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Accorsi A, Guo L, Marshall WF, Mommersteeg MTM, Nakajima YI. Extraordinary model systems for regeneration. Development 2024; 151:dev203083. [PMID: 39012059 DOI: 10.1242/dev.203083] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/17/2024]
Abstract
Regeneration is the remarkable phenomenon through which an organism can regrow lost or damaged parts with fully functional replacements, including complex anatomical structures, such as limbs. In 2019, Development launched its 'Model systems for regeneration' collection, a series of articles introducing some of the most popular model organisms for studying regeneration in vivo. To expand this topic further, this Perspective conveys the voices of five expert biologists from the field of regenerative biology, each of whom showcases some less well-known, but equally extraordinary, species for studying regeneration.
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Affiliation(s)
- Alice Accorsi
- University of California Davis, Department of Molecular and Cellular Biology, Davis, CA 95616, USA
| | - Longhua Guo
- Department of Molecular & Integrative Physiology, University of Michigan, Ann Arbor, MI 48109, USA
- Institute of Gerontology, Geriatrics Center, University of Michigan, Ann Arbor, MI 48109, USA
| | - Wallace F Marshall
- Deptartment of Biochemistry & Biophysics, University of California, San Francisco, 600 16th Street, San Francisco, CA 94158, USA
| | - Mathilda T M Mommersteeg
- Institute of Developmental & Regenerative Medicine (IDRM), Department of Physiology, Anatomy & Genetics, IMS-Tetsuya Nakamura Building, Old Road Campus, Roosevelt Drive, Headington, Oxford OX3 7TY, UK
| | - Yu-Ichiro Nakajima
- Graduate School of Pharmaceutical Sciences, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-0033, Japan
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Fišer Ž, Whitehorn H, Furness T, Trontelj P, Protas M. Genetic bias in repeated evolution of pigment loss in cave populations of the Asellus aquaticus species complex. JOURNAL OF EXPERIMENTAL ZOOLOGY. PART B, MOLECULAR AND DEVELOPMENTAL EVOLUTION 2024; 342:425-436. [PMID: 38828691 DOI: 10.1002/jez.b.23256] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/04/2024] [Revised: 04/26/2024] [Accepted: 05/01/2024] [Indexed: 06/05/2024]
Abstract
Similar phenotypes can evolve repeatedly under the same evolutionary pressures. A compelling example is the evolution of pigment loss and eye loss in cave-dwelling animals. While specific genomic regions or genes associated with these phenotypes have been identified in model species, it remains uncertain whether a bias towards particular genetic mechanisms exists. An isopod crustacean, Asellus aquaticus, is an ideal model organism to investigate this phenomenon. It inhabits surface freshwaters throughout Europe but has colonized groundwater on multiple independent occasions and evolved several cave populations with distinct ecomorphology. Previous studies have demonstrated that three different cave populations utilized common genetic regions, potentially the same genes, in the evolution of pigment and eye loss. Expanding on this, we conducted analysis on two additional cave populations, distinct either phylogenetically or biogeographically from those previously examined. We generated F2 hybrids from cave × surface crosses and tested phenotype-genotype associations, as well as conducted complementation tests by crossing individuals from different cave populations. Our findings revealed that pigment loss and orange eye pigment in additional cave populations were associated with the same genomic regions as observed in the three previously tested cave populations. Moreover, the lack of complementation across all cross combinations suggests that the same gene likely drives pigment loss. These results substantiate a genetic bias in the recurrent evolution of pigment loss in this model system. Future investigations should focus on the cause behind this bias, possibly arising from allele recruitment from ancestral surface populations' genetic variation or advantageous allele effects via pleiotropy.
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Affiliation(s)
- Žiga Fišer
- Department of Biology, Biotechnical Faculty, University of Ljubljana, Ljubljana, Slovenia
| | - Hana Whitehorn
- Department of Natural Sciences and Mathematics, Dominican University of California, San Rafael, California, USA
| | - Tia Furness
- Department of Natural Sciences and Mathematics, Dominican University of California, San Rafael, California, USA
| | - Peter Trontelj
- Department of Biology, Biotechnical Faculty, University of Ljubljana, Ljubljana, Slovenia
| | - Meredith Protas
- Department of Natural Sciences and Mathematics, Dominican University of California, San Rafael, California, USA
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Valchářová T, Horký P, Douda K, Slavík O. The effect of parasitism on boldness and sheltering behaviour in albino and pigmented European catfish (Silurus glanis). Sci Rep 2024; 14:17531. [PMID: 39080432 PMCID: PMC11289108 DOI: 10.1038/s41598-024-67645-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2023] [Accepted: 07/15/2024] [Indexed: 08/02/2024] Open
Abstract
Parasites can change the behaviour of their hosts, but little attention has been given to the relationship between parasite effects on host behaviour and colouration. The correlation between disrupted melanin production and alterations in various physiological and behavioural traits, e.g., aggression, shoaling behaviour, stress responsiveness and sensitivity to brood parasitism, has been reported in albino fish. We hypothesized that parasitism would affect the behaviour of albino and pigmented conspecifics differently. In laboratory conditions, we infested a group of pigmented and a group of albino individuals of European catfish Silurus glanis with glochidia of two Uninoidea species, namely, the native species Anodonta anatina and the invasive species Sinanodonta woodiana, and investigated the effect of parasitization on the boldness and sheltering behaviour of the hosts. The behaviour of albino individuals differed from that of pigmented conspecifics both before and after parasitization. Parasitization with glochidia did not affect sheltering behaviour, but it increased boldness in pigmented individuals, whereas albino individuals did not exhibit any changes in behaviour. Sheltering results were consistent in both binomial and continuous variable analyses, whereas boldness was significant only in the binomial analyses. Our results demonstrate the reduced susceptibility of the albino phenotype to glochidia infestation, together with questions of the choice of analyses.
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Affiliation(s)
- Tereza Valchářová
- Department of Zoology and Fisheries, Faculty of Agrobiology, Food and Natural Resources, Czech University of Life Sciences Prague, Kamýcká 129, Suchdol, Prague 6, Suchdol, 165 21, Czech Republic.
| | - Pavel Horký
- Department of Zoology and Fisheries, Faculty of Agrobiology, Food and Natural Resources, Czech University of Life Sciences Prague, Kamýcká 129, Suchdol, Prague 6, Suchdol, 165 21, Czech Republic
| | - Karel Douda
- Department of Zoology and Fisheries, Faculty of Agrobiology, Food and Natural Resources, Czech University of Life Sciences Prague, Kamýcká 129, Suchdol, Prague 6, Suchdol, 165 21, Czech Republic
| | - Ondřej Slavík
- Department of Zoology and Fisheries, Faculty of Agrobiology, Food and Natural Resources, Czech University of Life Sciences Prague, Kamýcká 129, Suchdol, Prague 6, Suchdol, 165 21, Czech Republic
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Kozol RA, Canavan A, Tolentino B, Keene AC, Kowalko JE, Duboué ER. Evolution of a central dopamine circuit underlies adaptation of light-evoked sensorimotor response in the blind cavefish, Astyanax mexicanus. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.07.25.605141. [PMID: 39091880 PMCID: PMC11291158 DOI: 10.1101/2024.07.25.605141] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 08/04/2024]
Abstract
Adaptive behaviors emerge in novel environments through functional changes in neural circuits. While relationships between circuit function and behavior have been well studied, how evolution shapes those circuits and leads to behavioral adpation is poorly understood. The Mexican cavefish , Astyanax mexicanus , provides a unique genetically amendable model system, equipped with above ground eyed surface fish and multiple evolutionarily divergent populations of blind cavefish that have evolved in complete darkness. These differences in environment and vision provide an opprotunity to examine how a neural circuit is functionally influenced by the presence of light. Here, we examine differences in the detection, and behavioral response induced by non visual light reception. Both populations exhibit photokinetic behavior, with surface fish becoming hyperactive following sudden darkness and cavefish becoming hyperactive following sudden illumination. To define these photokinetic neural circuits, we integrated whole brain functional imaging with our Astyanax brain atlas for surface and cavefish responding to light changes. We identified the caudal posterior tuberculum as the central modulator for both light or dark stimulated photokinesis. To unconver how spatiotemporal neuronal activity differed between surface fish and cavefish, we used stable pan-neuronal GCaMP Astyanax transgenics to show that a subpopulation of darkness sensitve neurons in surface fish are now light senstive in cavefish. Further functional analysis revealed that this integrative switch is dependent on dopmane signaling, suggesting a key role for dopamine and a highly conserved dopamine circuit in modulating the evolution of a circuit driving an essential behavior. Together, these data shed light into how neural circuits evolved to adapte to novel settings, and reveal the power of Astyanax as a model to elucidate mechanistic ingiths underlying sensory adaptation. Abstract Figure
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Gallman K, Rastogi A, North O, O'Gorman M, Hutton P, Lloyd E, Warren W, Kowalko JE, Duboue ER, Rohner N, Keene AC. Postprandial sleep in short-sleeping Mexican cavefish. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.07.03.602003. [PMID: 39005273 PMCID: PMC11244998 DOI: 10.1101/2024.07.03.602003] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/16/2024]
Abstract
Interaction between sleep and feeding behaviors are critical for adaptive fitness. Diverse species suppress sleep when food is scarce to increase the time spent foraging. Post-prandial sleep, an increase in sleep time following a feeding event, has been documented in vertebrate and invertebrate animals. While interactions between sleep and feeding appear to be highly conserved, the evolution of postprandial sleep in response to changes in food availability remains poorly understood. Multiple populations of the Mexican cavefish, Astyanax mexicanus, have independently evolved sleep loss and increased food consumption compared to surface-dwelling fish of the same species, providing the opportunity to investigate the evolution of interactions between sleep and feeding. Here, we investigate effects of feeding on sleep in larval and adult surface fish, and two parallelly evolved cave populations of A. mexicanus. Larval surface and cave populations of A. mexicanus increase sleep immediately following a meal, providing the first evidence of postprandial sleep in a fish model. The amount of sleep was not correlated to meal size and occurred independently of feeding time. In contrast to larvae, postprandial sleep was not detected in adult surface or cavefish, that can survive for months without food. Together, these findings reveal that postprandial sleep is present in multiple short-sleeping populations of cavefish, suggesting sleep-feeding interactions are retained despite the evolution of sleep loss. These findings raise the possibility that postprandial sleep is critical for energy conservation and survival in larvae that are highly sensitive to food deprivation.
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Affiliation(s)
- Kathryn Gallman
- Department of Biology, Texas A&M University, College Station, TX 77840
| | - Aakriti Rastogi
- Department of Biology, Texas A&M University, College Station, TX 77840
| | - Owen North
- Department of Biology, Texas A&M University, College Station, TX 77840
| | - Morgan O'Gorman
- Department of Biology, Texas A&M University, College Station, TX 77840
| | - Pierce Hutton
- Department of Biology, Texas A&M University, College Station, TX 77840
| | - Evan Lloyd
- Department of Biology, Texas A&M University, College Station, TX 77840
| | - Wes Warren
- Department of Genomics, University of Missouri, Columbia, MO 65201
| | - Johanna E Kowalko
- Department of Biological Sciences, Lehigh University, Bethlehem, PA 18015
| | | | - Nicolas Rohner
- Stowers Institute for Medical Research, Kansas City, MO 64110
| | - Alex C Keene
- Department of Biology, Texas A&M University, College Station, TX 77840
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Choy S, Thakur S, Polyakov E, Abdelaziz J, Lloyd E, Enriquez M, Jayan N, Fily Y, McGaugh S, Keene AC, Kowalko JE. Mutations in the albinism gene oca2 alter vision-dependent prey capture behavior in the Mexican tetra. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.06.17.599419. [PMID: 38948816 PMCID: PMC11212897 DOI: 10.1101/2024.06.17.599419] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/02/2024]
Abstract
Understanding the phenotypic consequences of naturally occurring genetic changes, as well as their impact on fitness, is fundamental to understanding how organisms adapt to an environment. This is critical when genetic variants have pleiotropic effects, as determining how each phenotype impacted by a gene contributes to fitness is essential to understand how and why traits have evolved. A striking example of a pleiotropic gene contributing to trait evolution is the oca2 gene, coding mutations in which underlie albinism and reductions of sleep in the blind Mexican cavefish, Astyanax mexicanus. Here, we characterize the effects of mutations in the oca2 gene on larval prey capture. We find that when conspecific surface fish with engineered mutations in the oca2 allele are hunting, they use cave-like, wide angle strikes to capture prey. However, unlike cavefish or surface fish in the dark, which rely on lateral line mediated hunting, oca2 mutant surface fish use vision when striking at prey from wide angles. Finally, we find that while oca2 mutant surface fish do not outcompete pigmented surface siblings in the dark, pigmented fish outcompete albino fish in the light. This raises the possibility that albinism is detrimental to larval feeding in a surface-like lighted environment, but does not have negative consequences for fish in cave-like, dark environments. Together, these results demonstrate that oca2 plays a role in larval feeding behavior in A. mexicanus. Further, they expand our understanding of the pleiotropic phenotypic consequences of oca2 in cavefish evolution.
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Affiliation(s)
- Stefan Choy
- Department of Biological Sciences, Lehigh University, Bethlehem, PA
| | - Sunishka Thakur
- Department of Integrative Biology, University of Texas at Austin, Austin, TX
| | - Ellen Polyakov
- Wilkes Honors College, Florida Atlantic University, Jupiter, FL
| | - Jennah Abdelaziz
- Department of Biological Sciences, Lehigh University, Bethlehem, PA
| | | | - Maya Enriquez
- Department of Ecology, Evolution, and Behavior, University of Minnesota, St. Paul, MN
| | - Nikita Jayan
- Wilkes Honors College, Florida Atlantic University, Jupiter, FL
| | - Yaouen Fily
- Wilkes Honors College, Florida Atlantic University, Jupiter, FL
| | - Suzanne McGaugh
- Department of Ecology, Evolution, and Behavior, University of Minnesota, St. Paul, MN
| | - Alex C Keene
- Department of Biology, Texas A&M, College Station, TX
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Drabeck DH, Wiese J, Gilbertson E, Arroyave J, Stiassny MLJ, Alter SE, Borowsky R, Hendrickson DA, Arcila D, McGaugh SE. Gene loss and relaxed selection of plaat1 in vertebrates adapted to low-light environments. Proc Biol Sci 2024; 291:20232847. [PMID: 38864338 DOI: 10.1098/rspb.2023.2847] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2023] [Accepted: 05/03/2024] [Indexed: 06/13/2024] Open
Abstract
Gene loss is an important mechanism for evolution in low-light or cave environments where visual adaptations often involve a reduction or loss of eyesight. The plaat gene family encodes phospholipases essential for the degradation of organelles in the lens of the eye. These phospholipases translocate to damaged organelle membranes, inducing them to rupture. This rupture is required for lens transparency and is essential for developing a functioning eye. Plaat3 is thought to be responsible for this role in mammals, while plaat1 is thought to be responsible in other vertebrates. We used a macroevolutionary approach and comparative genomics to examine the origin, loss, synteny and selection of plaat1 across bony fishes and tetrapods. We showed that plaat1 (probably ancestral to all bony fish + tetrapods) has been lost in squamates and is significantly degraded in lineages of low-visual-acuity and blind mammals and fishes. Our findings suggest that plaat1 is important for visual acuity across bony vertebrates, and that its loss through relaxed selection and pseudogenization may have played a role in the repeated evolution of visual systems in low-light environments. Our study sheds light on the importance of gene-loss in trait evolution and provides insights into the mechanisms underlying visual acuity in low-light environments.
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Affiliation(s)
- Danielle H Drabeck
- Department of Ecology, Evolution and Behavior, University of Minnesota Twin Cities, 1475 Gortner Ave, St, Paul, MN 55108, USA
| | - Jonathan Wiese
- Department of Ecology, Evolution and Behavior, University of Minnesota Twin Cities, 1475 Gortner Ave, St, Paul, MN 55108, USA
| | - Erin Gilbertson
- Department of Epidemiology and Biostatistics, University of San Francisco, University of California, San Francisco, CA, USA
| | - Jairo Arroyave
- Instituto de Biología, Universidad Nacional Autónoma de México (UNAM), Ciudad de México, México
| | - Melanie L J Stiassny
- Department of Ichthyology, American Museum of Natural History, New York, NY 10024, USA
| | - S Elizabeth Alter
- Biology and Chemistry Department, California State University Monterey Bay, Chapman Academic Science Center, Seaside, CA, USA
| | - Richard Borowsky
- Department of Biology, New York University, Washington Square, New York, NY 10003, USA
| | - Dean A Hendrickson
- Biodiversity Center, Texas Natural History Collections, University of Texas at Austin, Austin, TX 78758, USA
| | - Dahiana Arcila
- Scripps Institution of Oceanography, University of California San Diego, La Jolla, CA 92093, USA
| | - Suzanne E McGaugh
- Department of Ecology, Evolution and Behavior, University of Minnesota Twin Cities, 1475 Gortner Ave, St, Paul, MN 55108, USA
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Wiese J, Richards E, Kowalko JE, McGaugh SE. Loci associated with cave-derived traits concentrate in specific regions of the Mexican cavefish genome. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.03.29.587360. [PMID: 38585759 PMCID: PMC10996652 DOI: 10.1101/2024.03.29.587360] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/09/2024]
Abstract
A major goal of modern evolutionary biology is connecting phenotypic evolution with its underlying genetic basis. The Mexican cavefish (Astyanax mexicanus), a characin fish species comprised of a surface ecotype and a cave-derived ecotype, is well suited as a model to study the genetic mechanisms underlying adaptation to extreme environments. Here we map 206 previously published quantitative trait loci (QTL) for cave-derived traits in A. mexicanus to the newest version of the surface fish genome assembly, AstMex3. This analysis revealed that QTL cluster in the genome more than expected by chance, and this clustering is not explained by the distribution of genes in the genome. To investigate whether certain characteristics of the genome facilitate phenotypic evolution, we tested whether genomic characteristics, such as highly mutagenic CpG sites, are reliable predictors of the sites of trait evolution but did not find any significant trends. Finally, we combined the QTL map with previously collected expression and selection data to identify a list of 36 candidate genes that may underlie the repeated evolution of cave phenotypes, including rgrb which is predicted to be involved in phototransduction. We found this gene has disrupted exons in all non-hybrid cave populations but intact reading frames in surface fish. Overall, our results suggest specific "evolutionary hotspots" in the genome may play significant roles in driving adaptation to the cave environment in Astyanax mexicanus and demonstrate how this compiled dataset can facilitate our understanding of the genetic basis of repeated evolution in the Mexican cavefish.
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Affiliation(s)
- Jonathan Wiese
- Department of Ecology, Evolution, and Behavior, University of Minnesota, St. Paul, MN
| | - Emilie Richards
- Department of Ecology, Evolution, and Behavior, University of Minnesota, St. Paul, MN
| | | | - Suzanne E McGaugh
- Department of Ecology, Evolution, and Behavior, University of Minnesota, St. Paul, MN
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Lunghi E, Bilandžija H. Telomere length and dynamics in Astyanax mexicanus cave and surface morphs. PeerJ 2024; 12:e16957. [PMID: 38435987 PMCID: PMC10908260 DOI: 10.7717/peerj.16957] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2023] [Accepted: 01/25/2024] [Indexed: 03/05/2024] Open
Abstract
Background Telomeres are non-coding DNA repeats at the chromosome ends and their shortening is considered one of the major causes of aging. However, they also serve as a biomarker of environmental exposures and their length and attrition is affected by various stressors. In this study, we examined the average telomere length in Astyanax mexicanus, a species that has both surface-dwelling and cave-adapted populations. The cave morph descended from surface ancestors and adapted to a markedly different environment characterized by specific biotic and abiotic stressors, many of which are known to affect telomere length. Our objective was to explore whether telomere length differs between the two morphs and whether it serves as a biological marker of aging or correlates with the diverse environments the morphs are exposed to. Methods We compared telomere length and shortening between laboratory-reared Pachón cavefish and Rio Choy surface fish of A. mexicanus across different tissues and ages. Results Astyanax mexicanus surface fish exhibited longer average telomere length compared to cavefish. In addition, we did not observe telomere attrition in either cave or surface form as a result of aging in adults up to 9 years old, suggesting that efficient mechanisms prevent telomere-mediated senescence in laboratory stocks of this species, at least within this time frame. Our results suggest that telomere length in Astyanax may be considered a biomarker of environmental exposures. Cavefish may have evolved shorter and energetically less costly telomeres due to the absence of potential stressors known to affect surface species, such as predator pressure and ultra-violet radiation. This study provides the first insights into telomere dynamics in Astyanax morphs and suggests that shorter telomeres may have evolved as an adaptation to caves.
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Affiliation(s)
- Enrico Lunghi
- Department of Life, Health and Environmental Sciences, University of L’Aquila, L’Aquila, Italy
| | - Helena Bilandžija
- Division of Molecular Biology, Ruder Bošković Institute, Zagreb, Croatia
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Ding SS, Fox JL, Gordus A, Joshi A, Liao JC, Scholz M. Fantastic beasts and how to study them: rethinking experimental animal behavior. J Exp Biol 2024; 227:jeb247003. [PMID: 38372042 PMCID: PMC10911175 DOI: 10.1242/jeb.247003] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/20/2024]
Abstract
Humans have been trying to understand animal behavior at least since recorded history. Recent rapid development of new technologies has allowed us to make significant progress in understanding the physiological and molecular mechanisms underlying behavior, a key goal of neuroethology. However, there is a tradeoff when studying animal behavior and its underlying biological mechanisms: common behavior protocols in the laboratory are designed to be replicable and controlled, but they often fail to encompass the variability and breadth of natural behavior. This Commentary proposes a framework of 10 key questions that aim to guide researchers in incorporating a rich natural context into their experimental design or in choosing a new animal study system. The 10 questions cover overarching experimental considerations that can provide a template for interspecies comparisons, enable us to develop studies in new model organisms and unlock new experiments in our quest to understand behavior.
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Affiliation(s)
- Siyu Serena Ding
- Max Planck Institute of Animal Behavior, 78464 Konstanz, Germany
- Centre for the Advanced Study of Collective Behaviour, University of Konstanz, 78464 Konstanz, Germany
| | - Jessica L. Fox
- Department of Biology, Case Western Reserve University, Cleveland, OH 44106, USA
| | - Andrew Gordus
- Department of Biology, Johns Hopkins University, Baltimore, MD 21218, USA
| | - Abhilasha Joshi
- Departments of Physiology and Psychiatry, University of California, San Francisco, CA 94158, USA
| | - James C. Liao
- Department of Biology, The Whitney Laboratory for Marine Bioscience, University of Florida, St. Augustine, FL 32080, USA
| | - Monika Scholz
- Max Planck Research Group Neural Information Flow, Max Planck Institute for Neurobiology of Behavior – caesar, 53175 Bonn, Germany
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Swaminathan A, Xia F, Rohner N. From darkness to discovery: evolutionary, adaptive, and translational genetic insights from cavefish. Trends Genet 2024; 40:24-38. [PMID: 38707509 PMCID: PMC11068324 DOI: 10.1016/j.tig.2023.10.002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/07/2024]
Abstract
How genotype determines phenotype is a well-explored question, but genotype-environment interactions and their heritable impact on phenotype over the course of evolution are not as thoroughly investigated. The fish Astyanax mexicanus, consisting of surface and cave ecotypes, is an ideal emerging model to study the genetic basis of adaptation to new environments. This model has permitted quantitative trait locus mapping and whole-genome comparisons to identify the genetic bases of traits such as albinism and insulin resistance and has helped to better understand fundamental evolutionary mechanisms. In this review, we summarize recent advances in A. mexicanus genetics and discuss their broader impact on the fields of adaptation and evolutionary genetics.
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Affiliation(s)
| | - Fanning Xia
- Stowers Institute for Medical Research, Kansas City, MO, USA
| | - Nicolas Rohner
- Stowers Institute for Medical Research, Kansas City, MO, USA
- Department of Cell Biology and Physiology, University of Kansas Medical Center, Kansas City, KS, USA
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Drabeck DH, Wiese J, Gilbertson E, Arroyave J, Arcila D, Alter SE, Borowsky R, Hendrickson D, Stiassny M, McGaugh SE. Gene loss and relaxed selection of plaat1 in vertebrates adapted to low-light environments. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.12.12.571336. [PMID: 38168154 PMCID: PMC10760033 DOI: 10.1101/2023.12.12.571336] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/05/2024]
Abstract
Gene loss is an important mechanism for evolution in low-light or cave environments where visual adaptations often involve a reduction or loss of eyesight. The plaat gene family are phospholipases essential for the degradation of organelles in the lens of the eye. They translocate to damaged organelle membranes, inducing them to rupture. This rupture is required for lens transparency and is essential for developing a functioning eye. Plaat3 is thought to be responsible for this role in mammals, while plaat1 is thought to be responsible in other vertebrates. We used a macroevolutionary approach and comparative genomics to examine the origin, loss, synteny, and selection of plaat1 across bony fishes and tetrapods. We show that plaat1 (likely ancestral to all bony fish + tetrapods) has been lost in squamates and is significantly degraded in lineages of low-visual acuity and blind mammals and fish. Our findings suggest that plaat1 is important for visual acuity across bony vertebrates, and that its loss through relaxed selection and pseudogenization may have played a role in the repeated evolution of visual systems in low-light-environments. Our study sheds light on the importance of gene-loss in trait evolution and provides insights into the mechanisms underlying visual acuity in low-light environments.
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Affiliation(s)
- Danielle H Drabeck
- Department of Ecology, Evolution and Behavior, University of Minnesota Twin Cities, 1475 Gortner Ave, St. Paul, MN 55108
| | - Jonathan Wiese
- Department of Ecology, Evolution and Behavior, University of Minnesota Twin Cities, 1475 Gortner Ave, St. Paul, MN 55108
| | - Erin Gilbertson
- University of San Francisco, Department of Epidemiology and Biostatistics, University of California, San Francisco, CA
| | - Jairo Arroyave
- Instituto de Biología, Universidad Nacional Autónoma de México (UNAM), Ciudad de México, México
| | - Dahiana Arcila
- Marine Vertebrate Collection, Scripps Institution of Oceanography, University of California San Diego, La Jolla, California, 92093, USA
| | - S Elizabeth Alter
- California State University Monterey Bay, Biology and Chemistry Department, Chapman Academic Science Center, Seaside, CA
| | - Richard Borowsky
- Department of Biology, New York University, Washington Square, New York, NY, 10003, USA
| | - Dean Hendrickson
- Biodiversity Center, Texas Natural History Collections, University of Texas at Austin, Austin, TX 78758, United States
| | - Melanie Stiassny
- Department of Ichthyology, American Museum of Natural History, New York, NY 10024, USA
| | - Suzanne E McGaugh
- Department of Ecology, Evolution and Behavior, University of Minnesota Twin Cities, 1475 Gortner Ave, St. Paul, MN 55108
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Iwashita M, Tran A, Garcia M, Cashon J, Burbano D, Salgado V, Hasegawa M, Balmilero-Unciano R, Politan K, Wong M, Lee RWY, Yoshizawa M. Metabolic shift toward ketosis in asocial cavefish increases social-like affinity. BMC Biol 2023; 21:219. [PMID: 37840141 PMCID: PMC10577988 DOI: 10.1186/s12915-023-01725-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2023] [Accepted: 10/04/2023] [Indexed: 10/17/2023] Open
Abstract
BACKGROUND Social affinity and collective behavior are nearly ubiquitous in the animal kingdom, but many lineages feature evolutionarily asocial species. These solitary species may have evolved to conserve energy in food-sparse environments. However, the mechanism by which metabolic shifts regulate social affinity is not well investigated. RESULTS In this study, we used the Mexican tetra (Astyanax mexicanus), which features riverine sighted surface (surface fish) and cave-dwelling populations (cavefish), to address the impact of metabolic shifts on asociality and other cave-associated behaviors in cavefish, including repetitive turning, sleeplessness, swimming longer distances, and enhanced foraging behavior. After 1 month of ketosis-inducing ketogenic diet feeding, asocial cavefish exhibited significantly higher social affinity, whereas social affinity regressed in cavefish fed the standard diet. The ketogenic diet also reduced repetitive turning and swimming in cavefish. No major behavioral shifts were found regarding sleeplessness and foraging behavior, suggesting that other evolved behaviors are not largely regulated by ketosis. We further examined the effects of the ketogenic diet via supplementation with exogenous ketone bodies, revealing that ketone bodies are pivotal molecules positively associated with social affinity. CONCLUSIONS Our study indicated that fish that evolved to be asocial remain capable of exhibiting social affinity under ketosis, possibly linking the seasonal food availability and sociality.
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Affiliation(s)
- Motoko Iwashita
- School of Life Sciences, University of Hawai'I at Mānoa, Honolulu, HI, 96822, USA
| | - Amity Tran
- School of Life Sciences, University of Hawai'I at Mānoa, Honolulu, HI, 96822, USA
| | - Marianne Garcia
- School of Life Sciences, University of Hawai'I at Mānoa, Honolulu, HI, 96822, USA
| | - Jia Cashon
- Hawai'i Institute of Marine Biology, University of Hawai'i at Mānoa, Kāne'ohe, HI, 96744, USA
| | - Devanne Burbano
- School of Life Sciences, University of Hawai'I at Mānoa, Honolulu, HI, 96822, USA
| | - Vanessa Salgado
- School of Life Sciences, University of Hawai'I at Mānoa, Honolulu, HI, 96822, USA
| | - Malia Hasegawa
- School of Life Sciences, University of Hawai'I at Mānoa, Honolulu, HI, 96822, USA
| | | | - Kaylah Politan
- School of Life Sciences, University of Hawai'I at Mānoa, Honolulu, HI, 96822, USA
| | - Miki Wong
- Nā Pu'uwai Native Hawaiian Healthcare System, Kaunakakai, HI, 96748, USA
- Nutrition Services Department, Shriners Hospitals for Children, Honolulu, HI, 96826, USA
| | - Ryan W Y Lee
- Medical Staff Department, Shriners Hospitals for Children, Honolulu, HI, 96826, USA
| | - Masato Yoshizawa
- School of Life Sciences, University of Hawai'I at Mānoa, Honolulu, HI, 96822, USA.
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14
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Ponnimbaduge Perera P, Perez Guerra D, Riddle MR. The Mexican Tetra, Astyanax mexicanus, as a Model System in Cell and Developmental Biology. Annu Rev Cell Dev Biol 2023; 39:23-44. [PMID: 37437210 DOI: 10.1146/annurev-cellbio-012023-014003] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/14/2023]
Abstract
Our understanding of cell and developmental biology has been greatly aided by a focus on a small number of model organisms. However, we are now in an era where techniques to investigate gene function can be applied across phyla, allowing scientists to explore the diversity and flexibility of developmental mechanisms and gain a deeper understanding of life. Researchers comparing the eyeless cave-adapted Mexican tetra, Astyanax mexicanus, with its river-dwelling counterpart are revealing how the development of the eyes, pigment, brain, cranium, blood, and digestive system evolves as animals adapt to new environments. Breakthroughs in our understanding of the genetic and developmental basis of regressive and constructive trait evolution have come from A. mexicanus research. They include understanding the types of mutations that alter traits, which cellular and developmental processes they affect, and how they lead to pleiotropy. We review recent progress in the field and highlight areas for future investigations that include evolution of sex differentiation, neural crest development, and metabolic regulation of embryogenesis.
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Affiliation(s)
| | | | - Misty R Riddle
- Department of Biology, University of Nevada, Reno, Nevada, USA;
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15
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Sifuentes-Romero I, Aviles AM, Carter JL, Chan-Pong A, Clarke A, Crotty P, Engstrom D, Meka P, Perez A, Perez R, Phelan C, Sharrard T, Smirnova MI, Wade AJ, Kowalko JE. Trait Loss in Evolution: What Cavefish Have Taught Us about Mechanisms Underlying Eye Regression. Integr Comp Biol 2023; 63:393-406. [PMID: 37218721 PMCID: PMC10445413 DOI: 10.1093/icb/icad032] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2023] [Revised: 04/18/2023] [Accepted: 04/24/2023] [Indexed: 05/24/2023] Open
Abstract
Reduction or complete loss of traits is a common occurrence throughout evolutionary history. In spite of this, numerous questions remain about why and how trait loss has occurred. Cave animals are an excellent system in which these questions can be answered, as multiple traits, including eyes and pigmentation, have been repeatedly reduced or lost across populations of cave species. This review focuses on how the blind Mexican cavefish, Astyanax mexicanus, has been used as a model system for examining the developmental, genetic, and evolutionary mechanisms that underlie eye regression in cave animals. We focus on multiple aspects of how eye regression evolved in A. mexicanus, including the developmental and genetic pathways that contribute to eye regression, the effects of the evolution of eye regression on other traits that have also evolved in A. mexicanus, and the evolutionary forces contributing to eye regression. We also discuss what is known about the repeated evolution of eye regression, both across populations of A. mexicanus cavefish and across cave animals more generally. Finally, we offer perspectives on how cavefish can be used in the future to further elucidate mechanisms underlying trait loss using tools and resources that have recently become available.
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Affiliation(s)
- Itzel Sifuentes-Romero
- Harriet L. Wilkes Honors College, Florida Atlantic University, Jupiter FL 33458, USA
- Department of Ecology, Evolution, and Organismal Biology, Iowa State University, Ames, IA 50011, USA
| | - Ari M Aviles
- Harriet L. Wilkes Honors College, Florida Atlantic University, Jupiter FL 33458, USA
- Department of Cell Biology and Genetics, Texas A&M University, College Station, TX 77843, USA
| | - Joseph L Carter
- Harriet L. Wilkes Honors College, Florida Atlantic University, Jupiter FL 33458, USA
| | - Allen Chan-Pong
- Harriet L. Wilkes Honors College, Florida Atlantic University, Jupiter FL 33458, USA
| | - Anik Clarke
- Harriet L. Wilkes Honors College, Florida Atlantic University, Jupiter FL 33458, USA
| | - Patrick Crotty
- Harriet L. Wilkes Honors College, Florida Atlantic University, Jupiter FL 33458, USA
| | - David Engstrom
- Harriet L. Wilkes Honors College, Florida Atlantic University, Jupiter FL 33458, USA
| | - Pranav Meka
- Harriet L. Wilkes Honors College, Florida Atlantic University, Jupiter FL 33458, USA
- Charles E. Schmidt College of Medicine, Florida Atlantic University, Boca Raton, FL 33431, USA
| | - Alexandra Perez
- Harriet L. Wilkes Honors College, Florida Atlantic University, Jupiter FL 33458, USA
| | - Riley Perez
- Harriet L. Wilkes Honors College, Florida Atlantic University, Jupiter FL 33458, USA
| | - Christine Phelan
- Harriet L. Wilkes Honors College, Florida Atlantic University, Jupiter FL 33458, USA
| | - Taylor Sharrard
- Harriet L. Wilkes Honors College, Florida Atlantic University, Jupiter FL 33458, USA
| | - Maria I Smirnova
- Harriet L. Wilkes Honors College, Florida Atlantic University, Jupiter FL 33458, USA
- Charles E. Schmidt College of Medicine, Florida Atlantic University, Boca Raton, FL 33431, USA
- Stiles–Nicholson Brain Institute, Florida Atlantic University, Jupiter, FL 33458, USA
- Charles E. Schmidt College of Science, Florida Atlantic University, Boca Raton, FL 33431, USA
| | - Amanda J Wade
- Harriet L. Wilkes Honors College, Florida Atlantic University, Jupiter FL 33458, USA
| | - Johanna E Kowalko
- Harriet L. Wilkes Honors College, Florida Atlantic University, Jupiter FL 33458, USA
- Department of Biological Sciences, Lehigh University, Bethlehem, PA 18015, USA
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16
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Kozol RA, Conith AJ, Yuiska A, Cree-Newman A, Tolentino B, Benesh K, Paz A, Lloyd E, Kowalko JE, Keene AC, Albertson C, Duboue ER. A brain-wide analysis maps structural evolution to distinct anatomical module. eLife 2023; 12:e80777. [PMID: 37498318 PMCID: PMC10435234 DOI: 10.7554/elife.80777] [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: 06/03/2022] [Accepted: 07/26/2023] [Indexed: 07/28/2023] Open
Abstract
The vertebrate brain is highly conserved topologically, but less is known about neuroanatomical variation between individual brain regions. Neuroanatomical variation at the regional level is hypothesized to provide functional expansion, building upon ancestral anatomy needed for basic functions. Classically, animal models used to study evolution have lacked tools for detailed anatomical analysis that are widely used in zebrafish and mice, presenting a barrier to studying brain evolution at fine scales. In this study, we sought to investigate the evolution of brain anatomy using a single species of fish consisting of divergent surface and cave morphs, that permits functional genetic testing of regional volume and shape across the entire brain. We generated a high-resolution brain atlas for the blind Mexican cavefish Astyanax mexicanus and coupled the atlas with automated computational tools to directly assess variability in brain region shape and volume across all populations. We measured the volume and shape of every grossly defined neuroanatomical region of the brain and assessed correlations between anatomical regions in surface fish, cavefish, and surface × cave F2 hybrids, whose phenotypes span the range of surface to cave. We find that dorsal regions of the brain are contracted, while ventral regions have expanded, with F2 hybrid data providing support for developmental constraint along the dorsal-ventral axis. Furthermore, these dorsal-ventral relationships in anatomical variation show similar patterns for both volume and shape, suggesting that the anatomical evolution captured by these two parameters could be driven by similar developmental mechanisms. Together, these data demonstrate that A. mexicanus is a powerful system for functionally determining basic principles of brain evolution and will permit testing how genes influence early patterning events to drive brain-wide anatomical evolution.
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Affiliation(s)
- Robert A Kozol
- Jupiter Life Science Initiative, Florida Atlantic UniversityJupiterUnited States
| | - Andrew J Conith
- Department of Biology, University of Massachusetts AmherstAmherstUnited States
| | - Anders Yuiska
- Jupiter Life Science Initiative, Florida Atlantic UniversityJupiterUnited States
| | - Alexia Cree-Newman
- Jupiter Life Science Initiative, Florida Atlantic UniversityJupiterUnited States
| | - Bernadeth Tolentino
- Jupiter Life Science Initiative, Florida Atlantic UniversityJupiterUnited States
| | - Kasey Benesh
- Jupiter Life Science Initiative, Florida Atlantic UniversityJupiterUnited States
| | - Alexandra Paz
- Jupiter Life Science Initiative, Florida Atlantic UniversityJupiterUnited States
| | - Evan Lloyd
- Department of Biology, Texas A&M UniversityCollege StationUnited States
| | - Johanna E Kowalko
- Department of Biological Sciences, Lehigh UniversityBethlehemUnited States
| | - Alex C Keene
- Department of Biology, Texas A&M UniversityCollege StationUnited States
| | - Craig Albertson
- Department of Biology, University of Massachusetts AmherstAmherstUnited States
| | - Erik R Duboue
- Jupiter Life Science Initiative, Florida Atlantic UniversityJupiterUnited States
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17
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Batista da Silva I, Aciole Barbosa D, Kavalco KF, Nunes LR, Pasa R, Menegidio FB. Discovery of putative long non-coding RNAs expressed in the eyes of Astyanax mexicanus (Actinopterygii: Characidae). Sci Rep 2023; 13:12051. [PMID: 37491348 PMCID: PMC10368750 DOI: 10.1038/s41598-023-34198-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2023] [Accepted: 04/25/2023] [Indexed: 07/27/2023] Open
Abstract
Astyanax mexicanus is a well-known model species, that has two morphotypes, cavefish, from subterranean rivers and surface fish, from surface rivers. They are morphologically distinct due to many troglomorphic traits in the cavefish, such as the absence of eyes. Most studies on A. mexicanus are focused on eye development and protein-coding genes involved in the process. However, lncRNAs did not get the same attention and very little is known about them. This study aimed to fill this knowledge gap, identifying, describing, classifying, and annotating lncRNAs expressed in the embryo's eye tissue of cavefish and surface fish. To do so, we constructed a concise workflow to assemble and evaluate transcriptomes, annotate protein-coding genes, ncRNAs families, predict the coding potential, identify putative lncRNAs, map them and predict interactions. This approach resulted in the identification of 33,069 and 19,493 putative lncRNAs respectively mapped in cavefish and surface fish. Thousands of these lncRNAs were annotated and identified as conserved in human and several species of fish. Hundreds of them were validated in silico, through ESTs. We identified lncRNAs associated with genes related to eye development. This is the case of a few lncRNAs associated with sox2, which we suggest being isomorphs of the SOX2-OT, a lncRNA that can regulate the expression of sox2. This work is one of the first studies to focus on the description of lncRNAs in A. mexicanus, highlighting several lncRNA targets and opening an important precedent for future studies focusing on lncRNAs expressed in A. mexicanus.
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Affiliation(s)
- Iuri Batista da Silva
- Institute of Biological Sciences, Federal University of Minas Gerais, Belo Horizonte, MG, 31270-901, Brazil
- Laboratory of Ecological and Evolutionary Genetics, Institute of Biological and Health Sciences, Federal University of Viçosa Campus Rio Paranaíba, Rio Paranaíba, MG, 38810-000, Brazil
| | - David Aciole Barbosa
- Integrated Biotechnology Center, University of Mogi das Cruzes (UMC), Av. Dr. Cândido X. de Almeida and Souza, 200 - Centro Cívico, Mogi das Cruzes, SP, 08780-911, Brazil
| | - Karine Frehner Kavalco
- Laboratory of Ecological and Evolutionary Genetics, Institute of Biological and Health Sciences, Federal University of Viçosa Campus Rio Paranaíba, Rio Paranaíba, MG, 38810-000, Brazil
| | - Luiz R Nunes
- Center for Natural and Human Sciences, Federal University of ABC, São Bernardo do Campo, SP, 09606-045, Brazil
| | - Rubens Pasa
- Laboratory of Ecological and Evolutionary Genetics, Institute of Biological and Health Sciences, Federal University of Viçosa Campus Rio Paranaíba, Rio Paranaíba, MG, 38810-000, Brazil.
| | - Fabiano B Menegidio
- Integrated Biotechnology Center, University of Mogi das Cruzes (UMC), Av. Dr. Cândido X. de Almeida and Souza, 200 - Centro Cívico, Mogi das Cruzes, SP, 08780-911, Brazil.
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18
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Borowsky R. Selection Maintains the Phenotypic Divergence of Cave and Surface Fish. Am Nat 2023; 202:55-63. [PMID: 37384766 DOI: 10.1086/724661] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2023]
Abstract
AbstractGenetic divergence in the presence of gene flow has been well documented, but there is little information on the specific factors maintaining divergence. The present study investigates this in the Mexican tetra (Astyanax mexicanus), an excellent model for studying this question because surface and cave populations differ markedly in phenotype and genotype but are interfertile. Previous population studies documented significant gene flow among cave and surface populations, but they focused on analyses of neutral markers whose evolutionary dynamics likely differ from those of genes involved in cave adaptation. The present study advances our understanding of this question by focusing specifically on the genetics responsible for eye and pigmentation reduction, signature traits of cave populations. Direct observations of two cave populations over the course of 63 years verify that surface fish frequently move into the caves and even hybridize with the cave fish. Importantly, however, historical records show that surface alleles for pigmentation and eye size do not persist but are rapidly eliminated from the cave gene pool. It has been argued that regression of eyes and pigmentation was driven by drift, but the results of this study suggest that strong selection actively eliminates surface alleles from the cave populations.
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19
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Moran RL, Richards EJ, Ornelas-García CP, Gross JB, Donny A, Wiese J, Keene AC, Kowalko JE, Rohner N, McGaugh SE. Selection-driven trait loss in independently evolved cavefish populations. Nat Commun 2023; 14:2557. [PMID: 37137902 PMCID: PMC10156726 DOI: 10.1038/s41467-023-37909-8] [Citation(s) in RCA: 10] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2022] [Accepted: 04/03/2023] [Indexed: 05/05/2023] Open
Abstract
Laboratory studies have demonstrated that a single phenotype can be produced by many different genotypes; however, in natural systems, it is frequently found that phenotypic convergence is due to parallel genetic changes. This suggests a substantial role for constraint and determinism in evolution and indicates that certain mutations are more likely to contribute to phenotypic evolution. Here we use whole genome resequencing in the Mexican tetra, Astyanax mexicanus, to investigate how selection has shaped the repeated evolution of both trait loss and enhancement across independent cavefish lineages. We show that selection on standing genetic variation and de novo mutations both contribute substantially to repeated adaptation. Our findings provide empirical support for the hypothesis that genes with larger mutational targets are more likely to be the substrate of repeated evolution and indicate that features of the cave environment may impact the rate at which mutations occur.
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Affiliation(s)
- Rachel L Moran
- Department of Ecology, Evolution, and Behavior, University of Minnesota, Saint Paul, MN, USA.
- Department of Biology, Texas A&M University, College Station, TX, USA.
| | - Emilie J Richards
- Department of Ecology, Evolution, and Behavior, University of Minnesota, Saint Paul, MN, USA
| | - Claudia Patricia Ornelas-García
- Colección Nacional de Peces, Departamento de Zoología, Instituto de Biología, Universidad Nacional Autónoma de México, Tercer Circuito Exterior S/N. CP 04510, D. F. México, México City, México
| | - Joshua B Gross
- Department of Biological Sciences, University of Cincinnati, Cincinnati, OH, USA
| | - Alexandra Donny
- Department of Ecology, Evolution, and Behavior, University of Minnesota, Saint Paul, MN, USA
| | - Jonathan Wiese
- Department of Ecology, Evolution, and Behavior, University of Minnesota, Saint Paul, MN, USA
| | - Alex C Keene
- Department of Biology, Texas A&M University, College Station, TX, USA
| | - Johanna E Kowalko
- Department of Biological Sciences, Lehigh University, Bethlehem, PA, USA
| | - Nicolas Rohner
- Stowers Institute for Medical Research, Kansas City, MO, USA
- Department of Molecular & Integrative Physiology, KU Medical Center, Kansas City, KS, USA
| | - Suzanne E McGaugh
- Department of Ecology, Evolution, and Behavior, University of Minnesota, Saint Paul, MN, USA
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20
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Kozol RA, Yuiska A, Han JH, Tolentino B, Lopatto A, Lewis P, Paz A, Keene AC, Kowalko JE, Duboué ER. Novel Husbandry Practices Result in Rapid Rates of Growth and Sexual Maturation Without Impacting Adult Behavior in the Blind Mexican Cavefish. Zebrafish 2023; 20:86-94. [PMID: 37071855 PMCID: PMC10123811 DOI: 10.1089/zeb.2023.0001] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/20/2023] Open
Abstract
Animal model systems are dependent on the standardization of husbandry protocols that maximize growth and reduce generation time. The Mexican tetra, Astyanax mexicanus, exists as eyed surface and blind cave dwelling populations. The opportunity for comparative approaches between independently evolved populations has led to the rapid growth of A. mexicanus as a model for evolution and biomedical research. However, a slow and inconsistent growth rate remains a major limitation to the expanded application of A. mexicanus. Fortunately, this temporal limitation can be addressed through husbandry changes that accelerate growth rates while maintaining optimal health outcomes. Here, we describe a husbandry protocol that produces rapid growth rates through changes in diet, feeding frequency, growth sorting and progressive changes in tank size. This protocol produced robust growth rates and decreased the age of sexual maturity in comparison to our previous protocol. To determine whether changes in feeding impacted behavior, we tested fish in exploration and schooling assays. We found no difference in behavior between the two groups, suggesting that increased feeding and rapid growth will not impact the natural variation in behavioral traits. Taken together, this standardized husbandry protocol will accelerate the development of A. mexicanus as a genetic model.
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Affiliation(s)
- Robert A. Kozol
- College of Arts and Sciences, Florida Atlantic University, Jupiter, Florida, USA
| | - Anders Yuiska
- College of Arts and Sciences, Florida Atlantic University, Jupiter, Florida, USA
| | - Ji Heon Han
- Department of Biological Sciences, Florida Atlantic University, Jupiter, Florida, USA
| | - Bernadeth Tolentino
- Department of Biology, University of Southern California, Los Angeles, California, USA
| | - Arthur Lopatto
- College of Arts and Sciences, Florida Atlantic University, Jupiter, Florida, USA
| | - Peter Lewis
- College of Arts and Sciences, Florida Atlantic University, Jupiter, Florida, USA
| | - Alexandra Paz
- College of Arts and Sciences, Florida Atlantic University, Jupiter, Florida, USA
| | - Alex C. Keene
- Department of Biology, Texas A&M, College Station, Texas, USA
| | - Johanna E. Kowalko
- Department of Biological Sciences, Lehigh University, Bethlehem, Pennsylvania, USA
| | - Erik R. Duboué
- College of Arts and Sciences, Florida Atlantic University, Jupiter, Florida, USA
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21
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Miranda-Gamboa R, Espinasa L, Verde-Ramírez MDLA, Hernández-Lozano J, Lacaille JL, Espinasa M, Ornelas-García CP. A new cave population of Astyanax mexicanus from Northern Sierra de El Abra, Tamaulipas, Mexico. SUBTERRANEAN BIOLOGY 2023. [DOI: 10.3897/subtbiol.45.98434] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/08/2023] Open
Abstract
The Astyanax genus represents an extraordinary example of phenotypic evolution, being their most extreme examples the blind and depigmented morphs, which have evolved from independent surface-dwelling lineages. Among cave organisms, Astyanax cavefish is a prominent model system to study regressive evolution. Before this study, 34 cave populations were known for the Astyanax genus to be inhabited by the cave morph. The majority of those cave populations are distributed in Northeast México, at the Sierra Madre Oriental (32 cavefish), in three main areas: Sierra de Guatemala, Sierra de El Abra, and Micos, and two in the Balsas basin in the state of Guerrero, Mexico. In the present study, we describe a new cave population found 4.5 km Southward of Pachón cave, the most northern cave population known for the Sierra de El Abra limestone. El Refugio cave is a resurgence with a mixed population of fish with different levels of troglomorphism, and surface fish, resembling other hybrid populations within the Sierra de El Abra. Based on a mitochondrial DNA characterization of the 16S ribosomal DNA sequence, we could identify the mitochondrial lineage of this population, which was placed closely related to the “New Lineage”, sharing haplotypes with the surface (i.e. Arroyo Lagartos) and Pachón populations, instead of with the cave populations from Central Sierra de El Abra (e.g. Tinaja cave). El Refugio cave population gives additional evidence of the intricate history of this system, where migration, drift, and selection have shaped the evolution of the cave morphs through the independent episodes of the Astyanax mexicanus history.
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22
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Rodas LR, Sarbu SM, Bancila R, Price D, Fišer Ž, Protas M. Standing genetic variation as a potential mechanism of novel cave phenotype evolution in the freshwater isopod, Asellus aquaticus. Evol Dev 2023; 25:137-152. [PMID: 36755467 DOI: 10.1111/ede.12428] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2022] [Revised: 12/14/2022] [Accepted: 01/07/2023] [Indexed: 02/10/2023]
Abstract
Novel phenotypes can come about through a variety of mechanisms including standing genetic variation from a founding population. Cave animals are an excellent system in which to study the evolution of novel phenotypes such as loss of pigmentation and eyes. Asellus aquaticus is a freshwater isopod crustacean found in Europe and has both a surface and a cave ecomorph which vary in multiple phenotypic traits. An orange eye phenotype was previously revealed by F2 crosses and backcrosses to the cave parent within two examined Slovenian cave populations. Complete loss of pigmentation, both in eye and body, is epistatic to the orange eye phenotype and therefore the orange eye phenotype is hidden within the cave populations. Our goal was to investigate the origin of the orange eye alleles within the Slovenian cave populations by examining A. aquaticus individuals from Slovenian and Romanian surface populations and Asellus aquaticus infernus individuals from a Romanian cave population. We found orange eye individuals present in lab raised surface populations of A. aquaticus from both Slovenia and Romania. Using a mapping approach with crosses between individuals of two surface populations, we found that the region known to be responsible for the orange eye phenotype within the two previously examined Slovenian cave populations was also responsible within both the Slovenian and the Romanian surface populations. Complementation crosses between orange eye Slovenian and orange eye Romanian surface individuals suggest that the same gene is responsible for the orange eye phenotype in both surface populations. Additionally, we observed a low frequency phenotype of eye loss in crosses generated between the two surface populations and also in the Romanian surface population. Finally, in a cave population from Romania, A. aquaticus infernus, we found that the same region is also responsible for the orange eye phenotype as the Slovenian cave populations and the Slovenian and Romanian surface populations. Therefore, we present evidence that variation present in the cave populations could originate from standing variation present in the surface populations and/or transgressive hybridization of different surface phylogenetic lineages rather than de novo mutations.
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Affiliation(s)
- Lizet R Rodas
- Department of Natural Sciences and Mathematics, Dominican University of California, San Rafael, California, USA
| | - Serban M Sarbu
- Department of Biospeleology and Karst Edaphobiology, "Emil Racoviţă" Institute of Speleology of Romanian Academy of Sciences, Bucharest, Romania.,Department of Biological Sciences, California State University, Chico, California, USA
| | - Raluca Bancila
- Department of Biospeleology and Karst Edaphobiology, "Emil Racoviţă" Institute of Speleology of Romanian Academy of Sciences, Bucharest, Romania
| | - Devon Price
- Department of Natural Sciences and Mathematics, Dominican University of California, San Rafael, California, USA
| | - Žiga Fišer
- Department of Biology, Biotechnical Faculty, University of Ljubljana, Ljubljana, Slovenia
| | - Meredith Protas
- Department of Natural Sciences and Mathematics, Dominican University of California, San Rafael, California, USA
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23
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Martínez Sosa F, Pilot M. Molecular Mechanisms Underlying Vertebrate Adaptive Evolution: A Systematic Review. Genes (Basel) 2023; 14:416. [PMID: 36833343 PMCID: PMC9957108 DOI: 10.3390/genes14020416] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2022] [Revised: 01/24/2023] [Accepted: 02/01/2023] [Indexed: 02/08/2023] Open
Abstract
Adaptive evolution is a process in which variation that confers an evolutionary advantage in a specific environmental context arises and is propagated through a population. When investigating this process, researchers have mainly focused on describing advantageous phenotypes or putative advantageous genotypes. A recent increase in molecular data accessibility and technological advances has allowed researchers to go beyond description and to make inferences about the mechanisms underlying adaptive evolution. In this systematic review, we discuss articles from 2016 to 2022 that investigated or reviewed the molecular mechanisms underlying adaptive evolution in vertebrates in response to environmental variation. Regulatory elements within the genome and regulatory proteins involved in either gene expression or cellular pathways have been shown to play key roles in adaptive evolution in response to most of the discussed environmental factors. Gene losses were suggested to be associated with an adaptive response in some contexts. Future adaptive evolution research could benefit from more investigations focused on noncoding regions of the genome, gene regulation mechanisms, and gene losses potentially yielding advantageous phenotypes. Investigating how novel advantageous genotypes are conserved could also contribute to our knowledge of adaptive evolution.
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Affiliation(s)
| | - Małgorzata Pilot
- Museum and Institute of Zoology, Polish Academy of Sciences, 80-680 Gdańsk, Poland
- Faculty of Biology, University of Gdańsk, 80-308 Gdańsk, Poland
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Culver DC, Kowalko JE, Pipan T. Natural selection versus neutral mutation in the evolution of subterranean life: A false dichotomy? Front Ecol Evol 2023. [DOI: 10.3389/fevo.2023.1080503] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023] Open
Abstract
Throughout the evolutionary tree, there are gains and losses of morphological features, physiological processes, and behavioral patterns. Losses are perhaps nowhere so prominent as for subterranean organisms, which typically show reductions or losses of eyes and pigment. These losses seem easy to explain without recourse to natural selection. Its most modern form is the accumulation of selectively neutral, structurally reducing mutations. Selectionist explanations include direct selection, often involving metabolic efficiency in resource poor subterranean environments, and pleiotropy, where genes affecting eyes and pigment have other effects, such as increasing extra-optic sensory structures. This dichotomy echoes the debate in evolutionary biology in general about the sufficiency of natural selection as an explanation of evolution, e.g., Kimura’s neutral mutation theory. Tests of the two hypotheses have largely been one-sided, with data supporting that one or the other processes is occurring. While these tests have utilized a variety of subterranean organisms, the Mexican cavefish, Astyanax mexicanus, which has eyed extant ancestral-like surface fish conspecifics, is easily bred in the lab, and whose whole genome has been sequenced, is the favored experimental organism. However, with few exceptions, tests for selection versus neutral mutations contain limitations or flaws. Notably, these tests are often one sided, testing for the presence of one or the other process. In fact, it is most likely that both processes occur and make a significant contribution to the two most studied traits in cave evolution: eye and pigment reduction. Furthermore, narrow focus on neutral mutation hypothesis versus selection to explain cave-evolved traits often fails, at least in the simplest forms of these hypotheses, to account for aspects that are likely essential for understanding cave evolution: migration or epigenetic effects. Further, epigenetic effects and phenotypic plasticity have been demonstrated to play an important role in cave evolution in recent studies. Phenotypic plasticity does not by itself result in genetic change of course, but plasticity can reveal cryptic genetic variation which then selection can act on. These processes may result in a radical change in our thinking about evolution of subterranean life, especially the speed with which it may occur. Thus, perhaps it is better to ask what role the interaction of genes and environment plays, in addition to natural selection and neutral mutation.
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Oliva C, Hinz NK, Robinson W, Barrett Thompson AM, Booth J, Crisostomo LM, Zanineli S, Tanner M, Lloyd E, O'Gorman M, McDole B, Paz A, Kozol R, Brown EB, Kowalko JE, Fily Y, Duboue ER, Keene AC. Characterizing the genetic basis of trait evolution in the Mexican cavefish. Evol Dev 2022; 24:131-144. [PMID: 35924750 PMCID: PMC9786752 DOI: 10.1111/ede.12412] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2021] [Revised: 04/20/2022] [Accepted: 04/26/2022] [Indexed: 12/30/2022]
Abstract
Evolution in response to a change in ecology often coincides with various morphological, physiological, and behavioral traits. For most organisms little is known about the genetic and functional relationship between evolutionarily derived traits, representing a critical gap in our understanding of adaptation. The Mexican tetra, Astyanax mexicanus, consists of largely independent populations of fish that inhabit at least 30 caves in Northeast Mexico, and a surface fish population, that inhabit the rivers of Mexico and Southern Texas. The recent application of molecular genetic approaches combined with behavioral phenotyping have established A. mexicanus as a model for studying the evolution of complex traits. Cave populations of A. mexicanus are interfertile with surface populations and have evolved numerous traits including eye degeneration, insomnia, albinism, and enhanced mechanosensory function. The interfertility of different populations from the same species provides a unique opportunity to define the genetic relationship between evolved traits and assess the co-evolution of behavioral and morphological traits with one another. To define the relationships between morphological and behavioral traits, we developed a pipeline to test individual fish for multiple traits. This pipeline confirmed differences in locomotor activity, prey capture, and startle reflex between surface and cavefish populations. To measure the relationship between traits, individual F2 hybrid fish were characterized for locomotor behavior, prey-capture behavior, startle reflex, and morphological attributes. Analysis revealed an association between body length and slower escape reflex, suggesting a trade-off between increased size and predator avoidance in cavefish. Overall, there were few associations between individual behavioral traits, or behavioral and morphological traits, suggesting independent genetic changes underlie the evolution of the measured behavioral and morphological traits. Taken together, this approach provides a novel system to identify genetic underpinnings of naturally occurring variation in morphological and behavioral traits.
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Affiliation(s)
- Camila Oliva
- NIH U‐RISE ProgramFlorida Atlantic UniversityJupiterFloridaUSA
| | | | - Wayne Robinson
- NIH U‐RISE ProgramFlorida Atlantic UniversityJupiterFloridaUSA
| | | | - Julianna Booth
- NIH U‐RISE ProgramFlorida Atlantic UniversityJupiterFloridaUSA
| | | | | | - Maureen Tanner
- NIH U‐RISE ProgramFlorida Atlantic UniversityJupiterFloridaUSA
| | - Evan Lloyd
- Jupiter Life Science InitiativeFlorida Atlantic UniversityJupiterFloridaUSA,Department of BiologyTexas A&M UniversityCollege StationTexasUSA
| | - Morgan O'Gorman
- Jupiter Life Science InitiativeFlorida Atlantic UniversityJupiterFloridaUSA,Department of BiologyTexas A&M UniversityCollege StationTexasUSA
| | - Brittnee McDole
- Jupiter Life Science InitiativeFlorida Atlantic UniversityJupiterFloridaUSA
| | - Alexandra Paz
- Jupiter Life Science InitiativeFlorida Atlantic UniversityJupiterFloridaUSA
| | - Rob Kozol
- Jupiter Life Science InitiativeFlorida Atlantic UniversityJupiterFloridaUSA
| | - Elizabeth B. Brown
- Jupiter Life Science InitiativeFlorida Atlantic UniversityJupiterFloridaUSA
| | - Johanna E. Kowalko
- Jupiter Life Science InitiativeFlorida Atlantic UniversityJupiterFloridaUSA,Department of Biological SciencesLehigh UniversityBethlehemPennsylvaniaUSA
| | - Yaouen Fily
- Jupiter Life Science InitiativeFlorida Atlantic UniversityJupiterFloridaUSA
| | - Erik R. Duboue
- Jupiter Life Science InitiativeFlorida Atlantic UniversityJupiterFloridaUSA
| | - Alex C. Keene
- Jupiter Life Science InitiativeFlorida Atlantic UniversityJupiterFloridaUSA,Department of BiologyTexas A&M UniversityCollege StationTexasUSA
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Clark B, Elkin J, Marconi A, Turner GF, Smith AM, Joyce D, Miska EA, Juntti SA, Santos ME. Oca2 targeting using CRISPR/Cas9 in the Malawi cichlid Astatotilapia calliptera. ROYAL SOCIETY OPEN SCIENCE 2022; 9:220077. [PMID: 35601449 PMCID: PMC9019512 DOI: 10.1098/rsos.220077] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 01/20/2022] [Accepted: 03/22/2022] [Indexed: 05/03/2023]
Abstract
Identifying genetic loci underlying trait variation provides insights into the mechanisms of diversification, but demonstrating causality and characterizing the role of genetic loci requires testing candidate gene function, often in non-model species. Here we establish CRISPR/Cas9 editing in Astatotilapia calliptera, a generalist cichlid of the remarkably diverse Lake Malawi radiation. By targeting the gene oca2 required for melanin synthesis in other vertebrate species, we show efficient editing and germline transmission. Gene edits include indels in the coding region, probably a result of non-homologous end joining, and a large deletion in the 3' untranslated region due to homology-directed repair. We find that oca2 knock-out A. calliptera lack melanin, which may be useful for developmental imaging in embryos and studying colour pattern formation in adults. As A. calliptera resembles the presumed generalist ancestor of the Lake Malawi cichlids radiation, establishing genome editing in this species will facilitate investigating speciation, adaptation and trait diversification in this textbook radiation.
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Affiliation(s)
- Bethan Clark
- Department of Zoology, University of Cambridge, UK
| | - Joel Elkin
- Department of Zoology, University of Cambridge, UK
| | | | - George F. Turner
- School of Natural Sciences, Bangor University, Gwynedd LL57 2TH, UK
| | - Alan M. Smith
- Department of Biological and Marine Sciences, University of Hull, UK
| | - Domino Joyce
- Department of Biological and Marine Sciences, University of Hull, UK
| | - Eric A. Miska
- Department of Genetics, University of Cambridge, UK
- Gurdon Institute, University of Cambridge, Cambridge CB2 1QN, UK
- Wellcome Sanger Institute, Wellcome Trust Genome Campus, Cambridge, UK
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Abstract
Albino cavefish sleep less than their pigmented siblings. A recent study used CRISPR-Cas9-directed mutation to establish unambiguously that loss of function of a single gene, ocular and cutaneous albinism2, underlies both phenotypes, one morphological, the other behavioral.
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Affiliation(s)
- Richard Borowsky
- Department of Biology, New York University, New York, NY 10003, USA.
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