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Contreras-Tapia RA, Benítez-Díaz Mirón MI, Garza Mouriño G, Castellanos-Páez ME. From hatching to juvenile: Larval development of Vieja fenestrata (Teleostei: Cichlidae). JOURNAL OF FISH BIOLOGY 2024. [PMID: 39126256 DOI: 10.1111/jfb.15898] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/18/2024] [Revised: 06/30/2024] [Accepted: 07/25/2024] [Indexed: 08/12/2024]
Abstract
This study delves into the early development of Vieja fenestrata (Cichlidae), with a specific focus on the description of external morphological and morphometric changes, and growth patterns from hatching to the loss of larval characters under controlled laboratory conditions at a temperature of 28°C. Asynchronous hatching was observed between 58 and 60 h postfertilization, with the posterior body emerging first. Over 14 days, significant morphological, physiological, and behavioral changes were observed, revealing a complex developmental trajectory. The initial developmental phases were characterized by rapid vascularization, fin differentiation, and heightened activity, and the subsequent days witnessed the flexion of the notochord, emergence of swim bladder functionality, and transition to exogenous feeding. Maturation progressed with the absorption of the yolk sac, regression of cement glands, and fin ray development, culminating in metamorphosis by 14 days post-hatching. Throughout this period, evolving pigmentation patterns and structural adaptations highlight the species' adaptive strategies. During the larval period of V. fenestrata, substantial changes in morphological proportions were observed. Before the inflection, tail length, trunk length, and body depth had negative allometric growth, and head length, eye diameter, and snout length had positive allometric growth. After the inflection, body depth and snout length showed positive allometric growth; head length and trunk length exhibited isometric growth, whereas tail length and eye diameter demonstrated negative allometric growth. These findings contribute insights into the intricate developmental dynamics of V. fenestrata. Moreover, further research may explore these developmental dynamics' ecological and evolutionary implications.
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Affiliation(s)
- Rubén Alonso Contreras-Tapia
- Laboratorio de Rotiferología y Biología Molecular de Plancton, Departamento El Hombre y su Ambiente, Universidad Autónoma Metropolitana, Unidad Xochimilco, Mexico City, Mexico
| | - Marcela Ivonne Benítez-Díaz Mirón
- Laboratorio de Rotiferología y Biología Molecular de Plancton, Departamento El Hombre y su Ambiente, Universidad Autónoma Metropolitana, Unidad Xochimilco, Mexico City, Mexico
| | - Gabriela Garza Mouriño
- Laboratorio de Rotiferología y Biología Molecular de Plancton, Departamento El Hombre y su Ambiente, Universidad Autónoma Metropolitana, Unidad Xochimilco, Mexico City, Mexico
| | - María Elena Castellanos-Páez
- Laboratorio de Rotiferología y Biología Molecular de Plancton, Departamento El Hombre y su Ambiente, Universidad Autónoma Metropolitana, Unidad Xochimilco, Mexico City, Mexico
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2
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Marconi A, Vernaz G, Karunaratna A, Ngochera MJ, Durbin R, Santos ME. Genetic and developmental divergence in the neural crest programme between cichlid fish species. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.01.30.578004. [PMID: 38352436 PMCID: PMC10862805 DOI: 10.1101/2024.01.30.578004] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Indexed: 02/23/2024]
Abstract
Neural crest (NC) is a vertebrate-specific embryonic progenitor cell population at the basis of important vertebrate features such as the craniofacial skeleton and pigmentation patterns. Despite the wide-ranging variation of NC-derived traits across vertebrates, the contribution of NC to species diversification remains underexplored. Here, leveraging the adaptive diversity of African Great Lakes' cichlid species, we combined comparative transcriptomics and population genomics to investigate the evolution of the NC genetic programme in the context of their morphological divergence. Our analysis revealed substantial differences in transcriptional landscapes across somitogenesis, an embryonic period coinciding with NC development and migration. This included dozens of genes with described functions in the vertebrate NC gene regulatory network, several of which showed signatures of positive selection. Among candidates showing between-species expression divergence, we focused on teleost-specific paralogs of the NC-specifier sox10 (sox10a and sox10b) as prime candidates to influence NC development. These genes, expressed in NC cells, displayed remarkable spatio-temporal variation in cichlids, suggesting their contribution to inter-specific morphological differences. Finally, through CRISPR/Cas9 mutagenesis, we demonstrated the functional divergence between cichlid sox10 paralogs, with the acquisition of a novel skeletogenic function by sox10a. When compared to the teleost models zebrafish and medaka, our findings reveal that sox10 duplication, although retained in most teleost lineages, had variable functional fates across their phylogeny. Altogether, our study suggests that NC-related processes - particularly those controlled by sox10s - might be involved in generating morphological diversification between species and lays the groundwork for further investigations into mechanisms underpinning vertebrate NC diversification.
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Affiliation(s)
| | | | | | - Maxon J. Ngochera
- Senga Bay Fisheries Research Center, Malawi Fisheries Department, P.O. Box 316, Salima, Malawi
| | - Richard Durbin
- Department of Genetics, University of Cambridge, United Kingdom
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3
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Tetrault E, Aaronson B, Gilbert MC, Albertson RC. Foraging-induced craniofacial plasticity is associated with an early, robust and dynamic transcriptional response. Proc Biol Sci 2024; 291:20240215. [PMID: 38654651 PMCID: PMC11040245 DOI: 10.1098/rspb.2024.0215] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2024] [Accepted: 03/19/2024] [Indexed: 04/26/2024] Open
Abstract
Phenotypic plasticity is the ability of a single genotype to vary its phenotype in response to the environment. Plasticity of the skeletal system in response to mechanical input is widely studied, but the timing of its transcriptional regulation is not well understood. Here, we used the cichlid feeding apparatus to examine the transcriptional dynamics of skeletal plasticity over time. Using three closely related species that vary in their ability to remodel bone and a panel of 11 genes, including well-studied skeletal differentiation markers and newly characterized environmentally sensitive genes, we examined plasticity at one, two, four and eight weeks following the onset of alternate foraging challenges. We found that the plastic species exhibited environment-specific bursts in gene expression beginning at one week, followed by a sharp decline in levels, while the species with more limited plasticity exhibited consistently low levels of gene expression. This trend held across nearly all genes, suggesting that it is a hallmark of the larger plasticity regulatory network. We conclude that plasticity of the cichlid feeding apparatus is not the result of slowly accumulating gene expression difference over time, but rather is stimulated by early bursts of environment-specific gene expression followed by a return to homeostatic levels.
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Affiliation(s)
- Emily Tetrault
- Molecular and Cell Biology Graduate Program, University of Massachusetts, Amherst, MA 01003, USA
| | - Ben Aaronson
- Department of Biology, University of Massachusetts, Amherst, MA 01003, USA
| | - Michelle C. Gilbert
- Department of Biology, Pennsylvania State University, State College, PA 16802, USA
| | - R. Craig Albertson
- Department of Biology, University of Massachusetts, Amherst, MA 01003, USA
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4
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Licitra R, Fronte B, Verri T, Marchese M, Sangiacomo C, Santorelli FM. Zebrafish Feed Intake: A Systematic Review for Standardizing Feeding Management in Laboratory Conditions. BIOLOGY 2024; 13:209. [PMID: 38666821 PMCID: PMC11047914 DOI: 10.3390/biology13040209] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/18/2024] [Revised: 03/19/2024] [Accepted: 03/20/2024] [Indexed: 04/28/2024]
Abstract
Zebrafish are one of the most used animal models in biological research and a cost-effective alternative to rodents. Despite this, nutritional requirements and standardized feeding protocols have not yet been established for this species. This is important to avoid nutritional effects on experimental outcomes, and especially when zebrafish models are used in preclinical studies, as many diseases have nutritional confounding factors. A key aspect of zebrafish nutrition is related to feed intake, the amount of feed ingested by each fish daily. With the goal of standardizing feeding protocols among the zebrafish community, this paper systematically reviews the available data from 73 studies on zebrafish feed intake, feeding regimes (levels), and diet composition. Great variability was observed regarding diet composition, especially regarding crude protein (mean 44.98 ± 9.87%) and lipid content (9.91 ± 5.40%). Interestingly, the gross energy levels of the zebrafish diets were similar across the reviewed studies (20.39 ± 2.10 kilojoules/g of feed). In most of the reviewed papers, fish received a predetermined quantity of feed (feed supplied). The authors fed the fish according to the voluntary intake and then calculated feed intake (FI) in only 17 papers. From a quantitative point of view, FI was higher than when a fixed quantity (pre-defined) of feed was supplied. Also, the literature showed that many biotic and abiotic factors may affect zebrafish FI. Finally, based on the FI data gathered from the literature, a new feeding protocol is proposed. In summary, a daily feeding rate of 9-10% of body weight is proposed for larvae, whereas these values are equal to 6-8% for juveniles and 5% for adults when a dry feed with a proper protein and energy content is used.
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Affiliation(s)
- Rosario Licitra
- Department of Neurobiology and Molecular Medicine, IRCCS Stella Maris Foundation, 56128 Pisa, Italy;
| | - Baldassare Fronte
- Department of Veterinary Sciences, University of Pisa, 56124 Pisa, Italy; (B.F.); (C.S.)
| | - Tiziano Verri
- Department of Biological and Environmental Sciences and Technologies, University of Salento, 73100 Lecce, Italy;
| | - Maria Marchese
- Department of Neurobiology and Molecular Medicine, IRCCS Stella Maris Foundation, 56128 Pisa, Italy;
| | - Chiara Sangiacomo
- Department of Veterinary Sciences, University of Pisa, 56124 Pisa, Italy; (B.F.); (C.S.)
| | - Filippo Maria Santorelli
- Department of Neurobiology and Molecular Medicine, IRCCS Stella Maris Foundation, 56128 Pisa, Italy;
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5
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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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6
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Matthews DG, Dial TR, Lauder GV. Genes, Morphology, Performance, and Fitness: Quantifying Organismal Performance to Understand Adaptive Evolution. Integr Comp Biol 2023; 63:843-859. [PMID: 37422435 DOI: 10.1093/icb/icad096] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2023] [Revised: 06/06/2023] [Accepted: 06/22/2023] [Indexed: 07/10/2023] Open
Abstract
To understand the complexities of morphological evolution, we must understand the relationships between genes, morphology, performance, and fitness in complex traits. Genomicists have made tremendous progress in finding the genetic basis of many phenotypes, including a myriad of morphological characters. Similarly, field biologists have greatly advanced our understanding of the relationship between performance and fitness in natural populations. However, the connection from morphology to performance has primarily been studied at the interspecific level, meaning that in most cases we lack a mechanistic understanding of how evolutionarily relevant variation among individuals affects organismal performance. Therefore, functional morphologists need methods that will allow for the analysis of fine-grained intraspecific variation in order to close the path from genes to fitness. We suggest three methodological areas that we believe are well suited for this research program and provide examples of how each can be applied within fish model systems to build our understanding of microevolutionary processes. Specifically, we believe that structural equation modeling, biological robotics, and simultaneous multi-modal functional data acquisition will open up fruitful collaborations among biomechanists, evolutionary biologists, and field biologists. It is only through the combined efforts of all three fields that we will understand the connection between evolution (acting at the level of genes) and natural selection (acting on fitness).
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Affiliation(s)
- David G Matthews
- Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, MA 02138, USA
- Museum of Comparative Zoology, Harvard University, Cambridge, MA 02138, USA
| | - Terry R Dial
- Department of Biology and Ecology Center, Utah State University, Moab, UT 84322, USA
- Department of Environment and Society, Utah State University, Moab, UT 84322, USA
| | - George V Lauder
- Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, MA 02138, USA
- Museum of Comparative Zoology, Harvard University, Cambridge, MA 02138, USA
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7
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Powers AK, Hyacinthe C, Riddle MR, Kim YK, Amaismeier A, Thiel K, Martineau B, Ferrante E, Moran RL, McGaugh SE, Boggs TE, Gross JB, Tabin CJ. Genetic mapping of craniofacial traits in the Mexican tetra reveals loci associated with bite differences between cave and surface fish. BMC Ecol Evol 2023; 23:41. [PMID: 37626324 PMCID: PMC10463419 DOI: 10.1186/s12862-023-02149-3] [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: 01/04/2023] [Accepted: 08/11/2023] [Indexed: 08/27/2023] Open
Abstract
BACKGROUND The Mexican tetra, Astyanax mexicanus, includes interfertile surface-dwelling and cave-dwelling morphs, enabling powerful studies aimed at uncovering genes involved in the evolution of cave-associated traits. Compared to surface fish, cavefish harbor several extreme traits within their skull, such as a protruding lower jaw, a wider gape, and an increase in tooth number. These features are highly variable between individual cavefish and even across different cavefish populations. RESULTS To investigate these traits, we created a novel feeding behavior assay wherein bite impressions could be obtained. We determined that fish with an underbite leave larger bite impressions with an increase in the number of tooth marks. Capitalizing on the ability to produce hybrids from surface and cavefish crosses, we investigated genes underlying these segregating orofacial traits by performing Quantitative Trait Loci (QTL) analysis with F2 hybrids. We discovered significant QTL for bite (underbite vs. overbite) that mapped to a single region of the Astyanax genome. Within this genomic region, multiple genes exhibit coding region mutations, some with known roles in bone development. Further, we determined that there is evidence that this genomic region is under natural selection. CONCLUSIONS This work highlights cavefish as a valuable genetic model for orofacial patterning and will provide insight into the genetic regulators of jaw and tooth development.
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Affiliation(s)
- Amanda K Powers
- Department of Genetics, Blavatnik Institute at Harvard Medical School, 77 Avenue Louis Pasteur, Boston, MA, 02115, USA
| | - Carole Hyacinthe
- Department of Genetics, Blavatnik Institute at Harvard Medical School, 77 Avenue Louis Pasteur, Boston, MA, 02115, USA
| | - Misty R Riddle
- Department of Biology, University of Nevada, Reno, 1664 N. Virginia St., Reno, NV, 89557, USA
| | - Young Kwang Kim
- Harvard School of Dental Medicine, 188 Longwood Ave., Boston, MA, 02115, USA
| | - Alleigh Amaismeier
- Department of Biology, Xavier University, 3800 Victory Pkwy., Cincinnati, OH, 45207, USA
| | - Kathryn Thiel
- Department of Biology, Xavier University, 3800 Victory Pkwy., Cincinnati, OH, 45207, USA
| | - Brian Martineau
- Department of Genetics, Blavatnik Institute at Harvard Medical School, 77 Avenue Louis Pasteur, Boston, MA, 02115, USA
| | - Emma Ferrante
- Department of Genetics, Blavatnik Institute at Harvard Medical School, 77 Avenue Louis Pasteur, Boston, MA, 02115, USA
| | - Rachel L Moran
- Department of Biology, Texas A & M University, 100 Butler Hall, College Station, TX, 77843, USA
| | - Suzanne E McGaugh
- Department of Ecology, Evolution and Behavior, University of Minnesota, 1500 Gortner Ave., Saint Paul, MN, 55108, USA
| | - Tyler E Boggs
- Department of Biological Sciences, University of Cincinnati, 312 College Dr., Cincinnati, OH, 45221, USA
| | - Joshua B Gross
- Department of Biological Sciences, University of Cincinnati, 312 College Dr., Cincinnati, OH, 45221, USA
| | - Clifford J Tabin
- Department of Genetics, Blavatnik Institute at Harvard Medical School, 77 Avenue Louis Pasteur, Boston, MA, 02115, USA.
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8
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Marconi A, Yang CZ, McKay S, Santos ME. Morphological and temporal variation in early embryogenesis contributes to species divergence in Malawi cichlid fishes. Evol Dev 2023; 25:170-193. [PMID: 36748313 PMCID: PMC10909517 DOI: 10.1111/ede.12429] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2022] [Revised: 12/18/2022] [Accepted: 01/20/2023] [Indexed: 02/08/2023]
Abstract
The cichlid fishes comprise the largest extant vertebrate family and are the quintessential example of rapid "explosive" adaptive radiations and phenotypic diversification. Despite low genetic divergence, East African cichlids harbor a spectacular intra- and interspecific morphological diversity, including the hyper-variable, neural crest (NC)-derived traits such as coloration and craniofacial skeleton. Although the genetic and developmental basis of these phenotypes has been investigated, understanding of when, and specifically how early, in ontogeny species-specific differences emerge, remains limited. Since adult traits often originate during embryonic development, the processes of embryogenesis could serve as a potential source of species-specific variation. Consequently, we designed a staging system by which we compare the features of embryogenesis between three Malawi cichlid species-Astatotilapia calliptera, Tropheops sp. 'mauve' and Rhamphochromis sp. "chilingali"-representing a wide spectrum of variation in pigmentation and craniofacial morphologies. Our results showed fundamental differences in multiple aspects of embryogenesis that could underlie interspecific divergence in adult adaptive traits. First, we identified variation in the somite number and signatures of temporal variation, or heterochrony, in the rates of somite formation. The heterochrony was also evident within and between species throughout ontogeny, up to the juvenile stages. Finally, the identified interspecific differences in the development of pigmentation and craniofacial cartilages, present at the earliest stages of their overt formation, provide compelling evidence that the species-specific trajectories begin divergence during early embryogenesis, potentially during somitogenesis and NC development. Altogether, our results expand our understanding of fundamental cichlid biology and provide new insights into the developmental origins of vertebrate morphological diversity.
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Affiliation(s)
| | | | - Samuel McKay
- Department of ZoologyUniversity of CambridgeCambridgeUK
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9
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Deepak V, Gower DJ, Cooper N. Diet and habit explain head-shape convergences in natricine snakes. J Evol Biol 2023; 36:399-411. [PMID: 36511814 DOI: 10.1111/jeb.14139] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2022] [Revised: 10/24/2022] [Accepted: 11/14/2022] [Indexed: 12/15/2022]
Abstract
The concept of ecomorphs, whereby species with similar ecologies have similar phenotypes regardless of their phylogenetic relatedness, is often central to discussions regarding the relationship between ecology and phenotype. However, some aspects of the concept have been questioned, and sometimes species have been grouped as ecomorphs based on phenotypic similarity without demonstrating ecological similarity. Within snakes, similar head shapes have convergently evolved in species living in comparable environments and/or with similar diets. Therefore, ecomorphs could exist in some snake lineages, but this assertion has rarely been tested for a wide-ranging group within a single framework. Natricine snakes (Natricinae) are ecomorphologically diverse and currently distributed in Asia, Africa, Europe and north-central America. They are primarily semiaquatic or ground-dwelling terrestrial snakes, but some are aquatic, burrowing or aquatic and burrowing in habit and may be generalist or specialist in diet. Thus, natricines present an interesting system to test whether snakes from different major habit categories represent ecomorphs. We quantify morphological similarity and disparity in head shape among 191 of the ca. 250 currently recognized natricine species and apply phylogenetic comparative methods to test for convergence. Natricine head shape is largely correlated with habit, but in some burrowers is better explained by dietary specialism. Convergence in head shape is especially strong for aquatic burrowing, semiaquatic and terrestrial ecomorphs and less strong for aquatic and burrowing ecomorphs. The ecomorph concept is useful for understanding natricine diversity and evolution, though would benefit from further refinement, especially for aquatic and burrowing taxa.
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Affiliation(s)
- V Deepak
- Science Group, Natural History Museum London, London, UK.,Senckenberg Dresden, Museum of Zoology (Museum für Tierkunde), Dresden, Germany
| | - David J Gower
- Science Group, Natural History Museum London, London, UK
| | - Natalie Cooper
- Science Group, Natural History Museum London, London, UK
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10
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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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11
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A phylogeographic assessment of the greater kudu (Tragelaphus strepsiceros) across South Africa. CONSERV GENET 2022. [DOI: 10.1007/s10592-022-01464-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
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12
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Ma Y, Xiao Y, Xiao Z, Wu Y, Zhao H, Gao G, Wu L, Wang T, Zhao N, Li J. Genome-wide identification, characterization and expression analysis of the BMP family associated with beak-like teeth in Oplegnathus. Front Genet 2022; 13:938473. [PMID: 35923711 PMCID: PMC9342863 DOI: 10.3389/fgene.2022.938473] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2022] [Accepted: 06/28/2022] [Indexed: 11/13/2022] Open
Abstract
Bone morphogenetic proteins (BMPs), which belong to the transforming growth factor beta (TGF-β) family, are critical for the control of developmental processes such as dorsal-ventral axis formation, somite and tooth formation, skeletal development, and limb formation. Despite Oplegnathus having typical healing beak-like teeth and tooth development showing a trend from discrete to healing, the potential role of BMPs in the development of the beak-like teeth is incompletely understood. In the present study, 19 and 16 BMP genes were found in O. fasciatus and O. punctatus, respectively, and divided into the BMP2/4/16, BMP5/6/7/8, BMP9/10, BMP12/13/14, BMP3/15 and BMP11 subfamilies. Similar TGFb and TGF_β gene domains and conserved protein motifs were found in the same subfamily; furthermore, two common tandem repeat genes (BMP9 and BMP3a-1) were identified in both Oplegnathus fasciatus and Oplegnathus punctatus. Selection pressure analysis revealed 13 amino acid sites in the transmembrane region of BMP3, BMP7, and BMP9 proteins of O. fasciatus and O. punctatus, which may be related to the diversity and functional differentiation of genes within the BMP family. The qPCR-based developmental/temporal expression patterns of BMPs showed a trend of high expression at 30 days past hatching (dph), which exactly corresponds to the ossification period of the bones and beak-like teeth in Oplegnathus. Tissue-specific expression was found for the BMP4 gene, which was upregulated in the epithelial and mesenchymal tissues of the beak-like teeth, suggesting that it also plays a regulatory role in the development of the beak-like teeth in O. punctatus. Our investigation not only provides a scientific basis for comprehensively understanding the BMP gene family but also helps screen the key genes responsible for beak-like tooth healing in O. punctatus and sheds light on the developmental regulatory mechanism.
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Affiliation(s)
- Yuting Ma
- School of Marine Science and Engineering, Qingdao Agricultural University, Qingdao, China
- CAS and Shandong Province Key Laboratory of Experimental Marine Biology, Center for Ocean Mega-Science, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, China
| | - Yongshuang Xiao
- CAS and Shandong Province Key Laboratory of Experimental Marine Biology, Center for Ocean Mega-Science, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, China
- Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), Guangzhou, China
- Laboratory for Marine Biology and Biotechnology, Qingdao National Laboratory for Marine Science and Technology, Qingdao, China
- *Correspondence: Yongshuang Xiao, ; Jun Li, ,
| | - Zhizhong Xiao
- CAS and Shandong Province Key Laboratory of Experimental Marine Biology, Center for Ocean Mega-Science, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, China
- Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), Guangzhou, China
- Laboratory for Marine Biology and Biotechnology, Qingdao National Laboratory for Marine Science and Technology, Qingdao, China
- College of Marine Science, University of Chinese Academy of Sciences, Beijing, China
- Weihai Haohuigan Marine Biotechnology Co., Weihai, China
| | - Yanduo Wu
- CAS and Shandong Province Key Laboratory of Experimental Marine Biology, Center for Ocean Mega-Science, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, China
- College of Marine Science, University of Chinese Academy of Sciences, Beijing, China
| | - Haixia Zhao
- CAS and Shandong Province Key Laboratory of Experimental Marine Biology, Center for Ocean Mega-Science, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, China
- College of Marine Science, University of Chinese Academy of Sciences, Beijing, China
| | - Guang Gao
- CAS and Shandong Province Key Laboratory of Experimental Marine Biology, Center for Ocean Mega-Science, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, China
- College of Marine Science, University of Chinese Academy of Sciences, Beijing, China
| | - Lele Wu
- CAS and Shandong Province Key Laboratory of Experimental Marine Biology, Center for Ocean Mega-Science, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, China
- College of Marine Science, University of Chinese Academy of Sciences, Beijing, China
| | - Tao Wang
- School of Marine Science and Engineering, Qingdao Agricultural University, Qingdao, China
- CAS and Shandong Province Key Laboratory of Experimental Marine Biology, Center for Ocean Mega-Science, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, China
| | - Ning Zhao
- CAS and Shandong Province Key Laboratory of Experimental Marine Biology, Center for Ocean Mega-Science, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, China
- College of Marine Science, University of Chinese Academy of Sciences, Beijing, China
| | - Jun Li
- CAS and Shandong Province Key Laboratory of Experimental Marine Biology, Center for Ocean Mega-Science, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, China
- Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), Guangzhou, China
- Laboratory for Marine Biology and Biotechnology, Qingdao National Laboratory for Marine Science and Technology, Qingdao, China
- *Correspondence: Yongshuang Xiao, ; Jun Li, ,
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13
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Evolutionary Divergence and Radula Diversification in Two Ecomorphs from an Adaptive Radiation of Freshwater Snails. Genes (Basel) 2022; 13:genes13061029. [PMID: 35741791 PMCID: PMC9222583 DOI: 10.3390/genes13061029] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2022] [Revised: 05/27/2022] [Accepted: 05/31/2022] [Indexed: 12/13/2022] Open
Abstract
(1) Background: Adaptive diversification of complex traits plays a pivotal role in the evolution of organismal diversity. In the freshwater snail genus Tylomelania, adaptive radiations were likely promoted by trophic specialization via diversification of their key foraging organ, the radula. (2) Methods: To investigate the molecular basis of radula diversification and its contribution to lineage divergence, we used tissue-specific transcriptomes of two sympatric Tylomelania sarasinorum ecomorphs. (3) Results: We show that ecomorphs are genetically divergent lineages with habitat-correlated abundances. Sequence divergence and the proportion of highly differentially expressed genes are significantly higher between radula transcriptomes compared to the mantle and foot. However, the same is not true when all differentially expressed genes or only non-synonymous SNPs are considered. Finally, putative homologs of some candidate genes for radula diversification (hh, arx, gbb) were also found to contribute to trophic specialization in cichlids and Darwin’s finches. (4) Conclusions: Our results are in line with diversifying selection on the radula driving Tylomelania ecomorph divergence and indicate that some molecular pathways may be especially prone to adaptive diversification, even across phylogenetically distant animal groups.
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14
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Wagner M, Bračun S, Duenser A, Sturmbauer C, Gessl W, Ahi EP. Expression variations in ectodysplasin-A gene (eda) may contribute to morphological divergence of scales in haplochromine cichlids. BMC Ecol Evol 2022; 22:28. [PMID: 35272610 PMCID: PMC8908630 DOI: 10.1186/s12862-022-01984-0] [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: 09/13/2021] [Accepted: 02/28/2022] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Elasmoid scales are one of the most common dermal appendages and can be found in almost all species of bony fish differing greatly in their shape. Whilst the genetic underpinnings behind elasmoid scale development have been investigated, not much is known about the mechanisms involved in moulding of scales. To investigate the links between gene expression differences and morphological divergence, we inferred shape variation of scales from two different areas of the body (anterior and posterior) stemming from ten haplochromine cichlid species from different origins (Lake Tanganyika, Lake Malawi, Lake Victoria and riverine). Additionally, we investigated transcriptional differences of a set of genes known to be involved in scale development and morphogenesis in fish. RESULTS We found that scales from the anterior and posterior part of the body strongly differ in their overall shape, and a separate look on scales from each body part revealed similar trajectories of shape differences considering the lake origin of single investigated species. Above all, nine as well as 11 out of 16 target genes showed expression differences between the lakes for the anterior and posterior dataset, respectively. Whereas in posterior scales four genes (dlx5, eda, rankl and shh) revealed significant correlations between expression and morphological differentiation, in anterior scales only one gene (eda) showed such a correlation. Furthermore, eda displayed the most significant expression difference between species of Lake Tanganyika and species of the other two younger lakes. Finally, we found genetic differences in downstream regions of eda gene (e.g., in the eda-tnfsf13b inter-genic region) that are associated with observed expression differences. This is reminiscent of a genetic difference in the eda-tnfsf13b inter-genic region which leads to gain or loss of armour plates in stickleback. CONCLUSION These findings provide evidence for cross-species transcriptional differences of an important morphogenetic factor, eda, which is involved in formation of ectodermal appendages. These expression differences appeared to be associated with morphological differences observed in the scales of haplochromine cichlids indicating potential role of eda mediated signal in divergent scale morphogenesis in fish.
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Affiliation(s)
- Maximilian Wagner
- Institute of Biology, University of Graz, Universitätsplatz 2, 8010, Graz, Austria.,Department of Biology, University of Antwerp, Groenenborgerlaan 171, 2020, Antwerp, Belgium
| | - Sandra Bračun
- Institute of Biology, University of Graz, Universitätsplatz 2, 8010, Graz, Austria
| | - Anna Duenser
- Institute of Biology, University of Graz, Universitätsplatz 2, 8010, Graz, Austria
| | - Christian Sturmbauer
- Institute of Biology, University of Graz, Universitätsplatz 2, 8010, Graz, Austria.
| | - Wolfgang Gessl
- Institute of Biology, University of Graz, Universitätsplatz 2, 8010, Graz, Austria
| | - Ehsan Pashay Ahi
- Institute of Biology, University of Graz, Universitätsplatz 2, 8010, Graz, Austria. .,Organismal and Evolutionary Biology Research Programme, University of Helsinki, Viikinkaari 9, 00014, Helsinki, Finland.
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15
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Martinez CM, Tovar AJ, Wainwright PC. A novel intramandibular joint facilitates feeding versatility in the sixbar distichodus. J Exp Biol 2022; 225:273910. [PMID: 34989395 DOI: 10.1242/jeb.243621] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2021] [Accepted: 12/23/2021] [Indexed: 11/20/2022]
Abstract
The intramandibular joint (IMJ) is a secondary point of movement between the two major bones of the lower jaw. It has independently evolved in several groups of teleost fishes, each time representing a departure from related species in which the mandible functions as a single structure rotating only at the quadratomandibular joint (QMJ). In this study, we examine kinematic consequences of the IMJ novelty in a freshwater characiform fish, the herbivorous Distichodus sexfasciatus. We combine traditional kinematic approaches with trajectory-based analysis of motion shapes to compare patterns of prey capture movements during substrate biting, the fish's native feeding mode, and suction of prey from the water column. We find that the IMJ enables complex jaw motions and contributes to feeding versatility by allowing the fish to modulate its kinematics in response to different prey and to various scenarios of jaw-substrate interaction. Implications of the IMJ include context-dependent movements of lower versus upper jaws, enhanced lower jaw protrusion, and the ability to maintain contact between the teeth and substrate throughout the jaw closing or biting phase of the motion. The IMJ in D. sexfasciatus appears to be an adaptation for removing attached benthic prey, consistent with its function in other groups that have evolved the joint. This study builds on our understanding of the role of the IMJ during prey capture and provides insights into broader implications of the innovative trait.
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Affiliation(s)
- Christopher M Martinez
- Department of Ecology and Evolutionary Biology, University of California, Irvine, CA 92697, USA.,Department of Evolution and Ecology, University of California, Davis, CA 95616, USA
| | - Angelly J Tovar
- Department of Evolution and Ecology, University of California, Davis, CA 95616, USA
| | - Peter C Wainwright
- Department of Evolution and Ecology, University of California, Davis, CA 95616, USA
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16
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Navon D, Hatini P, Zogbaum L, Albertson RC. The genetic basis of coordinated plasticity across functional units in a Lake Malawi cichlid mapping population. Evolution 2021; 75:672-687. [PMID: 33438760 DOI: 10.1111/evo.14157] [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: 04/16/2020] [Revised: 12/15/2020] [Accepted: 12/22/2020] [Indexed: 11/28/2022]
Abstract
Adaptive radiations are often stereotypical, as populations repeatedly specialize along conserved environmental axes. Phenotypic plasticity may be similarly stereotypical, as individuals respond to environmental cues. These parallel patterns of variation, which are often consistent across traits, have led researchers to propose that plasticity can facilitate predictable patterns of evolution along environmental gradients. This "flexible stem" model of evolution raises questions about the genetic nature of plasticity, including how complex is the genetic basis for plasticity? Is plasticity across traits mediated by many distinct loci, or few "global" regulators? To address these questions, we reared a hybrid cichlid mapping population on alternate diet regimes mimicking an important environmental axis. We show that plasticity across an array of ecologically relevant traits is generally morphologically integrated, such that traits respond in a coordinated manner, especially those with overlapping function. Our genetic data are more ambiguous. While our mapping experiment provides little evidence for global genetic regulators of plasticity, these data do contain a genetic signal for the integration of plasticity across traits. Overall, our data suggest a compromise between genetic modularity, whereby plasticity may evolve independently across traits, and low level but widespread genetic integration, establishing the potential for plasticity to experience coordinated evolution.
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Affiliation(s)
- Dina Navon
- Graduate Program in Organismal & Evolutionary Biology, University of Massachusetts Amherst, Amherst, Massachusetts, 01003.,Rutgers University Human Genetics Institute, Piscataway, New Jersey, 08854
| | - Paul Hatini
- Department of Biology, Morrill Science Center, University of Massachusetts Amherst, Amherst, Massachusetts, 01003
| | - Lily Zogbaum
- Biology Department, Swarthmore College, Swarthmore, Pennsylvania, 19081
| | - R Craig Albertson
- Graduate Program in Organismal & Evolutionary Biology, University of Massachusetts Amherst, Amherst, Massachusetts, 01003.,Department of Biology, Morrill Science Center, University of Massachusetts Amherst, Amherst, Massachusetts, 01003
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17
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Nicholson GM, Clements KD. Ecomorphological divergence and trophic resource partitioning in 15 syntopic Indo-Pacific parrotfishes (Labridae: Scarini). Biol J Linn Soc Lond 2021. [DOI: 10.1093/biolinnean/blaa210] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
Abstract
Adaptive diversification is a product of both phylogenetic constraint and ecological opportunity. The species-rich parrotfish genera Scarus and Chlorurus display considerable variation in trophic cranial morphology, but these parrotfishes are often described as generalist herbivores. Recent work has suggested that parrotfish partition trophic resources at very fine spatial scales, raising the question of whether interspecific differences in cranial morphology reflect trophic partitioning. We tested this hypothesis by comparing targeted feeding substrata with a previously published dataset of nine cranial morphological traits. We sampled feeding substrata of 15 parrotfish species at Lizard Island, Great Barrier Reef, Australia, by following individuals until focused biting was observed, then extracting a bite core 22 mm in diameter. Three indices were parameterized for each bite core: substratum taphonomy, maximum turf height and cover of crustose coralline algae. Parrotfish species were spread along a single axis of variation in feeding substrata: successional status of the substratum taphonomy and epilithic and endolithic biota. This axis of trophic variation was significantly correlated with cranial morphology, indicating that morphological disparity within this clade is associated with interspecific partitioning of feeding substrata. Phylogenetic signal and phylomorphospace analyses revealed that the evolution of this clade involved a hitherto-unrecognized level of trophic diversification.
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Affiliation(s)
| | - Kendall D Clements
- School of Biological Sciences, University of Auckland, Auckland, New Zealand
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18
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Santos-Santos JH, Audenaert L, Verheyen E, Adriaens D. Ontogenetic divergence generates novel phenotypes in hybrid cichlids. J Anat 2021; 238:1116-1127. [PMID: 33417249 PMCID: PMC8053579 DOI: 10.1111/joa.13375] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2020] [Revised: 11/10/2020] [Accepted: 11/16/2020] [Indexed: 12/20/2022] Open
Abstract
Hybridization is suggested to contribute to ecomorphological and taxonomic diversity in lacustrine East African cichlids. This is supported by studies demonstrating that genetic diversity within lake radiations has been influenced by hybridization events, leading to extensive phenotypic differentiation of genetically closely related species. Hybrid persistence and speciation in sympatry with gene flow can be explained by pleiotropy in traits involved in reproductive isolation; however, little attention has been given to how trait differentiation is established during hybrid ontogeny, and how this may relate to trophic and locomotor specialization. This study compares body shape changes in a Lake Victoria cichlid hybrid throughout its post-hatch ontogeny to those of its parental species. Across the considered age/size categories, hybrids occupy a distinct and intermediate morphological space, yet where several transgressive traits emerge. A between-group principal component analysis on body shapes across size categories reveals axes of shape variation exclusive to the hybrids in the youngest/smallest size categories. Shape differences in the hybrids involved morphological traits known to be implicated in trophic and locomotor specializations in the parental species. Combined, our findings suggest that phenotypic divergence in the hybrid can lead to functional differences that may potentially release them to some degree from competition with the parental species. These findings agree with recent literature that addresses the potential importance of hybridization for the unusually recent origin of the Lake Victoria cichlid super-species flock.
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Affiliation(s)
- Javier H Santos-Santos
- Evolutionary Morphology of Vertebrates, Ghent University, Gent, Belgium.,Department of Biogeography and Global Change, Museo Nacional de Ciencias Naturales, Consejo Superior de Investigaciones Científicas (MNCN-CSIC), Madrid, Spain
| | - Leen Audenaert
- OD Taxonomy and Phylogeny, Vertebrates, Royal Belgian Institute of Natural Sciences, Brussels, Belgium
| | - Erik Verheyen
- OD Taxonomy and Phylogeny, Vertebrates, Royal Belgian Institute of Natural Sciences, Brussels, Belgium.,Evolutionary Ecology Group, Biology Department, University of Antwerp, Antwerp, Belgium
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19
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Conith AJ, Hope SA, Chhouk BH, Albertson RC. Weak genetic signal for phenotypic integration implicates developmental processes as major regulators of trait covariation. Mol Ecol 2021; 30:464-480. [PMID: 33231336 PMCID: PMC8811731 DOI: 10.1111/mec.15748] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2020] [Revised: 11/03/2020] [Accepted: 11/04/2020] [Indexed: 12/30/2022]
Abstract
Phenotypic integration is an important metric that describes the degree of covariation among traits in a population, and is hypothesized to arise due to selection for shared functional processes. Our ability to identify the genetic and/or developmental underpinnings of integration is marred by temporally overlapping cell-, tissue- and structure-level processes that serve to continually 'overwrite' the structure of covariation among traits through ontogeny. Here, we examine whether traits that are integrated at the phenotypic level also exhibit a shared genetic basis (e.g. pleiotropy). We micro-CT scanned two hard tissue traits, and two soft tissue traits (mandible, pectoral girdle, atrium and ventricle, respectively) from an F5 hybrid population of Lake Malawi cichlids, and used geometric morphometrics to extract 3D shape information from each trait. Given the large degree of asymmetric variation that may reflect developmental instability, we separated symmetric from asymmetric components of shape variation. We then performed quantitative trait loci (QTL) analysis to determine the degree of genetic overlap between shapes. While we found ubiquitous associations among traits at the phenotypic level, except for a handful of notable exceptions, our QTL analysis revealed few overlapping genetic regions. Taken together, this indicates developmental interactions can play a large role in determining the degree of phenotypic integration among traits, and likely obfuscate the genotype to phenotype map, limiting our ability to gain a comprehensive picture of the genetic contributors responsible for phenotypic divergence.
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Affiliation(s)
- Andrew J. Conith
- Biology Department, University of Massachusetts Amherst, Amherst, MA, 01002
| | - Sylvie A. Hope
- Biology Department, University of Massachusetts Amherst, Amherst, MA, 01002
| | - Brian H Chhouk
- Biology Department, University of Massachusetts Amherst, Amherst, MA, 01002
| | - R. Craig Albertson
- Biology Department, University of Massachusetts Amherst, Amherst, MA, 01002
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20
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Long HK, Osterwalder M, Welsh IC, Hansen K, Davies JOJ, Liu YE, Koska M, Adams AT, Aho R, Arora N, Ikeda K, Williams RM, Sauka-Spengler T, Porteus MH, Mohun T, Dickel DE, Swigut T, Hughes JR, Higgs DR, Visel A, Selleri L, Wysocka J. Loss of Extreme Long-Range Enhancers in Human Neural Crest Drives a Craniofacial Disorder. Cell Stem Cell 2020; 27:765-783.e14. [PMID: 32991838 PMCID: PMC7655526 DOI: 10.1016/j.stem.2020.09.001] [Citation(s) in RCA: 79] [Impact Index Per Article: 19.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2020] [Revised: 06/09/2020] [Accepted: 09/02/2020] [Indexed: 01/09/2023]
Abstract
Non-coding mutations at the far end of a large gene desert surrounding the SOX9 gene result in a human craniofacial disorder called Pierre Robin sequence (PRS). Leveraging a human stem cell differentiation model, we identify two clusters of enhancers within the PRS-associated region that regulate SOX9 expression during a restricted window of facial progenitor development at distances up to 1.45 Mb. Enhancers within the 1.45 Mb cluster exhibit highly synergistic activity that is dependent on the Coordinator motif. Using mouse models, we demonstrate that PRS phenotypic specificity arises from the convergence of two mechanisms: confinement of Sox9 dosage perturbation to developing facial structures through context-specific enhancer activity and heightened sensitivity of the lower jaw to Sox9 expression reduction. Overall, we characterize the longest-range human enhancers involved in congenital malformations, directly demonstrate that PRS is an enhanceropathy, and illustrate how small changes in gene expression can lead to morphological variation.
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Affiliation(s)
- Hannah K Long
- Department of Chemical and Systems Biology, Stanford University School of Medicine, Stanford, CA 94305, USA; Department of Developmental Biology, Stanford University School of Medicine, Stanford, CA 94305, USA; Institute of Stem Cell Biology and Regenerative Medicine, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Marco Osterwalder
- Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
| | - Ian C Welsh
- Program in Craniofacial Biology, Department of Orofacial Sciences and Department of Anatomy, Institute of Human Genetics, Eli and Edythe Broad Center of Regeneration Medicine and Stem Cell Research, University of California, San Francisco, San Francisco, CA, USA
| | - Karissa Hansen
- Program in Craniofacial Biology, Department of Orofacial Sciences and Department of Anatomy, Institute of Human Genetics, Eli and Edythe Broad Center of Regeneration Medicine and Stem Cell Research, University of California, San Francisco, San Francisco, CA, USA
| | - James O J Davies
- MRC Molecular Haematology Unit, MRC Weatherall Institute of Molecular Medicine, Radcliffe Department of Medicine, University of Oxford, Oxford, UK
| | - Yiran E Liu
- Cancer Biology Program, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Mervenaz Koska
- Department of Chemical and Systems Biology, Stanford University School of Medicine, Stanford, CA 94305, USA; Department of Developmental Biology, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Alexander T Adams
- Department of Chemical and Systems Biology, Stanford University School of Medicine, Stanford, CA 94305, USA; Department of Biology, Stanford University, Stanford, CA 94305, USA
| | - Robert Aho
- Program in Craniofacial Biology, Department of Orofacial Sciences and Department of Anatomy, Institute of Human Genetics, Eli and Edythe Broad Center of Regeneration Medicine and Stem Cell Research, University of California, San Francisco, San Francisco, CA, USA
| | - Neha Arora
- Department of Chemical and Systems Biology, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Kazuya Ikeda
- Department of Pediatrics, Stanford University, Stanford, CA 94305, USA
| | - Ruth M Williams
- MRC Weatherall Institute of Molecular Medicine, Radcliffe Department of Medicine, University of Oxford, Oxford, UK
| | - Tatjana Sauka-Spengler
- MRC Weatherall Institute of Molecular Medicine, Radcliffe Department of Medicine, University of Oxford, Oxford, UK
| | - Matthew H Porteus
- Department of Pediatrics, Stanford University, Stanford, CA 94305, USA
| | - Tim Mohun
- The Francis Crick Institute, Mill Hill Laboratory, The Ridgeway, Mill Hill, London NW7 1AA, UK
| | - Diane E Dickel
- Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
| | - Tomek Swigut
- Department of Chemical and Systems Biology, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Jim R Hughes
- MRC Molecular Haematology Unit, MRC Weatherall Institute of Molecular Medicine, Radcliffe Department of Medicine, University of Oxford, Oxford, UK
| | - Douglas R Higgs
- MRC Molecular Haematology Unit, MRC Weatherall Institute of Molecular Medicine, Radcliffe Department of Medicine, University of Oxford, Oxford, UK; Laboratory of Gene Regulation, MRC Weatherall Institute of Molecular Medicine, Radcliffe Department of Medicine, University of Oxford, Oxford, UK
| | - Axel Visel
- Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA; US 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
| | - Licia Selleri
- Program in Craniofacial Biology, Department of Orofacial Sciences and Department of Anatomy, Institute of Human Genetics, Eli and Edythe Broad Center of Regeneration Medicine and Stem Cell Research, University of California, San Francisco, San Francisco, CA, USA
| | - Joanna Wysocka
- Department of Chemical and Systems Biology, Stanford University School of Medicine, Stanford, CA 94305, USA; Department of Developmental Biology, Stanford University School of Medicine, Stanford, CA 94305, USA; Institute of Stem Cell Biology and Regenerative Medicine, Stanford University School of Medicine, Stanford, CA 94305, USA; Howard Hughes Medical Institute, Stanford University School of Medicine, Stanford, CA 94305, USA.
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21
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Munyandamutsa P, Jere WL, Kassam D, Mtethiwa A. Species specificity and sexual dimorphism in tooth shape among the three sympatric haplochromine species in Lake Kivu cichlids. Ecol Evol 2020; 10:5694-5711. [PMID: 32607184 PMCID: PMC7319136 DOI: 10.1002/ece3.6309] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2019] [Revised: 03/24/2020] [Accepted: 03/26/2020] [Indexed: 01/06/2023] Open
Abstract
Tooth shape is used to differentiate between morphologically similar species of vertebrates, including fish. This study aimed to quantify tooth shape of three sympatric species: Haplochromis kamiranzovu, H. insidiae, and H. astatodon endemic to Lake Kivu, whose existing identification criteria are currently only qualitative. A quantitative tooth shape analysis was performed based on digitized tooth outline data with a subsequent elliptic Fourier analysis to test for differences among the three species. We looked at crown shape and size differences within H. kamiranzovu and H. insidiae at geographical, habitat, and gender levels. No comparison at habitat level was done for H. astatodon because it is found only in littoral zone. The analysis revealed significant tooth shape differences among the three species. Haplochromis astatodon had a significantly longer major cusp height and a longer and larger minor cusp than that of H. insidiae. It had also a longer major cusp height and a longer and larger minor cusp than that of H. kamiranzovu. Tooth shape differences of H. kamiranzovu and H. insidiae species were not significantly different between littoral and pelagic fish (p > .05) while differences were significant between southern and northern Lake Kivu populations (p < .05). Tooth sizes in H. kamiranzovu and H. insidiae were significantly different, both in height and width as well as in their ratios, and this was true at sex and geographic levels (p < .05), but not at habitat level (p > .05). Tooth shape was also significantly different with sharp teeth for males compared with females of southern populations versus northern ones. These shape- and size-related differences between sexes suggest differences in the foraging strategies toward available food resources in the lake habitat. Further research should explain the genetic basis of the observed pattern.
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Affiliation(s)
- Philippe Munyandamutsa
- Africa Centre of Excellence in Aquaculture and FisheriesDepartment of Aquaculture and Fisheries ScienceBunda CollegeLilongwe University of Agriculture and Natural Resources (LUANAR)LilongweMalawi
- Department of Animal ProductionCollege of Agriculture, Animal Sciences and Veterinary MedicineUniversity of Rwanda (UR)MusanzeRwanda
| | - Wilson Lazaro Jere
- Africa Centre of Excellence in Aquaculture and FisheriesDepartment of Aquaculture and Fisheries ScienceBunda CollegeLilongwe University of Agriculture and Natural Resources (LUANAR)LilongweMalawi
| | - Daud Kassam
- Africa Centre of Excellence in Aquaculture and FisheriesDepartment of Aquaculture and Fisheries ScienceBunda CollegeLilongwe University of Agriculture and Natural Resources (LUANAR)LilongweMalawi
| | - Austin Mtethiwa
- Africa Centre of Excellence in Aquaculture and FisheriesDepartment of Aquaculture and Fisheries ScienceBunda CollegeLilongwe University of Agriculture and Natural Resources (LUANAR)LilongweMalawi
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22
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Ahi EP, Singh P, Duenser A, Gessl W, Sturmbauer C. Divergence in larval jaw gene expression reflects differential trophic adaptation in haplochromine cichlids prior to foraging. BMC Evol Biol 2019; 19:150. [PMID: 31340758 PMCID: PMC6657104 DOI: 10.1186/s12862-019-1483-3] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2019] [Accepted: 07/18/2019] [Indexed: 12/11/2022] Open
Abstract
Background Understanding how variation in gene expression contributes to morphological diversity is a major goal in evolutionary biology. Cichlid fishes from the East African Great lakes exhibit striking diversity in trophic adaptations predicated on the functional modularity of their two sets of jaws (oral and pharyngeal). However, the transcriptional basis of this modularity is not so well understood, as no studies thus far have directly compared the expression of genes in the oral and pharyngeal jaws. Nor is it well understood how gene expression may have contributed to the parallel evolution of trophic morphologies across the replicate cichlid adaptive radiations in Lake Tanganyika, Malawi and Victoria. Results We set out to investigate the role of gene expression divergence in cichlid fishes from these three lakes adapted to herbivorous and carnivorous trophic niches. We focused on the development stage prior to the onset of exogenous feeding that is critical for understanding patterns of gene expression after oral and pharyngeal jaw skeletogenesis, anticipating environmental cues. This framework permitted us for the first time to test for signatures of gene expression underlying jaw modularity in convergent eco-morphologies across three independent adaptive radiations. We validated a set of reference genes, with stable expression between the two jaw types and across species, which can be important for future studies of gene expression in cichlid jaws. Next we found evidence of modular and non-modular gene expression between the two jaws, across different trophic niches and lakes. For instance, prdm1a, a skeletogenic gene with modular anterior-posterior expression, displayed higher pharyngeal jaw expression and modular expression pattern only in carnivorous species. Furthermore, we found the expression of genes in cichlids jaws from the youngest Lake Victoria to exhibit low modularity compared to the older lakes. Conclusion Overall, our results provide cross-species transcriptional comparisons of modularly-regulated skeletogenic genes in the two jaw types, implicating expression differences which might contribute to the formation of divergent trophic morphologies at the stage of larval independence prior to foraging. Electronic supplementary material The online version of this article (10.1186/s12862-019-1483-3) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Ehsan Pashay Ahi
- Institute of Biology, University of Graz, Universitätsplatz 2, A-8010, Graz, Austria. .,Evolutionary Biology Centre, Uppsala University, Norbyvägen 18A, 75236, Uppsala, Sweden.
| | - Pooja Singh
- Institute of Biology, University of Graz, Universitätsplatz 2, A-8010, Graz, Austria
| | - Anna Duenser
- Institute of Biology, University of Graz, Universitätsplatz 2, A-8010, Graz, Austria
| | - Wolfgang Gessl
- Institute of Biology, University of Graz, Universitätsplatz 2, A-8010, Graz, Austria
| | - Christian Sturmbauer
- Institute of Biology, University of Graz, Universitätsplatz 2, A-8010, Graz, Austria
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23
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Edgley DE, Genner MJ. Adaptive Diversification of the Lateral Line System during Cichlid Fish Radiation. iScience 2019; 16:1-11. [PMID: 31146127 PMCID: PMC6542376 DOI: 10.1016/j.isci.2019.05.016] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2018] [Revised: 03/06/2019] [Accepted: 05/10/2019] [Indexed: 01/19/2023] Open
Abstract
The mechanosensory lateral line system is used by fishes to sense hydrodynamic stimuli in their environment. It provides information about flow regimes, proximity to substrate, and the presence and identity of prey and predators and represents a means of receiving communication signals from other fish. Thus we may expect lateral line system structures to be under strong divergent selection during adaptive radiation. Here, we used X-ray micro-computed tomography scans to quantify variation in cranial lateral line canal morphology within the adaptive radiation of Lake Malawi cichlids. We report that cranial lateral line canal morphology is strongly correlated with diet and other aspects of craniofacial morphology, including the shape of oral jaws. These results indicate an adaptive role for the lateral line system in prey detection and suggest that diversification of this system has taken an important role in the spectacular evolution of Lake Malawi's cichlid fish diversity.
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Affiliation(s)
- Duncan E Edgley
- School of Biological Sciences, University of Bristol, Life Sciences Building, 24 Tyndall Avenue, Bristol BS8 1TQ, UK.
| | - Martin J Genner
- School of Biological Sciences, University of Bristol, Life Sciences Building, 24 Tyndall Avenue, Bristol BS8 1TQ, UK.
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24
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Huby A, Lowie A, Herrel A, Vigouroux R, Frédérich B, Raick X, Kurchevski G, Godinho AL, Parmentier E. Functional diversity in biters: the evolutionary morphology of the oral jaw system in pacus, piranhas and relatives (Teleostei: Serrasalmidae). Biol J Linn Soc Lond 2019. [DOI: 10.1093/biolinnean/blz048] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Abstract
Abstract
Serrasalmid fishes form a highly specialized group of biters that show a large trophic diversity, ranging from pacus able to crush seeds to piranhas capable of cutting flesh. Their oral jaw system has been hypothesized to be forceful, but variation in bite performance and morphology with respect to diet has not previously been investigated. We tested whether herbivorous species have higher bite forces, larger jaw muscles and more robust jaws than carnivorous species. We measured in vivo and theoretical bite forces in 27 serrasalmid species. We compared the size of the adductor mandibulae muscle, the jaw mechanical advantages, the type of jaw occlusion, and the size and shape of the lower jaw. We also examined the association between bite performance and functional morphological traits of the oral jaw system. Contrary to our predictions, carnivorous piranhas deliver stronger bites than their herbivorous counterparts. The size of the adductor mandibulae muscle varies with bite force and muscles are larger in carnivorous species. Our study highlights an underestimated level of functional morphological diversity in a fish group of exclusive biters. We provide evidence that the trophic specialization towards carnivory in piranhas results from changes in the configuration of the adductor mandibulae muscle and the lower jaw shape, which have major effects on bite performance and bite strategy.
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Affiliation(s)
- Alessia Huby
- Laboratory of Functional and Evolutionary Morphology, University of Liège, Liège, Belgium
| | - Aurélien Lowie
- Laboratory of Functional and Evolutionary Morphology, University of Liège, Liège, Belgium
- Evolutionary Morphology of Vertebrates, Ghent University, Gent, Belgium
| | - Anthony Herrel
- UMR7179 MNHN/CNRS, National Museum of Natural History, Paris, France
- Evolutionary Morphology of Vertebrates, Ghent University, Gent, Belgium
| | - Régis Vigouroux
- HYDRECO GUYANE, Laboratory Environment of Petit Saut, Kourou, French Guiana
| | - Bruno Frédérich
- Laboratory of Functional and Evolutionary Morphology, University of Liège, Liège, Belgium
| | - Xavier Raick
- Laboratory of Functional and Evolutionary Morphology, University of Liège, Liège, Belgium
| | - Gregório Kurchevski
- Fish Passage Center, Federal University of Minas Gerais, Belo Horizonte, Brazil
| | | | - Eric Parmentier
- Laboratory of Functional and Evolutionary Morphology, University of Liège, Liège, Belgium
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25
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Vasil’ev AG. Evolutionary Ecology in the 21st Century: New Concepts and Development Prospects. RUSS J ECOL+ 2019. [DOI: 10.1134/s1067413619020103] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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26
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Böhne A, Weber AAT, Rajkov J, Rechsteiner M, Riss A, Egger B, Salzburger W. Repeated Evolution Versus Common Ancestry: Sex Chromosome Evolution in the Haplochromine Cichlid Pseudocrenilabrus philander. Genome Biol Evol 2019; 11:439-458. [PMID: 30649313 PMCID: PMC6375353 DOI: 10.1093/gbe/evz003] [Citation(s) in RCA: 22] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 01/07/2019] [Indexed: 12/15/2022] Open
Abstract
Why sex chromosomes turn over and remain undifferentiated in some taxa, whereas they degenerate in others, is still an area of ongoing research. The recurrent occurrence of homologous and homomorphic sex chromosomes in distantly related taxa suggests their independent evolution or continued recombination since their first emergence. Fishes display a great diversity of sex-determining systems. Here, we focus on sex chromosome evolution in haplochromines, the most species-rich lineage of cichlid fishes. We investigate sex-specific signatures in the Pseudocrenilabrus philander species complex, which belongs to a haplochromine genus found in many river systems and ichthyogeographic regions in northern, eastern, central, and southern Africa. Using whole-genome sequencing and population genetic, phylogenetic, and read-coverage analyses, we show that one population of P. philander has an XX-XY sex-determining system on LG7 with a large region of suppressed recombination. However, in a second bottlenecked population, we did not find any sign of a sex chromosome. Interestingly, LG7 also carries an XX-XY system in the phylogenetically more derived Lake Malawi haplochromine cichlids. Although the genomic regions determining sex are the same in Lake Malawi cichlids and P. philander, we did not find evidence for shared ancestry, suggesting that LG7 evolved as sex chromosome at least twice in haplochromine cichlids. Hence, our work provides further evidence for the labile nature of sex determination in fishes and supports the hypothesis that the same genomic regions can repeatedly and rapidly be recruited as sex chromosomes in more distantly related lineages.
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Affiliation(s)
- Astrid Böhne
- Department of Environmental Sciences, Zoological Institute, University of Basel, Switzerland
| | - Alexandra Anh-Thu Weber
- Department of Environmental Sciences, Zoological Institute, University of Basel, Switzerland
- Museums Victoria, Melbourne, Victoria, Australia
| | - Jelena Rajkov
- Department of Environmental Sciences, Zoological Institute, University of Basel, Switzerland
| | - Michael Rechsteiner
- Department of Environmental Sciences, Zoological Institute, University of Basel, Switzerland
| | - Andrin Riss
- Department of Environmental Sciences, Zoological Institute, University of Basel, Switzerland
| | - Bernd Egger
- Department of Environmental Sciences, Zoological Institute, University of Basel, Switzerland
- Program Man Society Environment, University of Basel, Switzerland
| | - Walter Salzburger
- Department of Environmental Sciences, Zoological Institute, University of Basel, Switzerland
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27
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Conith AJ, Lam DT, Albertson RC. Muscle-induced loading as an important source of variation in craniofacial skeletal shape. Genesis 2018; 57:e23263. [PMID: 30418689 DOI: 10.1002/dvg.23263] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2018] [Revised: 10/25/2018] [Accepted: 10/27/2018] [Indexed: 01/01/2023]
Abstract
The shape of the craniofacial skeleton is constantly changing through ontogeny and reflects a balance between developmental patterning and mechanical-load-induced remodeling. Muscles are a major contributor to producing the mechanical environment that is crucial for "normal" skull development. Here, we use an F5 hybrid population of Lake Malawi cichlids to characterize the strength and types of associations between craniofacial bones and muscles. We focus on four bones/bone complexes, with different developmental origins, alongside four muscles with distinct functions. We used micro-computed tomography to extract 3D information on bones and muscles. 3D geometric morphometrics and volumetric measurements were used to characterize bone and muscle shape, respectively. Linear regressions were performed to test for associations between bone shape and muscle volume. We identified three types of associations between muscles and bones: weak, strong direct (i.e., muscles insert directly onto bone), and strong indirect (i.e., bone is influenced by muscles without a direct connection). In addition, we show that although the shape of some bones is relatively robust to muscle-induced mechanical stimulus, others appear to be highly sensitive to muscular input. Our results imply that the roles for muscular input on skeletal shape extend beyond specific points of origin or insertion and hold significant potential to influence broader patterns of craniofacial geometry. Thus, changes in the loading environment, either as a normal course of ontogeny or if an organism is exposed to a novel environment, may have pronounced effects on skeletal shape via near and far-ranging effects of muscular loading.
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Affiliation(s)
- Andrew J Conith
- Biology Department, University of Massachusetts Amherst, Amherst, Massachusetts
| | - Daniel T Lam
- Biology Department, University of Massachusetts Amherst, Amherst, Massachusetts
| | - R Craig Albertson
- Biology Department, University of Massachusetts Amherst, Amherst, Massachusetts
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28
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Ahi EP, Singh P, Lecaudey LA, Gessl W, Sturmbauer C. Maternal mRNA input of growth and stress-response-related genes in cichlids in relation to egg size and trophic specialization. EvoDevo 2018; 9:23. [PMID: 30519389 PMCID: PMC6271631 DOI: 10.1186/s13227-018-0112-3] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2018] [Accepted: 11/22/2018] [Indexed: 01/21/2023] Open
Abstract
BACKGROUND Egg size represents an important form of maternal effect determined by a complex interplay of long-term adaptation and short-term plasticity balancing egg size with brood size. Haplochromine cichlids are maternal mouthbrooders showing differential parental investment in different species, manifested in great variation in egg size, brood size and duration of maternal care. Little is known about maternally determined molecular characters of eggs in fishes and their relation to egg size and trophic specialization. Here we investigate maternal mRNA inputs of selected growth- and stress-related genes in eggs of mouthbrooding cichlid fishes adapted to different trophic niches from Lake Tanganyika, Lake Malawi, Lake Victoria and compare them to their riverine allies. RESULTS We first identified two reference genes, atf7ip and mid1ip1, to be suitable for cross-species quantification of mRNA abundance via qRT-PCR in the cichlid eggs. Using these reference genes, we found substantial variation in maternal mRNA input for a set of candidate genes related to growth and stress response across species and lakes. We observed negative correlation of mRNA abundance between two of growth hormone receptor paralogs (ghr1 and ghr2) across all haplochromine cichlid species which also differentiate the species in the two younger lakes, Malawi and Lake Victoria, from those in Lake Tanganyika and ancestral riverine species. Furthermore, we found correlations between egg size and maternal mRNA abundance of two growth-related genes igf2 and ghr2 across the haplochromine cichlids as well as distinct clustering of the species based on their trophic specialization using maternal mRNA abundance of five genes (ghr1, ghr2, igf2, gr and sgk1). CONCLUSIONS These findings indicate that variations in egg size in closely related cichlid species can be linked to differences in maternal RNA deposition of key growth-related genes. In addition, the cichlid species with contrasting trophic specialization deposit different levels of maternal mRNAs in their eggs for particular growth-related genes; however, it is unclear whether such differences contribute to differential morphogenesis at later stages of development. Our results provide first insights into this aspect of gene activation, as a basis for future studies targeting their role during ecomorphological specialization and adaptive radiation.
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Affiliation(s)
- Ehsan Pashay Ahi
- Institute of Biology, University of Graz, Universitätsplatz 2, 8010 Graz, Austria
- Evolutionary Biology Centre, Uppsala University, Norbyvägen 18A, 75236 Uppsala, Sweden
| | - Pooja Singh
- Institute of Biology, University of Graz, Universitätsplatz 2, 8010 Graz, Austria
| | | | - Wolfgang Gessl
- Institute of Biology, University of Graz, Universitätsplatz 2, 8010 Graz, Austria
| | - Christian Sturmbauer
- Institute of Biology, University of Graz, Universitätsplatz 2, 8010 Graz, Austria
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29
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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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30
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Lencer ES, McCune AR. An embryonic staging series up to hatching for Cyprinodon variegatus: An emerging fish model for developmental, evolutionary, and ecological research. J Morphol 2018; 279:1559-1578. [PMID: 30368863 DOI: 10.1002/jmor.20870] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2018] [Revised: 06/17/2018] [Accepted: 06/22/2018] [Indexed: 11/08/2022]
Abstract
Using multiple taxa to research development is necessary for making general conclusions about developmental patterns and mechanisms. We present a staging series for Cyprinodon variegatus as a basis for further study of the developmental biology of fishes in the genus Cyprinodon and for comparative work on teleost fishes beyond the standard models. Cyprinodon are small, euryhaline fishes, widely distributed in fresh, brackish, and hypersaline waters of southern and eastern North America. Cyprinodontids are closely related to fundulids, providing a comparative reference point to the embryological model, Fundulus heteroclitus. Ecologists and evolutionary biologists commonly study Cyprinodon, and we have been using Cyprinodon to study skull variation and its genetic basis among closely related species. We divided embryonic development of C. variegatus into 34 morphologically identifiable stages. We reference our staging series to that already defined for a related model species, Oryzias latipes (medaka) that is studied by a large community of researchers. We provide a description of the early chondrogenesis and ossification of skull and caudal fin bones during the latter stages of embryonic development. We show that Cyprinodon are tractable for studying development. Eggs can be obtained easily from breeding pairs and our study provides a staging system to facilitate future developmental studies.
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Affiliation(s)
- Ezra S Lencer
- Department of Ecology and Evolutionary Biology, Cornell University, Ithaca, New York
| | - Amy R McCune
- Department of Ecology and Evolutionary Biology, Cornell University, Ithaca, New York
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31
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Woltering JM, Holzem M, Schneider RF, Nanos V, Meyer A. The skeletal ontogeny of Astatotilapia burtoni - a direct-developing model system for the evolution and development of the teleost body plan. BMC DEVELOPMENTAL BIOLOGY 2018; 18:8. [PMID: 29614958 PMCID: PMC5883283 DOI: 10.1186/s12861-018-0166-4] [Citation(s) in RCA: 25] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/09/2017] [Accepted: 03/01/2018] [Indexed: 12/20/2022]
Abstract
Background The experimental approach to the evolution and development of the vertebrate skeleton has to a large extent relied on “direct-developing” amniote model organisms, such as the mouse and the chicken. These organisms can however only be partially informative where it concerns secondarily lost features or anatomical novelties not present in their lineages. The widely used anamniotes Xenopus and zebrafish are “indirect-developing” organisms that proceed through an extended time as free-living larvae, before adopting many aspects of their adult morphology, complicating experiments at these stages, and increasing the risk for lethal pleiotropic effects using genetic strategies. Results Here, we provide a detailed description of the development of the osteology of the African mouthbrooding cichlid Astatotilapia burtoni, primarily focusing on the trunk (spinal column, ribs and epicentrals) and the appendicular skeleton (pectoral, pelvic, dorsal, anal, caudal fins and scales), and to a lesser extent on the cranium. We show that this species has an extremely “direct” mode of development, attains an adult body plan within 2 weeks after fertilization while living off its yolk supply only, and does not pass through a prolonged larval period. Conclusions As husbandry of this species is easy, generation time is short, and the species is amenable to genetic targeting strategies through microinjection, we suggest that the use of this direct-developing cichlid will provide a valuable model system for the study of the vertebrate body plan, particularly where it concerns the evolution and development of fish or teleost specific traits. Based on our results we comment on the development of the homocercal caudal fin, on shared ontogenetic patterns between pectoral and pelvic girdles, and on the evolution of fin spines as novelty in acanthomorph fishes. We discuss the differences between “direct” and “indirect” developing actinopterygians using a comparison between zebrafish and A. burtoni development.
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Affiliation(s)
- Joost M Woltering
- Chair in Zoology and Evolutionary Biology, Department of Biology, University of Konstanz, Universitätsstraße 10, 78457, Constance, Germany.
| | - Michaela Holzem
- Chair in Zoology and Evolutionary Biology, Department of Biology, University of Konstanz, Universitätsstraße 10, 78457, Constance, Germany.,Current address: Department of Biological an Medical Sciences, Oxford Brookes University, Headington Campus, Oxford, OX3 0 BP, UK
| | - Ralf F Schneider
- Chair in Zoology and Evolutionary Biology, Department of Biology, University of Konstanz, Universitätsstraße 10, 78457, Constance, Germany
| | - Vasilios Nanos
- Chair in Zoology and Evolutionary Biology, Department of Biology, University of Konstanz, Universitätsstraße 10, 78457, Constance, Germany
| | - Axel Meyer
- Chair in Zoology and Evolutionary Biology, Department of Biology, University of Konstanz, Universitätsstraße 10, 78457, Constance, Germany.
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32
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Gunter HM, Schneider RF, Karner I, Sturmbauer C, Meyer A. Molecular investigation of genetic assimilation during the rapid adaptive radiations of East African cichlid fishes. Mol Ecol 2017; 26:6634-6653. [PMID: 29098748 DOI: 10.1111/mec.14405] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2016] [Revised: 08/06/2017] [Accepted: 08/24/2017] [Indexed: 12/19/2022]
Abstract
Adaptive radiations are characterized by adaptive diversification intertwined with rapid speciation within a lineage resulting in many ecologically specialized, phenotypically diverse species. It has been proposed that adaptive radiations can originate from ancestral lineages with pronounced phenotypic plasticity in adaptive traits, facilitating ecologically driven phenotypic diversification that is ultimately fixed through genetic assimilation of gene regulatory regions. This study aimed to investigate how phenotypic plasticity is reflected in gene expression patterns in the trophic apparatus of several lineages of East African cichlid fishes, and whether the observed patterns support genetic assimilation. This investigation used a split brood experimental design to compare adaptive plasticity in species from within and outside of adaptive radiations. The plastic response was induced in the crushing pharyngeal jaws through feeding individuals either a hard or soft diet. We find that nonradiating, basal lineages show higher levels of adaptive morphological plasticity than the derived, radiated lineages, suggesting that these differences have become partially genetically fixed during the formation of the adaptive radiations. Two candidate genes that may have undergone genetic assimilation, gif and alas1, were identified, in addition to alterations in the wiring of LPJ patterning networks. Taken together, our results suggest that genetic assimilation may have dampened the inducibility of plasticity related genes during the adaptive radiations of East African cichlids, flattening the reaction norms and canalizing their feeding phenotypes, driving adaptation to progressively more narrow ecological niches.
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Affiliation(s)
- Helen M Gunter
- Lehrstuhl für Zoologie und Evolutionsbiologie, Department of Biology, University of Konstanz, Konstanz, Germany.,Zukunftskolleg, University of Konstanz, Konstanz, Germany
| | - Ralf F Schneider
- Lehrstuhl für Zoologie und Evolutionsbiologie, Department of Biology, University of Konstanz, Konstanz, Germany.,International Max Planck Research School for Organismal Biology, University of Konstanz, Konstanz, Germany
| | | | | | - Axel Meyer
- Lehrstuhl für Zoologie und Evolutionsbiologie, Department of Biology, University of Konstanz, Konstanz, Germany.,International Max Planck Research School for Organismal Biology, University of Konstanz, Konstanz, Germany.,Radcliffe Institute for Advanced Study, Harvard University, Cambridge, MA, USA
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33
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Egger B, Roesti M, Böhne A, Roth O, Salzburger W. Demography and genome divergence of lake and stream populations of an East African cichlid fish. Mol Ecol 2017; 26:5016-5030. [DOI: 10.1111/mec.14248] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2017] [Accepted: 06/22/2017] [Indexed: 12/17/2022]
Affiliation(s)
- Bernd Egger
- Zoological Institute; University of Basel; Basel Switzerland
| | - Marius Roesti
- Zoological Institute; University of Basel; Basel Switzerland
- Department of Zoology; Biodiversity Research Centre; University of British Columbia; Vancouver BC Canada
| | - Astrid Böhne
- Zoological Institute; University of Basel; Basel Switzerland
| | - Olivia Roth
- Evolutionary Ecology of Marine Fishes; Helmholtz Zentrum für Ozeanforschung Kiel (GEOMAR); Kiel Germany
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34
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The Integrated Genomic Architecture and Evolution of Dental Divergence in East African Cichlid Fishes ( Haplochromis chilotes x H. nyererei). G3-GENES GENOMES GENETICS 2017; 7:3195-3202. [PMID: 28751505 PMCID: PMC5592944 DOI: 10.1534/g3.117.300083] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 02/03/2023]
Abstract
The independent evolution of the two toothed jaws of cichlid fishes is thought to have promoted their unparalleled ecological divergence and species richness. However, dental divergence in cichlids could exhibit substantial genetic covariance and this could dictate how traits like tooth numbers evolve in different African Lakes and on their two jaws. To test this hypothesis, we used a hybrid mapping cross of two trophically divergent Lake Victoria species (Haplochromis chilotes × Haplochromis nyererei) to examine genomic regions associated with cichlid tooth diversity. Surprisingly, a similar genomic region was found to be associated with oral jaw tooth numbers in cichlids from both Lake Malawi and Lake Victoria. Likewise, this same genomic location was associated with variation in pharyngeal jaw tooth numbers. Similar relationships between tooth numbers on the two jaws in both our Victoria hybrid population and across the phylogenetic diversity of Malawi cichlids additionally suggests that tooth numbers on the two jaws of haplochromine cichlids might generally coevolve owing to shared genetic underpinnings. Integrated, rather than independent, genomic architectures could be key to the incomparable evolutionary divergence and convergence in cichlid tooth numbers.
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35
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Matthews DG, Albertson RC. Effect of craniofacial genotype on the relationship between morphology and feeding performance in cichlid fishes. Evolution 2017; 71:2050-2061. [PMID: 28598501 DOI: 10.1111/evo.13289] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2016] [Revised: 05/12/2017] [Accepted: 05/22/2017] [Indexed: 01/11/2023]
Abstract
The relationship between morphology and performance is complex, but important for understanding the adaptive nature of morphological variation. Recent studies have sought to better understand this system by illuminating the interconnectedness of different functional systems; however, the role of genetics is often overlooked. In this study, we attempt to gain insights into this relationship by examining the effect of genotypic variation at putative craniofacial loci on the relationship between morphology and feeding performance in cichlids. We studied two morphologically disparate species, as well as a morphologically intermediate hybrid population. We assessed feeding performance, jaw protrusion, and general facial morphology for each fish. We also genotyped hybrid animals at six previously identified craniofacial loci. Cichlid species were found to differ in facial geometry, kinematic morphology, and performance. Significant correlations were also noted between these variables; however, the explanatory power of facial geometry in predicting performance was relatively poor. Notably, when hybrids were grouped by genotype, the relationship between shape and performance improved. This relationship was especially robust in animals with the specialist allele at sox9b, a well-characterized regulator of craniofacial development. These data suggest a novel role for genotype in influencing complex relationships between form and function.
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Affiliation(s)
- David G Matthews
- Department of Biology, University of Massachusetts Amherst, Amherst, Massachusetts, 01003
| | - R Craig Albertson
- Department of Biology, University of Massachusetts Amherst, Amherst, Massachusetts, 01003
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36
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Lencer ES, Warren WC, Harrison R, McCune AR. The Cyprinodon variegatus genome reveals gene expression changes underlying differences in skull morphology among closely related species. BMC Genomics 2017; 18:424. [PMID: 28558659 PMCID: PMC5450241 DOI: 10.1186/s12864-017-3810-7] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2017] [Accepted: 05/22/2017] [Indexed: 01/18/2023] Open
Abstract
BACKGROUND Understanding the genetic and developmental origins of phenotypic novelty is central to the study of biological diversity. In this study we identify modifications to the expression of genes at four developmental stages that may underlie jaw morphological differences among three closely related species of pupfish (genus Cyprinodon) from San Salvador Island, Bahamas. Pupfishes on San Salvador Island are trophically differentiated and include two endemic species that have evolved jaw morphologies unlike that of any other species in the genus Cyprinodon. RESULTS We find that gene expression differs significantly across recently diverged species of pupfish. Genes such as Bmp4 and calmodulin, previously implicated in jaw diversification in African cichlid fishes and Galapagos finches, were not found to be differentially expressed among species of pupfish. Instead we find multiple growth factors and cytokine/chemokine genes to be differentially expressed among these pupfish taxa. These include both genes and pathways known to affect craniofacial development, such as Wnt signaling, as well as novel genes and pathways not previously implicated in craniofacial development. These data highlight both shared and potentially unique sources of jaw diversity in pupfish and those identified in other evolutionary model systems such as Galapagos finches and African cichlids. CONCLUSIONS We identify modifications to the expression of genes involved in Wnt signaling, Igf signaling, and the inflammation response as promising avenues for future research. Our project provides insight into the magnitude of gene expression changes contributing to the evolution of morphological novelties, such as jaw structure, in recently diverged pupfish species.
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Affiliation(s)
- Ezra S Lencer
- Department of Ecology and Evolutionary Biology, Cornell University, Ithaca, NY, 14850, USA.
| | - Wesley C Warren
- McDonnell Genome Institute, Washington University School of Medicine, St Louis, MO, 63108, USA
| | - Richard Harrison
- Department of Ecology and Evolutionary Biology, Cornell University, Ithaca, NY, 14850, USA
| | - Amy R McCune
- Department of Ecology and Evolutionary Biology, Cornell University, Ithaca, NY, 14850, USA
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37
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Husemann M, Tobler M, McCauley C, Ding B, Danley PD. Body shape differences in a pair of closely related Malawi cichlids and their hybrids: Effects of genetic variation, phenotypic plasticity, and transgressive segregation. Ecol Evol 2017. [PMID: 28649345 PMCID: PMC5478046 DOI: 10.1002/ece3.2823] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
Abstract
Phenotypic differences may have genetic and plastic components. Here, we investigated the contributions of both for differences in body shape in two species of Lake Malawi cichlids using wild-caught specimens and a common garden experiment. We further hybridized the two species to investigate the mode of gene action influencing body shape differences and to examine the potential for transgressive segregation. We found that body shape differences between the two species observed in the field are maintained after more than 10 generations in a standardized environment. Nonetheless, both species experienced similar changes in the laboratory environment. Our hybrid cross experiment confirmed that substantial variation in body shape appears to be genetically determined. The data further suggest that the underlying mode of gene action is complex and cannot be explained by simple additive or additive-dominance models. Transgressive phenotypes were found in the hybrid generations, as hybrids occupied significantly more morphospace than both parentals combined. Further, the body shapes of transgressive individuals resemble the body shapes observed in other Lake Malawi rock-dwelling genera. Our findings indicate that body shape can respond to selection immediately, through plasticity, and over longer timescales through adaptation. In addition, our results suggest that hybridization may have played an important role in the diversification of Lake Malawi cichlids through creating new phenotypic variation.
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Affiliation(s)
- Martin Husemann
- Centrum für Naturkunde University of Hamburg Hamburg Germany.,Biology Department Baylor University Waco TX USA
| | - Michael Tobler
- Division of Biology Kansas State University Manhattan KS USA
| | - Cagney McCauley
- Biology Department Baylor University Waco TX USA.,Department of Biological Sciences Institute of Applied Sciences University of North Texas 282 Cr 332 Rosebud Denton TX USA
| | - Baoqing Ding
- Biology Department Baylor University Waco TX USA.,Department of Ecology and Evolutionary Biology University of Connecticut Storrs CT USA
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38
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Bloomquist RF, Fowler TE, Sylvester JB, Miro RJ, Streelman JT. A compendium of developmental gene expression in Lake Malawi cichlid fishes. BMC DEVELOPMENTAL BIOLOGY 2017; 17:3. [PMID: 28158974 PMCID: PMC5291978 DOI: 10.1186/s12861-017-0146-0] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/15/2016] [Accepted: 01/26/2017] [Indexed: 12/24/2022]
Abstract
BACKGROUND Lake Malawi cichlids represent one of a growing number of vertebrate models used to uncover the genetic and developmental basis of trait diversity. Rapid evolutionary radiation has resulted in species that share similar genomes but differ markedly in phenotypes including brains and behavior, nuptial coloration and the craniofacial skeleton. Research has begun to identify the genes, as well as the molecular and developmental pathways that underlie trait divergence. RESULTS We assemble a compendium of gene expression for Lake Malawi cichlids, across pharyngula (the phylotypic stage) and larval stages of development, encompassing hundreds of gene transcripts. We chart patterns of expression in Bone morphogenetic protein (BMP), Fibroblast growth factor (FGF), Hedgehog (Hh), Notch and Wingless (Wnt) signaling pathways, as well as genes involved in neurogenesis, calcium and endocrine signaling, stem cell biology, and numerous homeobox (Hox) factors-in three planes using whole-mount in situ hybridization. Because of low sequence divergence across the Malawi cichlid assemblage, the probes we employ are broadly applicable in hundreds of species. We tabulate gene expression across general tissue domains, and highlight examples of unexpected expression patterns. CONCLUSIONS On the heels of recently published genomes, this compendium of developmental gene expression in Lake Malawi cichlids provides a valuable resource for those interested in the relationship between evolution and development.
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Affiliation(s)
- R F Bloomquist
- Georgia Institute of Technology, School of Biological Sciences and Institute for Bioengineering and Bioscience, Atlanta, GA, USA.,Medical College of Georgia, School of Dentistry, Augusta, GA, USA
| | - T E Fowler
- Georgia Institute of Technology, School of Biological Sciences and Institute for Bioengineering and Bioscience, Atlanta, GA, USA
| | - J B Sylvester
- Georgia Institute of Technology, School of Biological Sciences and Institute for Bioengineering and Bioscience, Atlanta, GA, USA
| | - R J Miro
- Georgia Institute of Technology, School of Biological Sciences and Institute for Bioengineering and Bioscience, Atlanta, GA, USA
| | - J T Streelman
- Georgia Institute of Technology, School of Biological Sciences and Institute for Bioengineering and Bioscience, Atlanta, GA, USA.
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39
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Navon D, Olearczyk N, Albertson RC. Genetic and developmental basis for fin shape variation in African cichlid fishes. Mol Ecol 2016; 26:291-303. [DOI: 10.1111/mec.13905] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2016] [Revised: 10/05/2016] [Accepted: 10/07/2016] [Indexed: 12/29/2022]
Affiliation(s)
- Dina Navon
- Graduate Program in Organismic and Evolutionary Biology University of Massachusetts Amherst MA 01003 USA
| | - Nathan Olearczyk
- Department of Biology University of Massachusetts 611 North Pleasant Street Room 221 Morrill Science Center Amherst MA 01003 USA
| | - R. Craig Albertson
- Department of Biology University of Massachusetts 611 North Pleasant Street Room 221 Morrill Science Center Amherst MA 01003 USA
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40
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Ford AGP, Rüber L, Newton J, Dasmahapatra KK, Balarin JD, Bruun K, Day JJ. Niche divergence facilitated by fine-scale ecological partitioning in a recent cichlid fish adaptive radiation. Evolution 2016; 70:2718-2735. [PMID: 27659769 PMCID: PMC5132037 DOI: 10.1111/evo.13072] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2016] [Revised: 08/29/2016] [Accepted: 09/10/2016] [Indexed: 12/22/2022]
Abstract
Ecomorphological differentiation is a key feature of adaptive radiations, with a general trend for specialization and niche expansion following divergence. Ecological opportunity afforded by invasion of a new habitat is thought to act as an ecological release, facilitating divergence, and speciation. Here, we investigate trophic adaptive morphology and ecology of an endemic clade of oreochromine cichlid fishes (Alcolapia) that radiated along a herbivorous trophic axis following colonization of an isolated lacustrine environment, and demonstrate phenotype‐environment correlation. Ecological and morphological divergence of the Alcolapia species flock are examined in a phylogenomic context, to infer ecological niche occupation within the radiation. Species divergence is observed in both ecology and morphology, supporting the importance of ecological speciation within the radiation. Comparison with an outgroup taxon reveals large‐scale ecomorphological divergence but shallow genomic differentiation within the Alcolapia adaptive radiation. Ancestral morphological reconstruction suggests lake colonization by a generalist oreochromine phenotype that diverged in Lake Natron to varied herbivorous morphologies akin to specialist herbivores in Lakes Tanganyika and Malawi.
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Affiliation(s)
- Antonia G P Ford
- Department of Genetics, Evolution and Environment, University College London, London, WC1E 6BT, United Kingdom.,Current Address: School of Biological Sciences, Bangor University, ECW Building, Deiniol Road, Bangor, Gwynedd, LL57 2UW, Wales, United Kingdom
| | - Lukas Rüber
- Naturhistorisches Museum der Burgergemeinde Bern, Bernastrasse 15, 3005, Bern, Switzerland.,Institute of Ecology and Evolution, University of Bern, Baltzerstrasse 6, 3012, Bern, Switzerland
| | - Jason Newton
- NERC Life Sciences Mass Spectrometry Facility, SUERC, Rankine Avenue, Scottish Enterprise Technology Park, East Kilbride, G75 0QF, United Kingdom
| | | | | | - Kristoffer Bruun
- Department of Genetics, Evolution and Environment, University College London, London, WC1E 6BT, United Kingdom
| | - Julia J Day
- Department of Genetics, Evolution and Environment, University College London, London, WC1E 6BT, United Kingdom
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41
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Powder KE, Albertson RC. Cichlid fishes as a model to understand normal and clinical craniofacial variation. Dev Biol 2016; 415:338-346. [PMID: 26719128 PMCID: PMC4914429 DOI: 10.1016/j.ydbio.2015.12.018] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2015] [Revised: 12/14/2015] [Accepted: 12/21/2015] [Indexed: 01/26/2023]
Abstract
We have made great strides towards understanding the etiology of craniofacial disorders, especially for 'simple' Mendelian traits. However, the facial skeleton is a complex trait, and the full spectrum of genetic, developmental, and environmental factors that contribute to its final geometry remain unresolved. Forward genetic screens are constrained with respect to complex traits due to the types of genes and alleles commonly identified, developmental pleiotropy, and limited information about the impact of environmental interactions. Here, we discuss how studies in an evolutionary model - African cichlid fishes - can complement traditional approaches to understand the genetic and developmental origins of complex shape. Cichlids exhibit an unparalleled range of natural craniofacial morphologies that model normal human variation, and in certain instances mimic human facial dysmorphologies. Moreover, the evolutionary history and genomic architecture of cichlids make them an ideal system to identify the genetic basis of these phenotypes via quantitative trait loci (QTL) mapping and population genomics. Given the molecular conservation of developmental genes and pathways, insights from cichlids are applicable to human facial variation and disease. We review recent work in this system, which has identified lbh as a novel regulator of neural crest cell migration, determined the Wnt and Hedgehog pathways mediate species-specific bone morphologies, and examined how plastic responses to diet modulate adult facial shapes. These studies have not only revealed new roles for existing pathways in craniofacial development, but have identified new genes and mechanisms involved in shaping the craniofacial skeleton. In all, we suggest that combining work in traditional laboratory and evolutionary models offers significant potential to provide a more complete and comprehensive picture of the myriad factors that are involved in the development of complex traits.
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Affiliation(s)
- Kara E Powder
- Department of Biology, University of Massachusetts Amherst, 221 Morrill Science Center South, 611 North Pleasant Street, Amherst, MA 01003, USA.
| | - R Craig Albertson
- Department of Biology, University of Massachusetts Amherst, 221 Morrill Science Center South, 611 North Pleasant Street, Amherst, MA 01003, USA.
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42
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Ellis NA, Miller CT. Dissection and Flat-mounting of the Threespine Stickleback Branchial Skeleton. J Vis Exp 2016. [PMID: 27213248 DOI: 10.3791/54056] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023] Open
Abstract
The posterior pharyngeal segments of the vertebrate head give rise to the branchial skeleton, the primary site of food processing in fish. The morphology of the fish branchial skeleton is matched to a species' diet. Threespine stickleback fish (Gasterosteus aculeatus) have emerged as a model system to study the genetic and developmental basis of evolved differences in a variety of traits. Marine populations of sticklebacks have repeatedly colonized countless new freshwater lakes and creeks. Adaptation to the new diet in these freshwater environments likely underlies a series of craniofacial changes that have evolved repeatedly in independently derived freshwater populations. These include three major patterning changes to the branchial skeleton: reductions in the number and length of gill raker bones, increases in pharyngeal tooth number, and increased branchial bone lengths. Here we describe a detailed protocol to dissect and flat-mount the internal branchial skeleton in threespine stickleback fish. Dissection of the entire three-dimensional branchial skeleton and mounting it flat into a largely two-dimensional prep allows for the easy visualization and quantification of branchial skeleton morphology. This dissection method is inexpensive, fast, relatively easy, and applicable to a wide variety of fish species. In sticklebacks, this efficient method allows the quantification of skeletal morphology in genetic crosses to map genomic regions controlling craniofacial patterning.
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Affiliation(s)
- Nicholas A Ellis
- Department of Molecular and Cell Biology, University of California, Berkeley
| | - Craig T Miller
- Department of Molecular and Cell Biology, University of California, Berkeley;
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43
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Lencer ES, Riccio ML, McCune AR. Changes in growth rates of oral jaw elements produce evolutionary novelty in bahamian pupfish. J Morphol 2016; 277:935-47. [DOI: 10.1002/jmor.20547] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2016] [Revised: 03/29/2016] [Accepted: 04/01/2016] [Indexed: 11/11/2022]
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44
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Developmental basis of phenotypic integration in two Lake Malawi cichlids. EvoDevo 2016; 7:3. [PMID: 26798449 PMCID: PMC4721197 DOI: 10.1186/s13227-016-0040-z] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2015] [Accepted: 01/06/2016] [Indexed: 02/05/2023] Open
Abstract
Background Cichlid fishes from the Rift Lakes of East Africa have undergone the most spectacular adaptive radiations in vertebrate history. Eco-morphological adaptations in lakes Victoria, Malawi and Tanganyika have resulted in a vast array of skull shapes and sizes, yet primary axes of morphological variation are conserved in all three radiations, prominently including the size of the preorbital region of the skull. This conserved pattern suggests that development may constrain the trajectories of cichlid head morphological evolution. Results Here, we (1) present a comparative analysis of adult head morphology in two sand-dweller cichlids from Lake Malawi with preorbital size differences representative of the main axis of variation among the three lakes and (2) analyze the ontogeny of shape and size differences by focusing on known developmental modules throughout the head. We find that (1) developmental differences between the two species correlate with known developmental modules; (2) differences in embryonic cartilage development result in phenotypically integrated changes among all bones derived from a single cartilage, while differences in dermal bone development tend to influence isolated regions within a bone; and lastly (3) species-specific morphologies appear in the embryo as subtle differences, which become progressively amplified throughout ontogeny. We propose that this amplification takes place at skeletal growth zones, the locations and shapes of which are patterned during embryogenesis. Conclusions This study is the most anatomically comprehensive analysis of the developmental differences underlying cichlid skull evolution in the Rift Lakes of East Africa. The scale of our analysis reveals previously unnoticed correlations between developmental modules and patterns of phenotypic integration. We propose that the primary axes of morphological variation among East African cichlid adaptive radiations are constrained by the hierarchical modularity of the teleost head skeleton.
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45
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Kavembe GD, Kautt AF, Machado-Schiaffino G, Meyer A. Eco-morphological differentiation in Lake Magadi tilapia, an extremophile cichlid fish living in hot, alkaline and hypersaline lakes in East Africa. Mol Ecol 2016; 25:1610-25. [DOI: 10.1111/mec.13461] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2015] [Revised: 11/01/2015] [Accepted: 11/03/2015] [Indexed: 12/25/2022]
Affiliation(s)
- Geraldine D. Kavembe
- Chair in Zoology and Evolutionary Biology; Department of Biology; University of Konstanz; Universitätsstrasse 10 78457 Konstanz Germany
- Department of Biology; School of Pure and Applied Sciences; South Eastern Kenya University; P. O. Box 170 90200 Kitui Kenya
| | - Andreas F. Kautt
- Chair in Zoology and Evolutionary Biology; Department of Biology; University of Konstanz; Universitätsstrasse 10 78457 Konstanz Germany
- International Max Planck Research School for Organismal Biology; University of Konstanz; Universitätsstrasse 10 78457 Konstanz Germany
| | - Gonzalo Machado-Schiaffino
- Chair in Zoology and Evolutionary Biology; Department of Biology; University of Konstanz; Universitätsstrasse 10 78457 Konstanz Germany
| | - Axel Meyer
- Chair in Zoology and Evolutionary Biology; Department of Biology; University of Konstanz; Universitätsstrasse 10 78457 Konstanz Germany
- International Max Planck Research School for Organismal Biology; University of Konstanz; Universitätsstrasse 10 78457 Konstanz Germany
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46
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Gross JB, Stahl BA, Powers AK, Carlson BM. Natural bone fragmentation in the blind cave-dwelling fish, Astyanax mexicanus: candidate gene identification through integrative comparative genomics. Evol Dev 2016; 18:7-18. [PMID: 26153732 PMCID: PMC5226847 DOI: 10.1111/ede.12131] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
Abstract
Animals that colonize dark and nutrient-poor subterranean environments evolve numerous extreme phenotypes. These include dramatic changes to the craniofacial complex, many of which are under genetic control. These phenotypes can demonstrate asymmetric genetic signals wherein a QTL is detected on one side of the face but not the other. The causative gene(s) underlying QTL are difficult to identify with limited genomic resources. We approached this task by searching for candidate genes mediating fragmentation of the third suborbital bone (SO3) directly inferior to the orbit of the eye. We integrated positional genomic information using emerging Astyanax resources, and linked these intervals to homologous (syntenic) regions of the Danio rerio genome. We identified a discrete, approximately 6 Mb, conserved region wherein the gene causing SO3 fragmentation likely resides. We interrogated this interval for genes demonstrating significant differential expression using mRNA-seq analysis of cave and surface morphs across life history. We then assessed genes with known roles in craniofacial evolution and development based on GO term annotation. Finally, we screened coding sequence alterations in this region, identifying two key genes: transforming growth factor β3 (tgfb3) and bone morphogenetic protein 4 (bmp4). Of these candidates, tgfb3 is most promising as it demonstrates significant differential expression across multiple stages of development, maps close (<1 Mb) to the fragmentation critical locus, and is implicated in a variety of other animal systems (including humans) in non-syndromic clefting and malformations of the cranial sutures. Both abnormalities are analogous to the failure-to-fuse phenotype that we observe in SO3 fragmentation. This integrative approach will enable discovery of the causative genetic lesions leading to complex craniofacial features analogous to human craniofacial disorders. This work underscores the value of cave-dwelling fish as a powerful evolutionary model of craniofacial disease, and demonstrates the power of integrative system-level studies for informing the genetic basis of craniofacial aberrations in nature.
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Affiliation(s)
- Joshua B. Gross
- Department of Biological Sciences, University of Cincinnati, 312 Clifton Court, Cincinnati, Ohio 45221, USA
| | - Bethany A. Stahl
- Department of Biological Sciences, University of Cincinnati, 312 Clifton Court, Cincinnati, Ohio 45221, USA
| | - Amanda K. Powers
- Department of Biological Sciences, University of Cincinnati, 312 Clifton Court, Cincinnati, Ohio 45221, USA
| | - Brian M. Carlson
- Department of Biological Sciences, University of Cincinnati, 312 Clifton Court, Cincinnati, Ohio 45221, USA
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47
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Kratochwil CF, Geissler L, Irisarri I, Meyer A. Molecular Evolution of the Neural Crest Regulatory Network in Ray-Finned Fish. Genome Biol Evol 2015; 7:3033-46. [PMID: 26475317 PMCID: PMC5635593 DOI: 10.1093/gbe/evv200] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023] Open
Abstract
Gene regulatory networks (GRN) are central to developmental processes. They are composed of transcription factors and signaling molecules orchestrating gene expression modules that tightly regulate the development of organisms. The neural crest (NC) is a multipotent cell population that is considered a key innovation of vertebrates. Its derivatives contribute to shaping the astounding morphological diversity of jaws, teeth, head skeleton, or pigmentation. Here, we study the molecular evolution of the NC GRN by analyzing patterns of molecular divergence for a total of 36 genes in 16 species of bony fishes. Analyses of nonsynonymous to synonymous substitution rate ratios (dN/dS) support patterns of variable selective pressures among genes deployed at different stages of NC development, consistent with the developmental hourglass model. Model-based clustering techniques of sequence features support the notion of extreme conservation of NC-genes across the entire network. Our data show that most genes are under strong purifying selection that is maintained throughout ray-finned fish evolution. Late NC development genes reveal a pattern of increased constraints in more recent lineages. Additionally, seven of the NC-genes showed signs of relaxation of purifying selection in the famously species-rich lineage of cichlid fishes. This suggests that NC genes might have played a role in the adaptive radiation of cichlids by granting flexibility in the development of NC-derived traits-suggesting an important role for NC network architecture during the diversification in vertebrates.
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Affiliation(s)
- Claudius F Kratochwil
- Department of Biology, University of Konstanz, Germany Zukunftskolleg, University of Konstanz, Germany
| | | | - Iker Irisarri
- Department of Biology, University of Konstanz, Germany
| | - Axel Meyer
- Department of Biology, University of Konstanz, Germany
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48
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Ahi EP, Steinhäuser SS, Pálsson A, Franzdóttir SR, Snorrason SS, Maier VH, Jónsson ZO. Differential expression of the aryl hydrocarbon receptor pathway associates with craniofacial polymorphism in sympatric Arctic charr. EvoDevo 2015; 6:27. [PMID: 26388986 PMCID: PMC4574265 DOI: 10.1186/s13227-015-0022-6] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2015] [Accepted: 09/04/2015] [Indexed: 12/03/2022] Open
Abstract
Background The developmental basis of craniofacial morphology hinges on interactions of numerous signalling systems. Extensive craniofacial variation in the polymorphic Arctic charr, a member of the salmonid family, from Lake Thingvallavatn (Iceland), offers opportunities to find and study such signalling pathways and their key regulators, thereby shedding light on the developmental pathways, and the genetics of trophic divergence. Results To identify genes involved in the craniofacial differences between benthic and limnetic Arctic charr, we used transcriptome data from different morphs, spanning early development, together with data on craniofacial expression patterns and skeletogenesis in model vertebrate species. Out of 20 genes identified, 7 showed lower gene expression in benthic than in limnetic charr morphs. We had previously identified a conserved gene network involved in extracellular matrix (ECM) organization and skeletogenesis, showing higher expression in developing craniofacial elements of benthic than in limnetic Arctic charr morphs. The present study adds a second set of genes constituting an expanded gene network with strong, benthic–limnetic differential expression. To identify putative upstream regulators, we performed knowledge-based motif enrichment analyses on the regulatory sequences of the identified genes which yielded potential binding sites for a set of known transcription factors (TFs). Of the 8 TFs that we examined using qPCR, two (Ahr2b and Ap2) were found to be differentially expressed between benthic and limnetic charr. Expression analysis of several known AhR targets indicated higher activity of the AhR pathway during craniofacial development in benthic charr morphotypes. Conclusion These results suggest a key role of the aryl hydrocarbon receptor (AhR) pathway in the observed craniofacial differences between distinct charr morphotypes. Electronic supplementary material The online version of this article (doi:10.1186/s13227-015-0022-6) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Ehsan Pashay Ahi
- Institute of Life and Environmental Sciences, University of Iceland, Sturlugata 7, 101 Reykjavik, Iceland
| | - Sophie S Steinhäuser
- Biomedical Center, University of Iceland, Vatnsmýrarvegur 16, 101 Reykjavik, Iceland
| | - Arnar Pálsson
- Institute of Life and Environmental Sciences, University of Iceland, Sturlugata 7, 101 Reykjavik, Iceland ; Biomedical Center, University of Iceland, Vatnsmýrarvegur 16, 101 Reykjavik, Iceland
| | - Sigrídur Rut Franzdóttir
- Institute of Life and Environmental Sciences, University of Iceland, Sturlugata 7, 101 Reykjavik, Iceland
| | - Sigurdur S Snorrason
- Institute of Life and Environmental Sciences, University of Iceland, Sturlugata 7, 101 Reykjavik, Iceland
| | - Valerie H Maier
- Institute of Life and Environmental Sciences, University of Iceland, Sturlugata 7, 101 Reykjavik, Iceland ; Biomedical Center, University of Iceland, Vatnsmýrarvegur 16, 101 Reykjavik, Iceland
| | - Zophonías O Jónsson
- Institute of Life and Environmental Sciences, University of Iceland, Sturlugata 7, 101 Reykjavik, Iceland ; Biomedical Center, University of Iceland, Vatnsmýrarvegur 16, 101 Reykjavik, Iceland
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49
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Laland KN, Uller T, Feldman MW, Sterelny K, Müller GB, Moczek A, Jablonka E, Odling-Smee J. The extended evolutionary synthesis: its structure, assumptions and predictions. Proc Biol Sci 2015; 282:20151019. [PMID: 26246559 PMCID: PMC4632619 DOI: 10.1098/rspb.2015.1019] [Citation(s) in RCA: 344] [Impact Index Per Article: 38.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2015] [Accepted: 07/09/2015] [Indexed: 12/15/2022] Open
Abstract
Scientific activities take place within the structured sets of ideas and assumptions that define a field and its practices. The conceptual framework of evolutionary biology emerged with the Modern Synthesis in the early twentieth century and has since expanded into a highly successful research program to explore the processes of diversification and adaptation. Nonetheless, the ability of that framework satisfactorily to accommodate the rapid advances in developmental biology, genomics and ecology has been questioned. We review some of these arguments, focusing on literatures (evo-devo, developmental plasticity, inclusive inheritance and niche construction) whose implications for evolution can be interpreted in two ways—one that preserves the internal structure of contemporary evolutionary theory and one that points towards an alternative conceptual framework. The latter, which we label the 'extended evolutionary synthesis' (EES), retains the fundaments of evolutionary theory, but differs in its emphasis on the role of constructive processes in development and evolution, and reciprocal portrayals of causation. In the EES, developmental processes, operating through developmental bias, inclusive inheritance and niche construction, share responsibility for the direction and rate of evolution, the origin of character variation and organism-environment complementarity. We spell out the structure, core assumptions and novel predictions of the EES, and show how it can be deployed to stimulate and advance research in those fields that study or use evolutionary biology.
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Affiliation(s)
- Kevin N Laland
- School of Biology, University of St Andrews, St Andrews, Fife, UK
| | - Tobias Uller
- Edward Grey Institute, Department of Zoology, University of Oxford, Oxford, UK Department of Biology, University of Lund, Lund, Sweden
| | - Marcus W Feldman
- Department of Biology, Stanford University, Herrin Hall, Stanford, CA 94305, USA
| | - Kim Sterelny
- School of Philosophy, Australian National University, Canberra, Australia School of History, Philosophy, Political Science and International Relations, Victoria University of Wellington, Wellington, New Zealand
| | - Gerd B Müller
- Department of Theoretical Biology, University of Vienna, Vienna, Austria
| | - Armin Moczek
- Department of Biology, Indiana University, Bloomington, IN 47405-7107, USA
| | - Eva Jablonka
- Cohn Institute for the History of Philosophy of Science and Ideas, Tel Aviv University, Tel Aviv, Israel
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50
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Gudbrandsson J, Ahi EP, Franzdottir SR, Kapralova KH, Kristjansson BK, Steinhaeuser SS, Maier VH, Johannesson IM, Snorrason SS, Jonsson ZO, Palsson A. The developmental transcriptome of contrasting Arctic charr (Salvelinus alpinus) morphs. F1000Res 2015; 4:136. [PMID: 27635217 PMCID: PMC5007756 DOI: 10.12688/f1000research.6402.1] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 04/10/2024] Open
Abstract
Species and populations with parallel evolution of specific traits can help illuminate how predictable adaptations and divergence are at the molecular and developmental level. Following the last glacial period, dwarfism and specialized bottom feeding morphology evolved rapidly in several landlocked Arctic charrSalvelinus alpinuspopulations in Iceland. To study the genetic divergence between small benthic morphs and limnetic morphs, we conducted RNA-sequencing charr embryos at four stages in early development. We studied two stocks with contrasting morphologies: the small benthic (SB) charr from Lake Thingvallavatn and Holar aquaculture (AC) charr.The data reveal significant differences in expression of several biological pathways during charr development. There was also an expression difference between SB- and AC-charr in genes involved in energy metabolism and blood coagulation genes. We confirmed differing expression of five genes in whole embryos with qPCR, includinglysozymeandnatterin-likewhich was previously identified as a fish-toxin of a lectin family that may be a putative immunopeptide. We also verified differential expression of 7 genes in the developing head that associated consistently with benthic v.s.limnetic morphology (studied in 4 morphs). Comparison of single nucleotide polymorphism (SNP) frequencies reveals extensive genetic differentiation between the SB and AC-charr (~1300 with more than 50% frequency difference). Curiously, three derived alleles in the otherwise conserved 12s and 16s mitochondrial ribosomal RNA genes are found in benthic charr.The data implicate multiple genes and molecular pathways in divergence of small benthic charr and/or the response of aquaculture charr to domestication. Functional, genetic and population genetic studies on more freshwater and anadromous populations are needed to confirm the specific loci and mutations relating to specific ecological traits in Arctic charr.
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