- Department of Human Genetics, Graduate School of Public Health, University of Pittsburgh, Pittsburgh, PA 15219, USA
| | - Shannon Fisher
- Department of Pharmacology and Experimental Therapeutics, Boston University School of Medicine, Boston, MA 02118, USA
| | - Ana S Gonzalez-Reiche
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Joseph G Hacia
- Department of Biochemistry and Molecular Medicine, Keck School of Medicine, University of Southern California, Los Angeles, CA 90033, USA
| | - Benedikt Hallgrimsson
- Department of Cell Biology and Anatomy, Alberta Children's Hospital Research Institute, and McCaig Bone and Joint Institute, University of Calgary, Alberta, Canada
| | - Karissa Hansen
- Program in Craniofacial Biology, Departments of Orofacial Sciences and of Anatomy, Institute of Human Genetics, University of California San Francisco, San Francisco, CA 94143, USA
| | - Matthew P Harris
- Department of Orthopedic Research, Boston Children's Hospital and Department of Genetics, Harvard Medical School, Boston, MA 02115, USA
| | - Thach-Vu Ho
- Center for Craniofacial Molecular Biology, Herman Ostrow School of Dentistry, University of Southern California, Los Angeles, CA 90033, USA
| | - Greg Holmes
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Joan E Hooper
- Department of Cell and Developmental Biology, School of Medicine, University of Colorado, Aurora, CO 80045, USA
| | - Ethylin Wang Jabs
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Kenneth L Jones
- Department of Biochemistry and Molecular Genetics, School of Medicine, University of Colorado, Aurora, CO 80045, USA
| | - Carl Kesselman
- Information Sciences Institute, Viterbi School of Engineering, University of Southern California, Marina del Rey, CA 90292, USA
| | - Ophir D Klein
- Program in Craniofacial Biology, Departments of Orofacial Sciences and Pediatrics, Institute for Human Genetics, University of California San Francisco, San Francisco, CA 94143, USA
| | | | - Hong Li
- Department of Craniofacial Biology, School of Dental Medicine, University of Colorado, Aurora, CO 80045, USA
| | - Eric C Liao
- Massachusetts General Hospital, Plastic and Reconstructive Surgery, Boston, MA 02114, USA
| | - Hannah Long
- Departments of Chemical and Systems Biology and of Developmental Biology, Howard Hughes Medical Institute, School of Medicine, Stanford University, Stanford, CA 94305, USA
| | - Na Lu
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Richard L Maas
- Division of Genetics, Brigham and Women's Hospital, Harvard Medical School, Boston, MA 02115, USA
| | - Mary L Marazita
- Department of Human Genetics, Graduate School of Public Health, University of Pittsburgh, Pittsburgh, PA 15219, USA
- Center for Craniofacial and Dental Genetics, Department of Oral Biology, School of Dental Medicine, University of Pittsburgh, Pittsburgh, PA 15219, USA
- Clinical and Translational Science, School of Medicine, University of Pittsburgh, Pittsburgh, PA 15219, USA
| | - Jaaved Mohammed
- Departments of Chemical and Systems Biology and of Developmental Biology, Howard Hughes Medical Institute, School of Medicine, Stanford University, Stanford, CA 94305, USA
| | - Sara Prescott
- Departments of Chemical and Systems Biology and of Developmental Biology, Howard Hughes Medical Institute, School of Medicine, Stanford University, Stanford, CA 94305, USA
| | - Robert Schuler
- Information Sciences Institute, Viterbi School of Engineering, University of Southern California, Marina del Rey, CA 90292, USA
| | - Licia Selleri
- Program in Craniofacial Biology, Departments of Orofacial Sciences and of Anatomy, Institute of Human Genetics, University of California San Francisco, San Francisco, CA 94143, USA
| | - Richard A Spritz
- Human Medical Genetics and Genomics Program, School of Medicine, University of Colorado, Aurora, CO 80045, USA
| | - Tomek Swigut
- Departments of Chemical and Systems Biology and of Developmental Biology, Howard Hughes Medical Institute, School of Medicine, Stanford University, Stanford, CA 94305, USA
| | - Harm van Bakel
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Axel Visel
- Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
- U.S. Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
- School of Natural Sciences, University of California Merced, Merced, CA 95343, USA
| | - Ian Welsh
- Program in Craniofacial Biology, Departments of Orofacial Sciences and of Anatomy, Institute of Human Genetics, University of California San Francisco, San Francisco, CA 94143, USA
| | - Cristina Williams
- Information Sciences Institute, Viterbi School of Engineering, University of Southern California, Marina del Rey, CA 90292, USA
| | - Trevor J Williams
- Department of Craniofacial Biology, School of Dental Medicine, University of Colorado, Aurora, CO 80045, USA
| | - Joanna Wysocka
- Departments of Chemical and Systems Biology and of Developmental Biology, Howard Hughes Medical Institute, School of Medicine, Stanford University, Stanford, CA 94305, USA
| | - Yuan Yuan
- Center for Craniofacial Molecular Biology, Herman Ostrow School of Dentistry, University of Southern California, Los Angeles, CA 90033, USA
| | - Yang Chai
- Center for Craniofacial Molecular Biology, Herman Ostrow School of Dentistry, University of Southern California, Los Angeles, CA 90033, USA
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Hulsey CD, Cohen KE, Johanson Z, Karagic N, Meyer A, Miller CT, Sadier A, Summers AP, Fraser GJ. Grand Challenges in Comparative Tooth Biology. Integr Comp Biol 2020; 60:563-580. [PMID: 32533826 PMCID: PMC7821850 DOI: 10.1093/icb/icaa038] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
Teeth are a model system for integrating developmental genomics, functional morphology, and evolution. We are at the cusp of being able to address many open issues in comparative tooth biology and we outline several of these newly tractable and exciting research directions. Like never before, technological advances and methodological approaches are allowing us to investigate the developmental machinery of vertebrates and discover both conserved and excitingly novel mechanisms of diversification. Additionally, studies of the great diversity of soft tissues, replacement teeth, and non-trophic functions of teeth are providing new insights into dental diversity. Finally, we highlight several emerging model groups of organisms that are at the forefront of increasing our appreciation of the mechanisms underlying tooth diversification.
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Affiliation(s)
- C Darrin Hulsey
- Department of Biology, University of Konstanz, Konstanz, 78464, Germany
| | - Karly E Cohen
- Friday Harbor Laboratories, School of Aquatic and Fishery Sciences, Department of Biology, University of Washington, WA 98195, USA
| | - Zerina Johanson
- Department of Earth Sciences, Natural History Museum, London SW7 5HD, UK
| | - Nidal Karagic
- Department of Biology, University of Konstanz, Konstanz, 78464, Germany
| | - Axel Meyer
- Department of Biology, University of Konstanz, Konstanz, 78464, Germany
| | - Craig T Miller
- Department of Molecular and Cell Biology, University of California Berkeley, Berkeley, CA 94720, USA
| | - Alexa Sadier
- Department of Ecology and Evolution, University of California Los Angeles, Los Angeles, CA 90032, USA
| | - Adam P Summers
- Friday Harbor Laboratories, School of Aquatic and Fishery Sciences, Department of Biology, University of Washington, WA 98195, USA
| | - Gareth J Fraser
- Department of Biology, University of Florida, Gainesville, FL 32611, USA
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Sadier A, Santana SE, Sears KE. The role of core and variable Gene Regulatory Network modules in tooth development and evolution. Integr Comp Biol 2020; 63:icaa116. [PMID: 32761089 DOI: 10.1093/icb/icaa116] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2020] [Revised: 07/15/2020] [Accepted: 07/27/2020] [Indexed: 02/28/2024] Open
Abstract
Among the developmental processes that have been proposed to influence the direction of evolution, the modular organization of developmental gene regulatory networks (GRNs) has shown particular promise. In theory, GRNs have core modules comprised of essential, conserved circuits of genes, and sub-modules of downstream, secondary circuits of genes that are more susceptible to variation. While this idea has received considerable interest as of late, the field of evo-devo lacks the experimental systems needed to rigorously evaluate this hypothesis. Here, we introduce an experimental system, the vertebrate tooth, that has great potential as a model for testing this hypothesis. Tooth development and its associated GRN have been well studied and modeled in both model and non-model organisms. We propose that the existence of modules within the tooth GRN explains both the conservation of developmental mechanisms and the extraordinary diversity of teeth among vertebrates. Based on experimental data, we hypothesize that there is a conserved core module of genes that is absolutely necessary to ensure tooth or cusp initiation and development. In regard to tooth shape variation between species, we suggest that more relaxed sub-modules activated at later steps of tooth development, e.g., during the morphogenesis of the tooth and its cusps, control the different axes of tooth morphological variation.
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Affiliation(s)
- Alexa Sadier
- Department of Ecology and Evolutionary Biology, University of California at Los Angeles, Los Angeles, California
| | - Sharlene E Santana
- Department of Biology and Burke Museum of Natural History and Culture, University of Washington, Seattle, Washington
| | - Karen E Sears
- Department of Ecology and Evolutionary Biology, University of California at Los Angeles, Los Angeles, California
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Siomava N, Fuentes JSM, Diogo R. Deconstructing the long‐standing a priori assumption that serial homology generally involves ancestral similarity followed by anatomical divergence. J Morphol 2020; 281:1110-1132. [DOI: 10.1002/jmor.21236] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2020] [Revised: 06/18/2020] [Accepted: 07/07/2020] [Indexed: 12/26/2022]
Affiliation(s)
- Natalia Siomava
- Department of Anatomy Howard University College of Medicine Washington District of Columbia USA
| | | | - Rui Diogo
- Department of Anatomy Howard University College of Medicine Washington District of Columbia USA
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39
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Fish TNF and TNF receptors. SCIENCE CHINA-LIFE SCIENCES 2020; 64:196-220. [DOI: 10.1007/s11427-020-1712-4] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/02/2020] [Accepted: 05/12/2020] [Indexed: 12/29/2022]
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40
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Cohen KE, Weller HI, Summers AP. Not your father's homodonty-stress, tooth shape, and the functional homodont. J Anat 2020; 237:837-848. [PMID: 32683739 DOI: 10.1111/joa.13248] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2019] [Revised: 05/19/2020] [Accepted: 05/20/2020] [Indexed: 12/31/2022] Open
Abstract
Teeth tell the tale of interactions between predator and prey. If a dental battery is made up of teeth that look similar, they are morphologically homodont, but if there is an unspecified amount of regional specialization in size or shape, they are morphologically heterodont. These are vague terms with no useful functional implication because morphological homodonty does not necessarily equal functional homodonty. Teeth that look the same may not function the same. Conical teeth are prevalent in fishes, superficially tasked with the simple job of puncture. There is a great deal of variation in the shape and placement of conical teeth. Anterior teeth may be larger than posterior ones, larger teeth may be surrounded by small ones, and patches of teeth may all have the same size and shape. Such variations suggest that conical dentitions might represent a single morphological solution for different functional problems. We are interested in the concept of homodonty and using the conical tooth as a model to differentiate between tooth shape and performance. We consider the stress that a tooth can exert on prey as stress is what causes damage. To create a statistical measure of functional homodonty, stress was calculated from measurements of surface area, position, and applied force. Functional homodonty is then defined as the degree to which teeth along the jaw all bear/exert similar stresses despite changes in shape. We find that morphologically heterodont teeth are often functionally homodont and that position is a better predictor of performance than shape. Furthermore, the arrangement of teeth affects their function, such that there is a functional advantage to having several smaller teeth surrounding a singular large tooth. We demonstrate that this arrangement of teeth is useful to grab, rather than tear, prey upon puncture, with the smaller teeth dissipating large stress forces around the larger tooth. We show that measurements of how shape affects stress distribution in response to loading give us a clearer picture of the evolution of conically shaped teeth.
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Affiliation(s)
- Karly E Cohen
- Biology Department, University of Washington, Seattle, WA, USA.,Friday Harbor Labs, University of Washington, Friday Harbor, WA, USA
| | - Hannah I Weller
- Department of Ecology and Evolutionary Biology, Brown University, Providence, RI, USA
| | - Adam P Summers
- Biology Department, University of Washington, Seattle, WA, USA.,Friday Harbor Labs, University of Washington, Friday Harbor, WA, USA
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41
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Burress ED, Martinez CM, Wainwright PC. Decoupled jaws promote trophic diversity in cichlid fishes. Evolution 2020; 74:950-961. [PMID: 32246835 DOI: 10.1111/evo.13971] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2020] [Revised: 03/13/2020] [Accepted: 03/26/2020] [Indexed: 01/15/2023]
Abstract
Functional decoupling of oral and pharyngeal jaws is widely considered to have expanded the ecological repertoire of cichlid fishes. But, the degree to which the evolution of these jaw systems is decoupled and whether decoupling has impacted trophic diversification remains unknown. Focusing on the large Neotropical radiation of cichlids, we ask whether oral and pharyngeal jaw evolution is correlated and how their evolutionary rates respond to feeding ecology. In support of decoupling, we find relaxed evolutionary integration between the two jaw systems, resulting in novel trait combinations that potentially facilitate feeding mode diversification. These outcomes are made possible by escaping the mechanical trade-off between force transmission and mobility, which characterizes a single jaw system that functions in isolation. In spite of the structural independence of the two jaw systems, results using a Bayesian, state-dependent, relaxed-clock model of multivariate Brownian motion indicate strongly aligned evolutionary responses to feeding ecology. So, although decoupling of prey capture and processing functions released constraints on jaw evolution and promoted trophic diversity in cichlids, the natural diversity of consumed prey has also induced a moderate degree of evolutionary integration between the jaw systems, reminiscent of the original mechanical trade-off between force and mobility.
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Affiliation(s)
- Edward D Burress
- Department of Evolution and Ecology, Center for Population Biology, University of California, Davis, Davis, California, 95616
| | - Christopher M Martinez
- Department of Evolution and Ecology, Center for Population Biology, University of California, Davis, Davis, California, 95616
| | - Peter C Wainwright
- Department of Evolution and Ecology, Center for Population Biology, University of California, Davis, Davis, California, 95616
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42
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Kan S, Zhu G, Du Y, Fan L, Yang F, Lou S, Li D, Ma L, Pan Y. Non-syndromic cleft lip with or without palate-susceptible SNPs is associated with hyperdontia. Oral Dis 2019; 25:1751-1758. [PMID: 31233659 DOI: 10.1111/odi.13149] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2019] [Revised: 05/21/2019] [Accepted: 06/10/2019] [Indexed: 11/29/2022]
Abstract
BACKGROUND Non-syndromic supernumerary teeth (NSST) or hyperdontia may share common genetic determinants with non-syndromic cleft lip with or without palate (NSCL/P). The aim of this study was to test the associations between five genome-wide-associated NSCL/P-susceptible single nucleotide polymorphisms (SNPs) (rs2235371, rs7078160, rs8049367, rs4791774, and rs13041247) and the occurrence of NSST. MATERIALS AND METHODS A total of 163 cases and 326 controls were recruited and their genomic DNA was extracted from blood samples. Five NSCL/P-susceptible SNPs (rs2235371, rs7078160, rs8049367, rs4791774, and rs13041247) were genotyped by TaqMan method. Odds ratio (OR) and 95% confidence interval (CI) were used to estimate the associations between the SNPs and the risk of NSST by PLINK software. RESULTS Rs4791774 (A > G) and rs13041247 (T > C) were associated with risk of NSST (rs4791774: Padd = 0.011, OR, 95% CI = 0.62, 0.43-0.90; rs13041247: Phomo = 0.031, OR, 95% CI = 1.79, 1.05-3.05) and one supernumerary tooth (rs4791774: Pdom = 0.009, OR, 95% CI = 0.56, 0.36-0.87; rs13041247: Phomo = 0.034, OR, 95% CI = 1.82, 1.05-3.15). Rs4791774 (A > G) was also showed association with risk of upper arch supernumerary teeth only (Padd = 0.010, OR, 95% CI = 0.60, 0.41-0.89). CONCLUSION Non-syndromic cleft lip with or without palate-susceptible loci rs4791774 (A > G) and rs13041247 (T > C) were associated with the risk of supernumerary teeth.
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Affiliation(s)
- Shiyi Kan
- Jiangsu Key Laboratory of Oral Diseases, Nanjing Medical University, Nanjing, China.,Department of Orthodontics, Affiliated Hospital of Stomatology, Nanjing Medical University, Nanjing, China
| | - Guirong Zhu
- Jiangsu Key Laboratory of Oral Diseases, Nanjing Medical University, Nanjing, China.,Department of Orthodontics, Affiliated Hospital of Stomatology, Nanjing Medical University, Nanjing, China
| | - Yifei Du
- Jiangsu Key Laboratory of Oral Diseases, Nanjing Medical University, Nanjing, China.,Department of Oral-maxillary surgery, Affiliated Hospital of Stomatology, Nanjing Medical University, Nanjing, China
| | - Liwen Fan
- Jiangsu Key Laboratory of Oral Diseases, Nanjing Medical University, Nanjing, China.,Department of Orthodontics, Affiliated Hospital of Stomatology, Nanjing Medical University, Nanjing, China
| | - Fan Yang
- Jiangsu Key Laboratory of Oral Diseases, Nanjing Medical University, Nanjing, China.,Department of Orthodontics, Affiliated Hospital of Stomatology, Nanjing Medical University, Nanjing, China
| | - Shu Lou
- Jiangsu Key Laboratory of Oral Diseases, Nanjing Medical University, Nanjing, China.,Department of Orthodontics, Affiliated Hospital of Stomatology, Nanjing Medical University, Nanjing, China
| | - Dandan Li
- Jiangsu Key Laboratory of Oral Diseases, Nanjing Medical University, Nanjing, China.,Department of Orthodontics, Affiliated Hospital of Stomatology, Nanjing Medical University, Nanjing, China
| | - Lan Ma
- Jiangsu Key Laboratory of Oral Diseases, Nanjing Medical University, Nanjing, China.,Department of Orthodontics, Affiliated Hospital of Stomatology, Nanjing Medical University, Nanjing, China
| | - Yongchu Pan
- Jiangsu Key Laboratory of Oral Diseases, Nanjing Medical University, Nanjing, China.,Department of Orthodontics, Affiliated Hospital of Stomatology, Nanjing Medical University, Nanjing, China
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Bell KL, Nice CC, Hulsey D. Population Genomic Evidence Reveals Subtle Patterns of Differentiation in the Trophically Polymorphic Cuatro Ciénegas Cichlid, Herichthys minckleyi. J Hered 2019; 110:361-369. [PMID: 30657932 DOI: 10.1093/jhered/esz004] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2018] [Accepted: 01/16/2019] [Indexed: 11/12/2022] Open
Abstract
In recent decades, an increased understanding of molecular ecology has led to a reinterpretation of the role of gene flow during the evolution of reproductive isolation and biological novelty. For example, even in the face of ongoing gene flow strong selection may maintain divergent polymorphisms, or gene flow may introduce novel biological diversity via hybridization and introgression from a divergent species. Herein, we elucidate the evolutionary history and genomic basis of a trophically polymorphic trait in a species of cichlid fish, Herichthys minckleyi. We explored genetic variation at 3 hierarchical levels; between H. minckleyi (n = 69) and a closely related species Herichthys cyanoguttatus (n = 10), between H. minckleyi individuals from 2 geographic locations, and finally between individuals with alternate morphotypes at both a genome-wide and locus-specific scale. We found limited support for the hypothesis that the H. minckleyi polymorphism is the result of ongoing hybridization between the 2 species. Within H. minckleyi we found evidence of geographic genetic structure, and using traditional population genetic analyses found that individuals of alternate morphotypes within a pool appear to be panmictic. However, when we used a locus-specific approach to examine the relationship between multi-locus genotype, tooth size, and geographic sampling, we found the first evidence for molecular genetic differences between the H. minckleyi morphotypes.
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Affiliation(s)
- Katherine L Bell
- Department of Biology, Population and Conservation Biology Program, Texas State University, San Marcos, TX
| | - Chris C Nice
- Department of Biology, Population and Conservation Biology Program, Texas State University, San Marcos, TX
| | - Darrin Hulsey
- Department of Biology, University of Konstanz, Konstanz, Germany
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Calamari ZT, Kuang-Hsien Hu J, Klein OD. Tissue Mechanical Forces and Evolutionary Developmental Changes Act Through Space and Time to Shape Tooth Morphology and Function. Bioessays 2018; 40:e1800140. [PMID: 30387177 PMCID: PMC6516060 DOI: 10.1002/bies.201800140] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2018] [Revised: 10/06/2018] [Indexed: 12/24/2022]
Abstract
Efforts from diverse disciplines, including evolutionary studies and biomechanical experiments, have yielded new insights into the genetic, signaling, and mechanical control of tooth formation and functions. Evidence from fossils and non-model organisms has revealed that a common set of genes underlie tooth-forming potential of epithelia, and changes in signaling environments subsequently result in specialized dentitions, maintenance of dental stem cells, and other phenotypic adaptations. In addition to chemical signaling, tissue forces generated through epithelial contraction, differential growth, and skeletal constraints act in parallel to shape the tooth throughout development. Here recent advances in understanding dental development from these studies are reviewed and important gaps that can be filled through continued application of evolutionary and biomechanical approaches are discussed.
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Affiliation(s)
- Zachary T. Calamari
- Department of Natural Sciences, Baruch College, City University of New York, New York City, New York, 10010, USA
- Department of Orofacial Sciences and Program in Craniofacial Biology, University of California, San Francisco, San Francisco, California, 94143, USA
| | - Jimmy Kuang-Hsien Hu
- Department of Orofacial Sciences and Program in Craniofacial Biology, University of California, San Francisco, San Francisco, California, 94143, USA
| | - Ophir D. Klein
- Department of Orofacial Sciences and Program in Craniofacial Biology, University of California, San Francisco, San Francisco, California, 94143, USA
- Department of Pediatrics and Institute for Human Genetics, University of California, San Francisco, San Francisco, California, 94143, USA
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45
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Darrin Hulsey C, Zheng J, Holzman R, Alfaro ME, Olave M, Meyer A. Phylogenomics of a putatively convergent novelty: did hypertrophied lips evolve once or repeatedly in Lake Malawi cichlid fishes? BMC Evol Biol 2018; 18:179. [PMID: 30486792 PMCID: PMC6263179 DOI: 10.1186/s12862-018-1296-9] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2017] [Accepted: 11/16/2018] [Indexed: 01/22/2023] Open
Abstract
BACKGROUND Phylogenies provide critical information about convergence during adaptive radiation. To test whether there have been multiple origins of a distinctive trophic phenotype in one of the most rapidly radiating groups known, we used ultra-conserved elements (UCEs) to examine the evolutionary affinities of Lake Malawi cichlids lineages exhibiting greatly hypertrophied lips. RESULTS The hypertrophied lip cichlids Cheilochromis euchilus, Eclectochromis ornatus, Placidochromis "Mbenji fatlip", and Placidochromis milomo are all nested within the non-mbuna clade of Malawi cichlids based on both concatenated sequence and single nucleotide polymorphism (SNP) inferred phylogenies. Lichnochromis acuticeps that exhibits slightly hypertrophied lips also appears to have evolutionary affinities to this group. However, Chilotilapia rhoadesii that lacks hypertrophied lips was recovered as nested within the species Cheilochromis euchilus. Species tree reconstructions and analyses of introgression provided largely ambiguous patterns of Malawi cichlid evolution. CONCLUSIONS Contrary to mitochondrial DNA phylogenies, bifurcating trees based on our 1024 UCE loci supported close affinities of Lake Malawi lineages with hypertrophied lips. However, incomplete lineage sorting in Malawi tends to render these inferences more tenuous. Phylogenomic analyses will continue to provide powerful inferences about whether phenotypic novelties arose once or multiple times during adaptive radiation.
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Affiliation(s)
- C. Darrin Hulsey
- Department of Biology, University of Konstanz, Konstanz, Germany
| | - Jimmy Zheng
- Department of Ecology & Evolutionary Biology, University of California, Los Angeles, CA USA
| | - Roi Holzman
- Department of Zoology, Tel Aviv University and the Inter-University Institute for Marine Sciences in Eilat, 88103 Eilat, Israel
| | - Michael E. Alfaro
- Department of Ecology & Evolutionary Biology, University of California, Los Angeles, CA USA
| | - Melisa Olave
- Department of Biology, University of Konstanz, Konstanz, Germany
| | - Axel Meyer
- Department of Biology, University of Konstanz, Konstanz, Germany
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46
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Atukorala ADS, Bhatia V, Ratnayake R. Craniofacial skeleton of MEXICAN tetra (Astyanax mexicanus): As a bone disease model. Dev Dyn 2018; 248:153-161. [PMID: 30450697 DOI: 10.1002/dvdy.4] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2018] [Revised: 11/12/2018] [Accepted: 11/12/2018] [Indexed: 12/16/2022] Open
Abstract
A small fresh water fish, the Mexican tetra (Astyanax mexicanus) is a novel animal model in evolutionary developmental biology. The existence of morphologically distinct surface and cave morphs of this species allows simultaneous comparative analysis of phenotypic changes at different life stages. The cavefish harbors many favorable constructive traits (i.e., large jaws with an increased number of teeth, neuromast cells, enlarged olfactory pits and excess storage of adipose tissues) and regressive traits (i.e., reduced eye structures and pigmentation) which are essential for cave adaptation. A wide spectrum of natural craniofacial morphologies can be observed among the different cave populations. Recently, the Mexican tetra has been identified as a human disease model. The fully sequenced genome along with modern genome editing tools has allowed researchers to generate transgenic and targeted gene knockouts with phenotypes that resemble human pathological conditions. This review will discuss the anatomy of the craniofacial skeleton of A. mexicanus with a focus on morphologically variable facial bones, jaws that house continuously replacing teeth and pharyngeal skeleton. Furthermore, the possible applications of this model animal in identifying human congenital and metabolic skeletal disorders is addressed. Developmental Dynamics 248:153-161, 2019. © 2018 Wiley Periodicals, Inc.
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Affiliation(s)
- Atukorallaya Devi Sewvandini Atukorala
- Department of Oral Biology, Dr. Gerald Niznick College of Dentistry, Rady Faculty of Health Sciences, University of Manitoba, Winnipeg, Manitoba, Canada
| | - Vikram Bhatia
- Department of Oral Biology, Dr. Gerald Niznick College of Dentistry, Rady Faculty of Health Sciences, University of Manitoba, Winnipeg, Manitoba, Canada
| | - Ravindra Ratnayake
- Department of Oral Biology, Dr. Gerald Niznick College of Dentistry, Rady Faculty of Health Sciences, University of Manitoba, Winnipeg, Manitoba, Canada
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Savriama Y, Valtonen M, Kammonen JI, Rastas P, Smolander OP, Lyyski A, Häkkinen TJ, Corfe IJ, Gerber S, Salazar-Ciudad I, Paulin L, Holm L, Löytynoja A, Auvinen P, Jernvall J. Bracketing phenogenotypic limits of mammalian hybridization. ROYAL SOCIETY OPEN SCIENCE 2018; 5:180903. [PMID: 30564397 PMCID: PMC6281900 DOI: 10.1098/rsos.180903] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/06/2018] [Accepted: 10/29/2018] [Indexed: 05/09/2023]
Abstract
An increasing number of mammalian species have been shown to have a history of hybridization and introgression based on genetic analyses. Only relatively few fossils, however, preserve genetic material, and morphology must be used to identify the species and determine whether morphologically intermediate fossils could represent hybrids. Because dental and cranial fossils are typically the key body parts studied in mammalian palaeontology, here we bracket the potential for phenotypically extreme hybridizations by examining uniquely preserved cranio-dental material of a captive hybrid between grey and ringed seals. We analysed how distinct these species are genetically and morphologically, how easy it is to identify the hybrids using morphology and whether comparable hybridizations happen in the wild. We show that the genetic distance between these species is more than twice the modern human-Neanderthal distance, but still within that of morphologically similar species pairs known to hybridize. By contrast, morphological and developmental analyses show grey and ringed seals to be highly disparate, and that the hybrid is a predictable intermediate. Genetic analyses of the parent populations reveal introgression in the wild, suggesting that grey-ringed seal hybridization is not limited to captivity. Taken together, we postulate that there is considerable potential for mammalian hybridization between phenotypically disparate taxa.
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Affiliation(s)
- Yoland Savriama
- Developmental Biology Program, Institute of Biotechnology, University of Helsinki, PO Box 56, 00014 Helsinki, Finland
| | - Mia Valtonen
- Developmental Biology Program, Institute of Biotechnology, University of Helsinki, PO Box 56, 00014 Helsinki, Finland
- Department of Environmental and Biological Sciences, University of Eastern Finland, PO Box 111, 80101 Joensuu, Finland
| | - Juhana I. Kammonen
- Genome Biology Program, Institute of Biotechnology, University of Helsinki, PO Box 56, 00014 Helsinki, Finland
| | - Pasi Rastas
- Genome Biology Program, Institute of Biotechnology, University of Helsinki, PO Box 56, 00014 Helsinki, Finland
| | - Olli-Pekka Smolander
- Genome Biology Program, Institute of Biotechnology, University of Helsinki, PO Box 56, 00014 Helsinki, Finland
| | - Annina Lyyski
- Genome Biology Program, Institute of Biotechnology, University of Helsinki, PO Box 56, 00014 Helsinki, Finland
| | - Teemu J. Häkkinen
- Developmental Biology Program, Institute of Biotechnology, University of Helsinki, PO Box 56, 00014 Helsinki, Finland
| | - Ian J. Corfe
- Developmental Biology Program, Institute of Biotechnology, University of Helsinki, PO Box 56, 00014 Helsinki, Finland
| | - Sylvain Gerber
- Institut Systématique Evolution Biodiversité (ISYEB), Muséum national d'Histoire naturelle, CNRS, Sorbonne Université, EPHE, 45 rue Buffon, CP 50, 75005 Paris, France
| | - Isaac Salazar-Ciudad
- Developmental Biology Program, Institute of Biotechnology, University of Helsinki, PO Box 56, 00014 Helsinki, Finland
- Departament de Genètica i Microbiologia, Universitat Autònoma de Barcelona, 08193 Cerdanyola del Vallès, Spain
| | - Lars Paulin
- Genome Biology Program, Institute of Biotechnology, University of Helsinki, PO Box 56, 00014 Helsinki, Finland
| | - Liisa Holm
- Genome Biology Program, Institute of Biotechnology, University of Helsinki, PO Box 56, 00014 Helsinki, Finland
- Faculty of Biological and Environmental Sciences, University of Helsinki, PO Box 56, 00014 Helsinki, Finland
| | - Ari Löytynoja
- Genome Biology Program, Institute of Biotechnology, University of Helsinki, PO Box 56, 00014 Helsinki, Finland
- Authors for correspondence: Ari Löytynoja e-mail:
| | - Petri Auvinen
- Genome Biology Program, Institute of Biotechnology, University of Helsinki, PO Box 56, 00014 Helsinki, Finland
- Authors for correspondence: Petri Auvinen e-mail:
| | - Jukka Jernvall
- Developmental Biology Program, Institute of Biotechnology, University of Helsinki, PO Box 56, 00014 Helsinki, Finland
- Authors for correspondence: Jukka Jernvall e-mail:
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48
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Ripamonti U. Developmental pathways of periodontal tissue regeneration. J Periodontal Res 2018; 54:10-26. [DOI: 10.1111/jre.12596] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2018] [Revised: 07/06/2018] [Accepted: 07/12/2018] [Indexed: 12/13/2022]
Affiliation(s)
- Ugo Ripamonti
- Bone Research Laboratory; School of Oral Health Sciences; Faculty of Health Sciences; University of the Witwatersrand; Johannesburg South Africa
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49
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Maruska KP, Fernald RD. Astatotilapia burtoni: A Model System for Analyzing the Neurobiology of Behavior. ACS Chem Neurosci 2018. [PMID: 29522313 DOI: 10.1021/acschemneuro.7b00496] [Citation(s) in RCA: 52] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/16/2023] Open
Abstract
Most biomedical research is performed using a very limited number of "model" species. In part, this has resulted from a combination of full genomes, manipulation of genes, and short generation times in these species. However, the advent of low-cost sequencing and gene editing in any organism has increased the use of nontraditional organisms. Many scientists have paraphrased the adage by Krogh [ Krogh , A. ( 2018 ) Science 70 , 200 - 204 ] that for many biological problems some species will prove to be most convenient and useful to study. In particular, using organisms most suited to the specific research question can lead to novel insights about fundamental physiological, neurobiological, immunological, and neuroendocrine systems that can advance our understanding of the well-being and health of humans. In addition, such studies have led to new ideas about the evolution and mechanisms that control social behavior. Fishes constitute about 50% of all vertebrate species and are the most diverse vertebrate radiation. Here we review behavioral and neurobiological discoveries of plasticity in social behavior resulting from analysis of an African cichlid fish, showing how its unique behavioral system has facilitated a broad range of discoveries. For many future questions, Astatotilapia burtoni and other cichlid fishes may be ideally suited to study as we advance our understanding of the neural basis of social decisions.
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Affiliation(s)
- Karen P. Maruska
- Department of Biological Sciences, Louisiana State University, Baton Rouge, Louisiana 70803, United States
| | - Russell D. Fernald
- Biology Department, Stanford University, Stanford, California 94305, United States
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50
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Hart JC, Ellis NA, Eisen MB, Miller CT. Convergent evolution of gene expression in two high-toothed stickleback populations. PLoS Genet 2018; 14:e1007443. [PMID: 29897962 PMCID: PMC6016950 DOI: 10.1371/journal.pgen.1007443] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2018] [Revised: 06/25/2018] [Accepted: 05/23/2018] [Indexed: 12/30/2022] Open
Abstract
Changes in developmental gene regulatory networks enable evolved changes in morphology. These changes can be in cis regulatory elements that act in an allele-specific manner, or changes to the overall trans regulatory environment that interacts with cis regulatory sequences. Here we address several questions about the evolution of gene expression accompanying a convergently evolved constructive morphological trait, increases in tooth number in two independently derived freshwater populations of threespine stickleback fish (Gasterosteus aculeatus). Are convergently evolved cis and/or trans changes in gene expression associated with convergently evolved morphological evolution? Do cis or trans regulatory changes contribute more to gene expression changes accompanying an evolved morphological gain trait? Transcriptome data from dental tissue of ancestral low-toothed and two independently derived high-toothed stickleback populations revealed significantly shared gene expression changes that have convergently evolved in the two high-toothed populations. Comparing cis and trans regulatory changes using phased gene expression data from F1 hybrids, we found that trans regulatory changes were predominant and more likely to be shared among both high-toothed populations. In contrast, while cis regulatory changes have evolved in both high-toothed populations, overall these changes were distinct and not shared among high-toothed populations. Together these data suggest that a convergently evolved trait can occur through genetically distinct regulatory changes that converge on similar trans regulatory environments.
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Affiliation(s)
- James C. Hart
- Department of Molecular and Cell Biology, University of California-Berkeley, CA, United States of America
| | - Nicholas A. Ellis
- Department of Molecular and Cell Biology, University of California-Berkeley, CA, United States of America
| | - Michael B. Eisen
- Department of Molecular and Cell Biology, University of California-Berkeley, CA, United States of America
- Howard Hughes Medical Institute, University of California, Berkeley, CA, United States of America
| | - Craig T. Miller
- Department of Molecular and Cell Biology, University of California-Berkeley, CA, United States of America
- * E-mail:
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