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Leclercq J, Torres-Paz J, Policarpo M, Agnès F, Rétaux S. Evolution of the regulation of developmental gene expression in blind Mexican cavefish. Development 2024; 151:dev202610. [PMID: 39007346 DOI: 10.1242/dev.202610] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2023] [Accepted: 07/08/2024] [Indexed: 07/16/2024]
Abstract
Developmental evolution and diversification of morphology can arise through changes in the regulation of gene expression or protein-coding sequence. To unravel mechanisms underlying early developmental evolution in cavefish of the species Astyanax mexicanus, we compared transcriptomes of surface-dwelling and blind cave-adapted morphs at the end of gastrulation. Twenty percent of the transcriptome was differentially expressed. Allelic expression ratios in cave X surface hybrids showed that cis-regulatory changes are the quasi-exclusive contributors to inter-morph variations in gene expression. Among a list of 108 genes with change at the cis-regulatory level, we explored the control of expression of rx3, which is a master eye gene. We discovered that cellular rx3 levels are cis-regulated in a cell-autonomous manner, whereas rx3 domain size depends on non-autonomous Wnt and Bmp signalling. These results highlight how uncoupled mechanisms and regulatory modules control developmental gene expression and shape morphological changes. Finally, a transcriptome-wide search for fixed coding mutations and differential exon use suggested that variations in coding sequence have a minor contribution. Thus, during early embryogenesis, changes in gene expression regulation are the main drivers of cavefish developmental evolution.
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Affiliation(s)
- Julien Leclercq
- Paris-Saclay Institute of Neuroscience, CNRS and University Paris-Saclay, 91400 Saclay, France
| | - Jorge Torres-Paz
- Paris-Saclay Institute of Neuroscience, CNRS and University Paris-Saclay, 91400 Saclay, France
| | - Maxime Policarpo
- Paris-Saclay Institute of Neuroscience, CNRS and University Paris-Saclay, 91400 Saclay, France
| | - François Agnès
- Paris-Saclay Institute of Neuroscience, CNRS and University Paris-Saclay, 91400 Saclay, France
| | - Sylvie Rétaux
- Paris-Saclay Institute of Neuroscience, CNRS and University Paris-Saclay, 91400 Saclay, France
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2
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Zhao L, Xiao R, Zhang S, Zhang C, Zhang F. Environmental specificity of karst cave habitats evidenced by diverse symbiotic bacteria in Opiliones. BMC Ecol Evol 2024; 24:58. [PMID: 38720266 PMCID: PMC11080181 DOI: 10.1186/s12862-024-02248-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2023] [Accepted: 04/30/2024] [Indexed: 05/12/2024] Open
Abstract
BACKGROUND Karst caves serve as natural laboratories, providing organisms with extreme and constant conditions that promote isolation, resulting in a genetic relationship and living environment that is significantly different from those outside the cave. However, research on cave creatures, especially Opiliones, remains scarce, with most studies focused on water, soil, and cave sediments. RESULTS The structure of symbiotic bacteria in different caves were compared, revealing significant differences. Based on the alpha and beta diversity, symbiotic bacteria abundance and diversity in the cave were similar, but the structure of symbiotic bacteria differed inside and outside the cave. Microorganisms in the cave play an important role in material cycling and energy flow, particularly in the nitrogen cycle. Although microbial diversity varies inside and outside the cave, Opiliones in Beijing caves and Hainan Island exhibited a strong similarity, indicating that the two environments share commonalities. CONCLUSIONS The karst cave environment possesses high microbial diversity and there are noticeable differences among different caves. Different habitats lead to significant differences in the symbiotic bacteria in Opiliones inside and outside the cave, and cave microorganisms have made efforts to adapt to extreme environments. The similarity in symbiotic bacteria community structure suggests a potential similarity in host environments, providing an explanation for the appearance of Sinonychia martensi in caves in the north.
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Affiliation(s)
- Likun Zhao
- School of Life Sciences, Institute of Life Science and Green Development, Hebei University, Baoding, 071002, P.R. China
- The Key Laboratory of Microbial Diversity Research and Application of Hebei Province, Baoding, 071002, P. R. China
| | - Ruoyi Xiao
- School of Life Sciences, Institute of Life Science and Green Development, Hebei University, Baoding, 071002, P.R. China
| | - Shanfeng Zhang
- School of Life Sciences, Institute of Life Science and Green Development, Hebei University, Baoding, 071002, P.R. China
| | - Chao Zhang
- School of Life Sciences, Institute of Life Science and Green Development, Hebei University, Baoding, 071002, P.R. China.
- The Key Laboratory of Zoological Systematics and Application of Hebei Province, Baoding, 071002, P. R. China.
| | - Feng Zhang
- School of Life Sciences, Institute of Life Science and Green Development, Hebei University, Baoding, 071002, P.R. China.
- The Key Laboratory of Zoological Systematics and Application of Hebei Province, Baoding, 071002, P. R. China.
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3
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Jolles JW, Böhm A, Brinker A, Behrmann-Godel J. Unravelling the origins of boldness behaviour: a common garden experiment with cavefish ( Barbatula barbatula). ROYAL SOCIETY OPEN SCIENCE 2024; 11:231517. [PMID: 38204784 PMCID: PMC10776215 DOI: 10.1098/rsos.231517] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/06/2023] [Accepted: 12/06/2023] [Indexed: 01/12/2024]
Abstract
Many animals show an aversion to bright, open spaces, with significant variability seen across species, populations and individuals within populations. Although there is much interest in the underlying causes of this behaviour, few studies have been able to systematically isolate the role of heritable and environmental effects. Here, we addressed this gap using a common garden experiment with cavefish. Specifically, we bred and cross-bred cave loaches (Barbatula barbatula), Europe's only known cavefish, in the laboratory, raised the offspring in complete darkness or normal light conditions, and studied their light avoidance behaviour. Cavefish spent much more time in a light area and ventured further out, while surface fish spent considerable time in risk-assessment behaviour between the light and dark areas. Hybrids behaved most similarly to cavefish. Light treatment and eye quality and lens size only had a modest effect. Our results suggest light avoidance behaviour of cavefish has a heritable basis and is fundamentally linked to increased boldness rather than reduced vision, which is likely adaptive given the complete lack of macropredators in the cave environment. Our study provides novel experimental insights into the behavioural divergence of cavefish and contributes to our broader understanding of the evolution of boldness and behavioural adaptation.
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Affiliation(s)
- Jolle W. Jolles
- Limnological Institute, University of Konstanz, Konstanz, Baden-Württemberg, Germany
- Centre for Advanced Studies Blanes (CEAB), CSIC, Blanes, Catalunya, Spain
| | - Alexander Böhm
- Limnological Institute, University of Konstanz, Konstanz, Baden-Württemberg, Germany
| | - Alexander Brinker
- Limnological Institute, University of Konstanz, Konstanz, Baden-Württemberg, Germany
- Fisheries Research Station Baden-Württemberg, Langenargen, Germany
| | - Jasminca Behrmann-Godel
- Limnological Institute, University of Konstanz, Konstanz, Baden-Württemberg, Germany
- Ministry for Nutrition, Rural Affairs and Consumer Protection Baden-Württemberg (MLR), Stuttgart, Germany
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4
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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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5
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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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6
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Liu Y, Liu T, Wang Y, Liu J, Liu B, Gong L, Lü Z, Liu L. Genome Sequencing Provides Novel Insights into Mudflat Burrowing Adaptations in Eel Goby Taenioides sp. (Teleost: Amblyopinae). Int J Mol Sci 2023; 24:12892. [PMID: 37629073 PMCID: PMC10454203 DOI: 10.3390/ijms241612892] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2023] [Revised: 08/09/2023] [Accepted: 08/14/2023] [Indexed: 08/27/2023] Open
Abstract
Amblyopinae is one of the lineage of bony fish that preserves amphibious traits living in tidal mudflat habitats. In contrast to other active amphibious fish, Amblyopinae species adopt a seemly more passive lifestyle by living in deep burrows of mudflat to circumvent the typical negative effects associated with terrestriality. However, little is known about the genetic origin of these mudflat deep-burrowing adaptations in Amblyopinae. Here we sequenced the first genome of Amblyopinae species, Taenioides sp., to elucidate their mudflat deep-burrowing adaptations. Our results revealed an assembled genome size of 774.06 Mb with 23 pseudochromosomes anchored, which predicted 22,399 protein-coding genes. Phylogenetic analyses indicated that Taenioides sp. diverged from the active amphibious fish of mudskipper approximately 28.3 Ma ago. In addition, 185 and 977 putative gene families were identified to be under expansion, contraction and 172 genes were undergone positive selection in Taenioides sp., respectively. Enrichment categories of top candidate genes under significant expansion and selection were mainly associated with hematopoiesis or angiogenesis, DNA repairs and the immune response, possibly suggesting their involvement in the adaptation to the hypoxia and diverse pathogens typically observed in mudflat burrowing environments. Some carbohydrate/lipid metabolism, and insulin signaling genes were also remarkably alterated, illustrating physiological remolding associated with nutrient-limited subterranean environments. Interestingly, several genes related to visual perception (e.g., crystallins) have undergone apparent gene losses, pointing to their role in the small vestigial eyes development in Taenioides sp. Our work provide valuable resources for understanding the molecular mechanisms underlying mudflat deep-burrowing adaptations in Amblyopinae, as well as in other tidal burrowing teleosts.
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Affiliation(s)
- Yantao Liu
- National Engineering Laboratory of Marine Germplasm Resources Exploration and Utilization, College of Marine Sciences and Technology, Zhejiang Ocean University, Zhoushan 316022, China
| | - Tianwei Liu
- National Engineering Laboratory of Marine Germplasm Resources Exploration and Utilization, College of Marine Sciences and Technology, Zhejiang Ocean University, Zhoushan 316022, China
| | - Yuzhen Wang
- National Engineering Research Center for Facilitated Marine Aquaculture, Zhejiang Ocean University, Zhoushan 316022, China
| | - Jing Liu
- National Engineering Laboratory of Marine Germplasm Resources Exploration and Utilization, College of Marine Sciences and Technology, Zhejiang Ocean University, Zhoushan 316022, China
| | - Bingjian Liu
- National Engineering Laboratory of Marine Germplasm Resources Exploration and Utilization, College of Marine Sciences and Technology, Zhejiang Ocean University, Zhoushan 316022, China
| | - Li Gong
- National Engineering Laboratory of Marine Germplasm Resources Exploration and Utilization, College of Marine Sciences and Technology, Zhejiang Ocean University, Zhoushan 316022, China
| | - Zhenming Lü
- National Engineering Laboratory of Marine Germplasm Resources Exploration and Utilization, College of Marine Sciences and Technology, Zhejiang Ocean University, Zhoushan 316022, China
| | - Liqin Liu
- National Engineering Laboratory of Marine Germplasm Resources Exploration and Utilization, College of Marine Sciences and Technology, Zhejiang Ocean University, Zhoushan 316022, China
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7
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Wu L, Fan C, Lan C, Yu J, Wen H, Yang Q, Xiao N, Zhou J. A long-ignored unique ecosystem of cavefishes in the southern karst: achievements, challenges, and prospects. ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH INTERNATIONAL 2023; 30:90489-90499. [PMID: 37479926 DOI: 10.1007/s11356-023-28806-0] [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: 12/28/2022] [Accepted: 07/11/2023] [Indexed: 07/23/2023]
Abstract
Cavefishes represent a taxon that has experienced natural selection pressures. This paper summarizes the results with respect to the taxonomy, diversity, phylogeny, and adaptation aspects of cavefishes research. It showed that: 1) These studies suggest that cavefishes play important roles in the study of geologic history and adaptation to extreme environments, but the mechanisms involved 168 species of cavefishes belonging to 17 genera, four families, and two orders have been recorded in China. Meanwhile, more new species are being discovered recently, and the species diversity of cavefishes are still underestimated, indicating the need to strengthen the survey in field. 2) The biogeography of cavefishes have focused on Sinocyclocheilus and Triplophysa, that have helped understand the geomorphology of karst areas in southern China and the spatial pattern of species diversity. These studies revealed the influences of evolution and geological history in Sinocyclocheilus, but there are still many species that have not been studied accordingly. 3) Some adaptive mechanistic studies have been conducted on cavefishes, primarily focusing on eye and body color degradation and energy metabolism in the genus Sinocyclocheilus to reveal adaptive mechanisms in the dark environment. 4) The IUCN list of protected cavefishes species in China only includes 21 species. The List of Key Protected Wild Animals for 2021 includes all species of Sinocyclocheilus as National Class II.It is necessary to strengthen the research on the biodiversity and adaptation and need consider the conservation actions for cavefishes.
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Affiliation(s)
- Li Wu
- School of Karst Science, Guizhou Normal University, Guiyang, 550001, China
| | - Cui Fan
- School of Karst Science, Guizhou Normal University, Guiyang, 550001, China
| | - Changting Lan
- School of Life Sciences, Guizhou Normal University, Guiyang, 550001, China
| | - Jing Yu
- School of Life Sciences, Guizhou Normal University, Guiyang, 550001, China
| | - Huamei Wen
- College of Science, Qiongtai Normal University, Haikou, 571127, China
| | - Qin Yang
- School of Karst Science, Guizhou Normal University, Guiyang, 550001, China
| | - Ning Xiao
- Guiyang Healthcare Vocational University, Guiyang, 550081, Guizhou, China
| | - Jiang Zhou
- School of Karst Science, Guizhou Normal University, Guiyang, 550001, China.
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8
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Swanson NE, Gluesenkamp AG, Donny AE, Mcgaugh SE. Developmental environment contributes to rapid trait shifts among newly colonized subterranean habitats. Zool Res 2023; 44:808-820. [PMID: 37464938 PMCID: PMC10415762 DOI: 10.24272/j.issn.2095-8137.2022.488] [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: 05/16/2023] [Accepted: 07/12/2023] [Indexed: 07/20/2023] Open
Abstract
Recent colonization of extreme environments provides unique opportunities to study the early steps of adaptation and the potential for rapid convergent evolution. However, phenotypic shifts during recent colonization may also be due to plasticity in response to changes in the rearing environment. Here, we analyzed a suite of morphological and behavioral traits in paired surface, subterranean, and facultatively subterranean Mexican tetras ( Astyanax mexicanus) from recent introductions in two separate watersheds outside of their native range. We found a variety of phenotypic and behavioral shifts between subterranean and surface populations that are similar to those observed in relatively ancient populations in Mexico. Despite this rapid morphological divergence, we found that most of these trait differences were due to plasticity in response to rearing environments. While most trait assays in common-garden, lab-raised fish indicated that phenotypic shifts in wild fish were the result of plasticity, we also found evidence of genetic control in several traits present in subterranean populations. Interestingly, wall-following behavior, an important subterranean foraging behavior, was greater in lab-born subterranean fish than in lab-born surface fish, suggesting rapid divergence of this trait between subterranean and surface populations. Thus, this study sheds light on the early steps of subterranean evolution, identifies potential rapid behavioral evolution, and suggests that plasticity in traits involving exploratory behavior may facilitate subterranean colonization.
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Affiliation(s)
- Nathan E Swanson
- Department of Fisheries, Wildlife and Conservation Biology, University of Minnesota, Saint Paul, MN 55108, USA
- Department of Ecology and Evolutionary Biology, University of California Irvine, Irvine, CA 92697-2525, USA. E-mail:
| | - Andrew G Gluesenkamp
- Center for Conservation and Research, San Antonio Zoo, San Antonio, Texas 78212, USA
| | - Alexandra E Donny
- Ecology, Evolution, and Behavior, University of Minnesota, Saint Paul, MN 55108, USA
- Department of Biology, Stanford University, Stanford, CA 94305, USA
| | - Suzanne E Mcgaugh
- Ecology, Evolution, and Behavior, University of Minnesota, Saint Paul, MN 55108, USA. E-mail:
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9
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Drager KI, Rivera MD, Gibson JC, Ruzi SA, Hanisch PE, Achury R, Suarez AV. Testing the predictive value of functional traits in diverse ant communities. Ecol Evol 2023; 13:e10000. [PMID: 37091559 PMCID: PMC10115899 DOI: 10.1002/ece3.10000] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2022] [Revised: 03/22/2023] [Accepted: 03/24/2023] [Indexed: 04/25/2023] Open
Abstract
Associating morphological features with ecological traits is essential for understanding the connection between organisms and their roles in the environment. If applied successfully, functional trait approaches link form and function in an organism. However, functional trait data not associated with natural history information provide an incomplete picture of an organism's role in the ecosystem. Using data on the relative trophic position of 592 ant (Formicidae) samples comprising 393 species from 11 subfamilies and 19 widely distributed communities, we tested the extent to which commonly used functional proxies (i.e., morphometric traits) predict diet/trophic position as estimated from stable isotopes (δ15N). We chose ants as a group due to their ubiquity and abundance, as well as the wealth of available data on species traits and trophic levels. We measured 12 traits that have previously been identified as functionally significant, and corrected trait values for size and evolutionary history by using phylogenetically corrected trait residuals. Estimated trophic positions varied from 0.9 to 4.8 or roughly 4 trophic levels. Morphological data spanned nearly the entire size range seen in ants from the smallest (e.g., Strumigenys mitis total length 1.1 mm) to the largest species (e.g., Dinoponera australis total length 28.3 mm). We found overall body size, relative eye position, and scape length to be informative for predicting diet/trophic position in these communities, albeit with relatively weak predictive values. Specifically, trophic position was negatively correlated with body size and positively correlated with sensory traits (higher eye position and scape length). Our results suggest that functional trait-based approaches can be informative but should be used with caution unless clear links between form and function have been established.
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Affiliation(s)
- Kim I. Drager
- Department of Evolution, Ecology and BehaviorUniversity of Illinois505 S. Goodwin Ave. 515 Morrill HallUrbanaIllinois61801USA
| | - Michael D. Rivera
- Program in Ecology, Evolution and Conservation BiologyUniversity of Illinois505 S. Goodwin Ave. 515 Morrill HallUrbanaIllinois61801USA
| | - Joshua C. Gibson
- Department of EntomologyUniversity of Illinois505 S. Goodwin Ave. 320 Morrill HallUrbanaIllinois61801USA
- Beckman Institute for Advanced Science and TechnologyUniversity of Illinois at Urbana‐Champaign405 N. Mathews AveUrbanaIllinois61801USA
| | - Selina A. Ruzi
- Department of Applied EcologyNorth Carolina State University115 David Clark Labs, 100 Eugene Brooks AvenueRaleighNorth Carolina27695USA
| | - Priscila E. Hanisch
- Department of Animal Ecology and Tropical BiologyBiocenterUniversity of WürzburgAm Hubland 97074WürzburgGermany
- Museo Argentino de Ciencias Naturales “Bernardino Rivadavia” MACN‐CONICETBuenos AiresArgentina
| | - Rafael Achury
- Department of EntomologyUniversity of Illinois505 S. Goodwin Ave. 320 Morrill HallUrbanaIllinois61801USA
- Terrestrial Ecology Research GroupTechnical University of MunichHans‐Carl‐von‐Carlowitz‐Platz 2Freising85354Germany
| | - Andrew V. Suarez
- Department of Evolution, Ecology and BehaviorUniversity of Illinois505 S. Goodwin Ave. 515 Morrill HallUrbanaIllinois61801USA
- Program in Ecology, Evolution and Conservation BiologyUniversity of Illinois505 S. Goodwin Ave. 515 Morrill HallUrbanaIllinois61801USA
- Department of EntomologyUniversity of Illinois505 S. Goodwin Ave. 320 Morrill HallUrbanaIllinois61801USA
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10
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Fernandes VFL, Glaser Y, Iwashita M, Yoshizawa M. Evolution of left-right asymmetry in the sensory system and foraging behavior during adaptation to food-sparse cave environments. BMC Biol 2022; 20:295. [PMID: 36575431 PMCID: PMC9795734 DOI: 10.1186/s12915-022-01501-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2022] [Accepted: 12/12/2022] [Indexed: 12/28/2022] Open
Abstract
BACKGROUND Laterality in relation to behavior and sensory systems is found commonly in a variety of animal taxa. Despite the advantages conferred by laterality (e.g., the startle response and complex motor activities), little is known about the evolution of laterality and its plasticity in response to ecological demands. In the present study, a comparative study model, the Mexican tetra (Astyanax mexicanus), composed of two morphotypes, i.e., riverine surface fish and cave-dwelling cavefish, was used to address the relationship between environment and laterality. RESULTS The use of a machine learning-based fish posture detection system and sensory ablation revealed that the left cranial lateral line significantly supports one type of foraging behavior, i.e., vibration attraction behavior, in one cave population. Additionally, left-right asymmetric approaches toward a vibrating rod became symmetrical after fasting in one cave population but not in the other populations. CONCLUSION Based on these findings, we propose a model explaining how the observed sensory laterality and behavioral shift could help adaptation in terms of the tradeoff in energy gain and loss during foraging according to differences in food availability among caves.
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Affiliation(s)
| | - Yannik Glaser
- Department of Information and Computer Sciences, University of Hawai'i at Mānoa, Honolulu, Hawai'i, USA
| | - Motoko Iwashita
- School of Life Sciences, University of Hawai'i at Mānoa, Honolulu, Hawai'i, USA
| | - Masato Yoshizawa
- School of Life Sciences, University of Hawai'i at Mānoa, Honolulu, Hawai'i, USA.
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11
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Ren X, Léveillard T. Modulating antioxidant systems as a therapeutic approach to retinal degeneration. Redox Biol 2022; 57:102510. [PMID: 36274523 PMCID: PMC9596747 DOI: 10.1016/j.redox.2022.102510] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2022] [Revised: 10/11/2022] [Accepted: 10/11/2022] [Indexed: 11/21/2022] Open
Abstract
The human retina is facing a big challenge of reactive oxygen species (ROS) from endogenous and exogenous sources. Excessive ROS can cause damage to DNA, lipids, and proteins, triggering abnormal redox signaling, and ultimately lead to cell death. Thus, oxidative stress has been observed in inherited retinal diseases as a common hallmark. To counteract the detrimental effect of ROS, cells are equipped with various antioxidant defenses. In this review, we will focus on the antioxidant systems in the retina and how they can protect retina from oxidative stress. Both small antioxidants and antioxidant enzymes play a role in ROS removal. Particularly, the thioredoxin and glutaredoxin systems, as the major antioxidant systems in mammalian cells, exert functions in redox signaling regulation via modifying cysteines in proteins. In addition, the thioredoxin-like rod-derived cone viability factor (RdCVFL) and thioredoxin interacting protein (TXNIP) can modulate metabolism in photoreceptors and promote their survival. In conclusion, elevating the antioxidant capacity in retina is a promising therapy to curb the progress of inherited retinal degeneration.
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Affiliation(s)
- Xiaoyuan Ren
- Department of Genetics, Sorbonne Université, INSERM, CNRS, Institut de la Vision, 17 rue Moreau, F-75012 Paris, France; Division of Biochemistry, Department of Medical Biochemistry and Biophysics, Karolinska Institutet, Stockholm, 17177, Sweden.
| | - Thierry Léveillard
- Department of Genetics, Sorbonne Université, INSERM, CNRS, Institut de la Vision, 17 rue Moreau, F-75012 Paris, France.
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12
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Zhao Q, Shao F, Li Y, Yi SV, Peng Z. Novel genome sequence of Chinese cavefish (Triplophysa rosa) reveals pervasive relaxation of natural selection in cavefish genomes. Mol Ecol 2022; 31:5831-5845. [PMID: 36125323 PMCID: PMC9828065 DOI: 10.1111/mec.16700] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2021] [Accepted: 09/15/2022] [Indexed: 01/13/2023]
Abstract
All cavefishes, living exclusively in caves across the globe, exhibit similar phenotypic traits, including the characteristic loss of eyes. To understand whether such phenotypic convergence shares similar genomic bases, here we investigated genome-wide evolutionary signatures of cavefish phenotypes by comparing whole-genome sequences of three pairs of cavefishes and their surface fish relatives. Notably, we newly sequenced and generated a whole-genome assembly of the Chinese cavefish Triplophysa rosa. Our comparative analyses revealed several shared features of cavefish genome evolution. Cavefishes had lower mutation rates than their surface fish relatives. In contrast, the ratio of nonsynonymous to synonymous substitutions (ω) was significantly elevated in cavefishes compared to in surface fishes, consistent with the relaxation of purifying selection. In addition, cavefish genomes had an increased mutational load, including mutations that alter protein hydrophobicity profiles, which were considered harmful. Interestingly, however, we found no overlap in positively selected genes among different cavefish lineages, indicating that the phenotypic convergence in cavefishes was not caused by positive selection of the same sets of genes. Analyses of previously identified candidate genes associated with cave phenotypes supported this conclusion. Genes belonging to the lipid metabolism functional ontology were under relaxed purifying selection in all cavefish genomes, which may be associated with the nutrient-poor habitat of cavefishes. Our work reveals previously uncharacterized patterns of cavefish genome evolution and provides comparative insights into the evolution of cave-associated phenotypic traits.
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Affiliation(s)
- Qingyuan Zhao
- Key Laboratory of Freshwater Fish Reproduction and Development (Ministry of Education)Southwest University School of Life SciencesChongqingChina,Department of Laboratory Animal Science, College of Basic Medical SciencesArmy Medical University (Third Military Medical University)ChongqingChina
| | - Feng Shao
- Key Laboratory of Freshwater Fish Reproduction and Development (Ministry of Education)Southwest University School of Life SciencesChongqingChina
| | - Yanping Li
- Key Laboratory of Freshwater Fish Reproduction and Development (Ministry of Education)Southwest University School of Life SciencesChongqingChina,Key Laboratory of Sichuan Province for Fish Conservation and Utilization in the Upper Reaches of the Yangtze RiverNeijiang Normal University College of Life SciencesNeijiangChina
| | - Soojin V. Yi
- Department of Ecology, Evolution and Marine BiologyUniversity of CaliforniaSanta BarbaraCaliforniaUSA
| | - Zuogang Peng
- Key Laboratory of Freshwater Fish Reproduction and Development (Ministry of Education)Southwest University School of Life SciencesChongqingChina,Academy of Plateau Science and SustainabilityQinghai Normal UniversityXiningChina
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13
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Hodge BA, Meyerhof GT, Katewa SD, Lian T, Lau C, Bar S, Leung NY, Li M, Li-Kroeger D, Melov S, Schilling B, Montell C, Kapahi P. Dietary restriction and the transcription factor clock delay eye aging to extend lifespan in Drosophila Melanogaster. Nat Commun 2022; 13:3156. [PMID: 35672419 PMCID: PMC9174495 DOI: 10.1038/s41467-022-30975-4] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2021] [Accepted: 05/24/2022] [Indexed: 01/15/2023] Open
Abstract
Many vital processes in the eye are under circadian regulation, and circadian dysfunction has emerged as a potential driver of eye aging. Dietary restriction is one of the most robust lifespan-extending therapies and amplifies circadian rhythms with age. Herein, we demonstrate that dietary restriction extends lifespan in Drosophila melanogaster by promoting circadian homeostatic processes that protect the visual system from age- and light-associated damage. Altering the positive limb core molecular clock transcription factor, CLOCK, or CLOCK-output genes, accelerates visual senescence, induces a systemic immune response, and shortens lifespan. Flies subjected to dietary restriction are protected from the lifespan-shortening effects of photoreceptor activation. Inversely, photoreceptor inactivation, achieved via mutating rhodopsin or housing flies in constant darkness, primarily extends the lifespan of flies reared on a high-nutrient diet. Our findings establish the eye as a diet-sensitive modulator of lifespan and indicates that vision is an antagonistically pleiotropic process that contributes to organismal aging.
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Affiliation(s)
- Brian A Hodge
- Buck Institute for Research on Aging, 8001 Redwood Blvd, Novato, CA, 94945, USA.
| | - Geoffrey T Meyerhof
- Buck Institute for Research on Aging, 8001 Redwood Blvd, Novato, CA, 94945, USA
- Neuroscience Research Institute and Department of Molecular, Cellular and Developmental Biology, University of California, Santa Barbara, Santa Barbara, CA, 93106, USA
| | - Subhash D Katewa
- Buck Institute for Research on Aging, 8001 Redwood Blvd, Novato, CA, 94945, USA
- NGM Biopharmaceuticals, 333 Oyster Point Blvd, South San Francisco, CA, 94080, USA
| | - Ting Lian
- Buck Institute for Research on Aging, 8001 Redwood Blvd, Novato, CA, 94945, USA
- Sichuan Agricultural University, 46 Xinkang Rd, Yucheng District, Ya'an, Sichuan, China
| | - Charles Lau
- Buck Institute for Research on Aging, 8001 Redwood Blvd, Novato, CA, 94945, USA
| | - Sudipta Bar
- Buck Institute for Research on Aging, 8001 Redwood Blvd, Novato, CA, 94945, USA
| | - Nicole Y Leung
- Neuroscience Research Institute and Department of Molecular, Cellular and Developmental Biology, University of California, Santa Barbara, Santa Barbara, CA, 93106, USA
- Department of Psychiatry and Behavioral Sciences, Stanford University, Stanford, CA, 94305, USA
- Department of Neurobiology, Stanford University, Stanford, CA, 94305, USA
| | - Menglin Li
- Neuroscience Research Institute and Department of Molecular, Cellular and Developmental Biology, University of California, Santa Barbara, Santa Barbara, CA, 93106, USA
| | - David Li-Kroeger
- Department of Neurology, Baylor College of Medicine, Houston, TX, 77096, USA
| | - Simon Melov
- Buck Institute for Research on Aging, 8001 Redwood Blvd, Novato, CA, 94945, USA
| | - Birgit Schilling
- Buck Institute for Research on Aging, 8001 Redwood Blvd, Novato, CA, 94945, USA
| | - Craig Montell
- Neuroscience Research Institute and Department of Molecular, Cellular and Developmental Biology, University of California, Santa Barbara, Santa Barbara, CA, 93106, USA
| | - Pankaj Kapahi
- Buck Institute for Research on Aging, 8001 Redwood Blvd, Novato, CA, 94945, USA.
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14
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Lunghi E, Bilandžija H. Longevity in Cave Animals. Front Ecol Evol 2022. [DOI: 10.3389/fevo.2022.874123] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
An extraordinary longevity has been observed in some cave species, and this raised the hypothesis that a longer lifespan may be considered one of the characteristic traits of these animals. However, only a few cave species have been studied thus far, and a firm conclusion remains to be drawn. Here we review the available knowledge on the longevity of subterranean species, point out the limitations of previous studies, and provide suggestions for future studies to answer important questions regarding the longevity in cave animals, its adaptive value and the related promoting factors. We also argue that studying the longevity in cave animals will contribute to the field of aging, especially to understanding the evolution of this phenomenon.
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15
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Langille BL, Tierney SM, Bertozzi T, Beasley-Hall PG, Bradford TM, Fagan-Jeffries EP, Hyde J, Leijs R, Richardson M, Saint KM, Stringer DN, Villastrigo A, Humphreys WF, Austin AD, Cooper SJB. Parallel decay of vision genes in subterranean water beetles. Mol Phylogenet Evol 2022; 173:107522. [PMID: 35595008 DOI: 10.1016/j.ympev.2022.107522] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2022] [Revised: 04/19/2022] [Accepted: 04/20/2022] [Indexed: 11/19/2022]
Abstract
In the framework of neutral theory of molecular evolution, genes specific to the development and function of eyes in subterranean animals living in permanent darkness are expected to evolve by relaxed selection, ultimately becoming pseudogenes. However, definitive empirical evidence for the role of neutral processes in the loss of vision over evolutionary time remains controversial. In previous studies, we characterized an assemblage of independently-evolved water beetle (Dytiscidae) species from a subterranean archipelago in Western Australia, where parallel vision and eye loss have occurred. Using a combination of transcriptomics and exon capture, we present evidence of parallel coding sequence decay, resulting from the accumulation of frameshift mutations and premature stop codons, in eight phototransduction genes (arrestins, opsins, ninaC and transient receptor potential channel genes) in 32 subterranean species in contrast to surface species, where these genes have open reading frames. Our results provide strong evidence to support neutral evolutionary processes as a major contributing factor to the loss of phototransduction genes in subterranean animals, with the ultimate fate being the irreversible loss of a light detection system.
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Affiliation(s)
- Barbara L Langille
- Australian Centre for Evolutionary Biology and Biodiversity, Department of Ecology and Evolution, School of Biological Sciences, University of Adelaide, South Australia 5005, Australia.
| | - Simon M Tierney
- Australian Centre for Evolutionary Biology and Biodiversity, Department of Ecology and Evolution, School of Biological Sciences, University of Adelaide, South Australia 5005, Australia; Hawkesbury Institute for the Environment, Western Sydney University, Locked Bag 1797, Penrith, NSW 2751, Australia
| | - Terry Bertozzi
- Australian Centre for Evolutionary Biology and Biodiversity, Department of Ecology and Evolution, School of Biological Sciences, University of Adelaide, South Australia 5005, Australia; Evolutionary Biology Unit, South Australian Museum, North Terrace, Adelaide, South Australia 5000, Australia
| | - Perry G Beasley-Hall
- Australian Centre for Evolutionary Biology and Biodiversity, Department of Ecology and Evolution, School of Biological Sciences, University of Adelaide, South Australia 5005, Australia
| | - Tessa M Bradford
- Australian Centre for Evolutionary Biology and Biodiversity, Department of Ecology and Evolution, School of Biological Sciences, University of Adelaide, South Australia 5005, Australia; Evolutionary Biology Unit, South Australian Museum, North Terrace, Adelaide, South Australia 5000, Australia
| | - Erinn P Fagan-Jeffries
- Australian Centre for Evolutionary Biology and Biodiversity, Department of Ecology and Evolution, School of Biological Sciences, University of Adelaide, South Australia 5005, Australia; Evolutionary Biology Unit, South Australian Museum, North Terrace, Adelaide, South Australia 5000, Australia
| | - Josephine Hyde
- Australian Centre for Evolutionary Biology and Biodiversity, Department of Ecology and Evolution, School of Biological Sciences, University of Adelaide, South Australia 5005, Australia; Western Australia Department of Biodiversity Conservation and Attractions, Kensington, WA 6151, Australia
| | - Remko Leijs
- Evolutionary Biology Unit, South Australian Museum, North Terrace, Adelaide, South Australia 5000, Australia
| | - Matthew Richardson
- Australian Centre for Evolutionary Biology and Biodiversity, Department of Ecology and Evolution, School of Biological Sciences, University of Adelaide, South Australia 5005, Australia
| | - Kathleen M Saint
- Australian Centre for Evolutionary Biology and Biodiversity, Department of Ecology and Evolution, School of Biological Sciences, University of Adelaide, South Australia 5005, Australia; Evolutionary Biology Unit, South Australian Museum, North Terrace, Adelaide, South Australia 5000, Australia
| | - Danielle N Stringer
- Australian Centre for Evolutionary Biology and Biodiversity, Department of Ecology and Evolution, School of Biological Sciences, University of Adelaide, South Australia 5005, Australia; Evolutionary Biology Unit, South Australian Museum, North Terrace, Adelaide, South Australia 5000, Australia
| | - Adrián Villastrigo
- Evolutionary Biology Unit, South Australian Museum, North Terrace, Adelaide, South Australia 5000, Australia; Institute of Evolutionary Biology, Passeig Marítim de la Barceloneta, 37-49, 08003, Spain
| | - William F Humphreys
- Western Australian Museum, Locked Bag 40, Welshpool DC, WA 6986, Australia; School of Animal Biology, University of Western Australia, Nedlands, Western Australia, Australia
| | - Andrew D Austin
- Australian Centre for Evolutionary Biology and Biodiversity, Department of Ecology and Evolution, School of Biological Sciences, University of Adelaide, South Australia 5005, Australia; Evolutionary Biology Unit, South Australian Museum, North Terrace, Adelaide, South Australia 5000, Australia
| | - Steven J B Cooper
- Australian Centre for Evolutionary Biology and Biodiversity, Department of Ecology and Evolution, School of Biological Sciences, University of Adelaide, South Australia 5005, Australia; Evolutionary Biology Unit, South Australian Museum, North Terrace, Adelaide, South Australia 5000, Australia
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16
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Recknagel H, Trontelj P. From Cave Dragons to Genomics: Advancements in the Study of Subterranean Tetrapods. Bioscience 2022; 72:254-266. [PMID: 35241972 PMCID: PMC8888124 DOI: 10.1093/biosci/biab117] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Throughout most of the kingdom Animalia, evolutionary transitions from surface life to a life permanently bound to caves and other subterranean habitats have occurred innumerous times. Not so in tetrapods, where a mere 14 cave-obligate species-all plethodontid and proteid salamanders-are known. We discuss why cave tetrapods are so exceptional and why only salamanders have made the transition. Their evolution follows predictable and convergent, albeit independent pathways. Among the many known changes associated with transitions to subterranean life, eye degeneration, starvation resistance, and longevity are especially relevant to human biomedical research. Recently, sequences of salamander genomes have become available opening up genomic research for cave tetrapods. We discuss new genomic methods that can spur our understanding of the evolutionary mechanisms behind convergent phenotypic change, the relative roles of selective and neutral evolution, cryptic species diversity, and data relevant for conservation such as effective population size and demography.
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Affiliation(s)
- Hans Recknagel
- University of Ljubljana, Slovenia, working, Biotechnical Faculty, Dept. of Biology, Subterranean Biology Lab
| | - Peter Trontelj
- University of Ljubljana, Slovenia, working, Biotechnical Faculty, Dept. of Biology, Subterranean Biology Lab
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17
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Sadier A, Sears KE, Womack M. Unraveling the heritage of lost traits. JOURNAL OF EXPERIMENTAL ZOOLOGY. PART B, MOLECULAR AND DEVELOPMENTAL EVOLUTION 2022; 338:107-118. [PMID: 33528870 DOI: 10.1002/jez.b.23030] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/28/2020] [Revised: 12/22/2020] [Accepted: 01/03/2021] [Indexed: 12/22/2022]
Abstract
We synthesize ontogenetic work spanning the past century that show evolutionarily lost structures are rarely entirely absent from earlier developmental stages. We discuss morphological and genetic insights from developmental studies reveal about the evolution of trait loss and regain.
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Affiliation(s)
- Alexa Sadier
- Department of Ecology and Evolutionary Biology, University of California, Los Angeles, California, USA
| | - Karen E Sears
- Department of Ecology and Evolutionary Biology, University of California, Los Angeles, California, USA
| | - Molly Womack
- Department of Biology, Utah State University, Logan, Utah, USA
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18
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Devos L, Agnès F, Edouard J, Simon V, Legendre L, El Khallouki N, Barbachou S, Sohm F, Rétaux S. Eye morphogenesis in the blind Mexican cavefish. Biol Open 2021; 10:bio059031. [PMID: 34590124 PMCID: PMC8565469 DOI: 10.1242/bio.059031] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2021] [Accepted: 09/24/2021] [Indexed: 01/13/2023] Open
Abstract
The morphogenesis of the vertebrate eye consists of a complex choreography of cell movements, tightly coupled to axial regionalization and cell type specification processes. Disturbances in these events can lead to developmental defects and blindness. Here, we have deciphered the sequence of defective events leading to coloboma in the embryonic eye of the blind cavefish of the species Astyanax mexicanus. Using comparative live imaging on targeted enhancer-trap Zic1:hsp70:GFP reporter lines of both the normal, river-dwelling morph and the cave morph of the species, we identified defects in migratory cell behaviours during evagination that participate in the reduced optic vesicle size in cavefish, without proliferation defect. Further, impaired optic cup invagination shifts the relative position of the lens and contributes to coloboma in cavefish. Based on these results, we propose a developmental scenario to explain the cavefish phenotype and discuss developmental constraints to morphological evolution. The cavefish eye appears as an outstanding natural mutant model to study molecular and cellular processes involved in optic region morphogenesis.
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Affiliation(s)
- Lucie Devos
- Paris-Saclay Institute of Neuroscience, CNRS, Université Paris-Saclay, 91198 Gif sur Yvette, France
| | - François Agnès
- Paris-Saclay Institute of Neuroscience, CNRS, Université Paris-Saclay, 91198 Gif sur Yvette, France
| | - Joanne Edouard
- AMAGEN, CNRS, INRA, Université Paris-Saclay, 91198, Gif sur Yvette, France
| | - Victor Simon
- Paris-Saclay Institute of Neuroscience, CNRS, Université Paris-Saclay, 91198 Gif sur Yvette, France
- AMAGEN, CNRS, INRA, Université Paris-Saclay, 91198, Gif sur Yvette, France
| | - Laurent Legendre
- AMAGEN, CNRS, INRA, Université Paris-Saclay, 91198, Gif sur Yvette, France
| | - Naima El Khallouki
- AMAGEN, CNRS, INRA, Université Paris-Saclay, 91198, Gif sur Yvette, France
| | - Sosthène Barbachou
- AMAGEN, CNRS, INRA, Université Paris-Saclay, 91198, Gif sur Yvette, France
| | - Frédéric Sohm
- AMAGEN, CNRS, INRA, Université Paris-Saclay, 91198, Gif sur Yvette, France
| | - Sylvie Rétaux
- Paris-Saclay Institute of Neuroscience, CNRS, Université Paris-Saclay, 91198 Gif sur Yvette, France
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19
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Kostanjšek R, Diderichsen B, Recknagel H, Gunde-Cimerman N, Gostinčar C, Fan G, Kordiš D, Trontelj P, Jiang H, Bolund L, Luo Y. Toward the massive genome of Proteus anguinus-illuminating longevity, regeneration, convergent evolution, and metabolic disorders. Ann N Y Acad Sci 2021; 1507:5-11. [PMID: 34480358 DOI: 10.1111/nyas.14686] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2021] [Revised: 08/13/2021] [Accepted: 08/17/2021] [Indexed: 12/27/2022]
Abstract
Deciphering the genetic code of organisms with unusual phenotypes can help answer fundamental biological questions and provide insight into mechanisms relevant to human biomedical research. The cave salamander Proteus anguinus (Urodela: Proteidae), also known as the olm, is an example of a species with unique morphological and physiological adaptations to its subterranean environment, including regenerative abilities, resistance to prolonged starvation, and a life span of more than 100 years. However, the structure and sequence of the olm genome is still largely unknown owing to its enormous size, estimated at nearly 50 gigabases. An international Proteus Genome Research Consortium has been formed to decipher the olm genome. This perspective provides the scientific and biomedical rationale for exploring the olm genome and outlines potential outcomes, challenges, and methodological approaches required to analyze and annotate the genome of this unique amphibian.
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Affiliation(s)
- Rok Kostanjšek
- Department of Biology, Biotechnical Faculty, University of Ljubljana, Ljubljana, Slovenia
| | - Børge Diderichsen
- Department of Molecular Biology and Genetics, Aarhus University, Aarhus, Denmark
| | - Hans Recknagel
- Department of Biology, Biotechnical Faculty, University of Ljubljana, Ljubljana, Slovenia
| | - Nina Gunde-Cimerman
- Department of Biology, Biotechnical Faculty, University of Ljubljana, Ljubljana, Slovenia
| | - Cene Gostinčar
- Department of Biology, Biotechnical Faculty, University of Ljubljana, Ljubljana, Slovenia.,Lars Bolund Institute of Regenerative Medicine, Qingdao-Europe Advanced Institute for Life Sciences, BGI-Qingdao, BGI-Shenzhen, Qingdao, China
| | - Guangyi Fan
- Lars Bolund Institute of Regenerative Medicine, Qingdao-Europe Advanced Institute for Life Sciences, BGI-Qingdao, BGI-Shenzhen, Qingdao, China
| | - Dušan Kordiš
- Department of Molecular and Biomedical Sciences, Jožef Stefan Institute, Ljubljana, Slovenia
| | - Peter Trontelj
- Department of Biology, Biotechnical Faculty, University of Ljubljana, Ljubljana, Slovenia
| | | | - Lars Bolund
- Lars Bolund Institute of Regenerative Medicine, Qingdao-Europe Advanced Institute for Life Sciences, BGI-Qingdao, BGI-Shenzhen, Qingdao, China.,Department of Biomedicine, Aarhus University, Aarhus, Denmark
| | - Yonglun Luo
- Lars Bolund Institute of Regenerative Medicine, Qingdao-Europe Advanced Institute for Life Sciences, BGI-Qingdao, BGI-Shenzhen, Qingdao, China.,Department of Biomedicine, Aarhus University, Aarhus, Denmark.,Steno Diabetes Center Aarhus, Aarhus University Hospital, Aarhus, Denmark
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20
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Tovar RU, Cantu V, Fremaux B, Gonzalez Jr P, Spikes A, García DM. Comparative development and ocular histology between epigean and subterranean salamanders ( Eurycea) from central Texas. PeerJ 2021; 9:e11840. [PMID: 34395082 PMCID: PMC8325428 DOI: 10.7717/peerj.11840] [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: 10/20/2018] [Accepted: 07/01/2021] [Indexed: 11/24/2022] Open
Abstract
The salamander clade Eurycea from the karst regions of central Texas provides an ideal platform for comparing divergent nervous and sensory systems since some species exhibit extreme phenotypes thought to be associated with inhabiting a subterranean environment, including highly reduced eyes, while others retain an ancestral ocular phenotype appropriate for life above ground. We describe ocular morphology, comparing three salamander species representing two phenotypes-the surface-dwelling Barton Springs salamander (E. sosorum) and San Marcos salamander (E. nana) and the obligate subterranean Texas blind salamander (E. rathbuni) - in terms of structure and size of their eyes. Eyes were examined using confocal microscopy and measurements were made using ImageJ. Statistical analysis of data was carried out using R. We also provide a developmental series and track eye development and immunolocalization of Pax6 in E. sosorum and E. rathbuni. Adult histology of the surface-dwelling San Marcos salamander (E. nana) shows similarities to E. sosorum. The eyes of adults of the epigean species E. nana and E. sosorum appear fully developed with all the histological features of a fully functional eye. In contrast, the eyes of E. rathbuni adults have fewer layers, lack lenses and other features associated with vision as has been reported previously. However, in early developmental stages eye morphology did not differ significantly between E. rathbuni and E. sosorum. Parallel development is observed between the two phenotypes in terms of morphology; however, Pax6 labeling seems to decrease in the latter stages of development in E.rathbuni. We test for immunolabeling of the visual pigment proteins opsin and rhodopsin and observe immunolocalization around photoreceptor disks in E. nana and E. sosorum, but not in the subterranean E. rathbuni. Our results from examining developing salamanders suggest a combination of underdevelopment and degeneration contribute to the reduced eyes of adult E. rathbuni.
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Affiliation(s)
- Ruben U. Tovar
- Department of Biology, Texas State University, San Marcos, TX, United States of America
- Department of Integrative Biology, University of Texas at Austin, Austin, TX, United States of America
| | - Valentin Cantu
- San Marcos Aquatic Resources Center, U.S. Fish and Wildlife Service, San Marcos, TX, United States of America
- Uvalde National Fish Hatchery, U.S. Fish and Wildlife Service, Uvalde, TX, United States of America
| | - Brian Fremaux
- Department of Biology, Texas State University, San Marcos, TX, United States of America
| | - Pedro Gonzalez Jr
- Department of Biology, Texas State University, San Marcos, TX, United States of America
| | - Amanda Spikes
- Department of Biology, Texas State University, San Marcos, TX, United States of America
| | - Dana M. García
- Department of Biology, Texas State University, San Marcos, TX, United States of America
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21
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Schrader L, Pan H, Bollazzi M, Schiøtt M, Larabee FJ, Bi X, Deng Y, Zhang G, Boomsma JJ, Rabeling C. Relaxed selection underlies genome erosion in socially parasitic ant species. Nat Commun 2021; 12:2918. [PMID: 34006882 PMCID: PMC8131649 DOI: 10.1038/s41467-021-23178-w] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2020] [Accepted: 04/06/2021] [Indexed: 02/03/2023] Open
Abstract
Inquiline ants are highly specialized and obligate social parasites that infiltrate and exploit colonies of closely related species. They have evolved many times convergently, are often evolutionarily young lineages, and are almost invariably rare. Focusing on the leaf-cutting ant genus Acromyrmex, we compared genomes of three inquiline social parasites with their free-living, closely-related hosts. The social parasite genomes show distinct signatures of erosion compared to the host lineages, as a consequence of relaxed selective constraints on traits associated with cooperative ant colony life and of inquilines having very small effective population sizes. We find parallel gene losses, particularly in olfactory receptors, consistent with inquiline species having highly reduced social behavioral repertoires. Many of the genomic changes that we uncover resemble those observed in the genomes of obligate non-social parasites and intracellular endosymbionts that branched off into highly specialized, host-dependent niches.
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Affiliation(s)
- Lukas Schrader
- Centre for Social Evolution, Department of Biology, University of Copenhagen, Copenhagen, Denmark.
- Institute for Evolution and Biodiversity, University of Münster, Münster, Germany.
| | | | - Martin Bollazzi
- Entomología, Facultad de Agronomía, Universidad de la República, Montevideo, Uruguay
| | - Morten Schiøtt
- Centre for Social Evolution, Department of Biology, University of Copenhagen, Copenhagen, Denmark
| | - Fredrick J Larabee
- Department of Entomology, National Museum of Natural History, Smithsonian Institution, Washington, DC, USA
| | | | | | - Guojie Zhang
- Centre for Social Evolution, Department of Biology, University of Copenhagen, Copenhagen, Denmark
- BGI-Shenzhen, Shenzhen, China
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, China
| | - Jacobus J Boomsma
- Centre for Social Evolution, Department of Biology, University of Copenhagen, Copenhagen, Denmark.
| | - Christian Rabeling
- Department of Biology, University of Rochester, Rochester, NY, USA.
- School of Life Sciences, Arizona State University, Tempe, AZ, USA.
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22
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Feng S, Chen QH, Guo ZL. Integrative taxonomy uncovers a new stygobiotic Caridina species (Decapoda, Caridea, Atyidae) from Guizhou Province, China. Zookeys 2021; 1028:29-47. [PMID: 33883966 PMCID: PMC8041733 DOI: 10.3897/zookeys.1028.63822] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2021] [Accepted: 03/06/2021] [Indexed: 11/22/2022] Open
Abstract
Collecting much-needed information on the taxonomy, distribution, and ecology of cave-dwelling shrimp is vital for addressing the urgent challenges in conservation biodiversity in fragile cave ecosystems. Caridinaincolorsp. nov., a new atyid shrimp from an underground stream of Yaoshui Cave, Daqikong scenic area, Libo County, Guizhou Province, southwestern China is described based on morphology and DNA analysis (mitochondrial COI). Caridinaincolorsp. nov. differs from epigean congeners by its smaller eyes which range from reduced to completely blind; colorless body and appendages; long stylocerite and sixth abdominal segment; and relatively large eggs. In comparison to other cave species, Caridinaincolorsp. nov. presents a long rostrum and stylocerite; slender sixth abdominal segment; and unique shape of the appendix masculina. Data on the habitat, ecology, and levels of threat are provided and suggest that it should be categorized as Critically Endangered (CR) under the current IUCN criteria.
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Affiliation(s)
- Shuo Feng
- Department of Animal Science, School of Life Science and Engineering, Foshan University, Nanhai 528231, Guangdong Province, China Foshan University Nanhai China
| | - Qing-Hua Chen
- Department of Animal Science, School of Life Science and Engineering, Foshan University, Nanhai 528231, Guangdong Province, China Foshan University Nanhai China
| | - Zhao-Liang Guo
- Department of Animal Science, School of Life Science and Engineering, Foshan University, Nanhai 528231, Guangdong Province, China Foshan University Nanhai China
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He Y, Chen Y, Yang J, Page LM. Phylogenetic analysis and osteological comparison of the cave-dwelling spined loach, Bibarba parvoculus (Cypriniformes: Cobitidae), and its surface congener. Zool J Linn Soc 2021. [DOI: 10.1093/zoolinnean/zlaa073] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Abstract
Abstract
Bibarba parvoculus, a depigmented and small-eyed, spined loach, is endemic to a karst cave in southern China. Both mitochondrial Cytb and nuclear RAG1 gene analyses indicate that B. parvoculus and its only surface congener, B. bibarba, form the basal-most lineage in the so-called Northern Clade of Cobitidae. Genetic divergence for Cytb is 10.3 % between B. parvoculus and B. bibarba. A duplication of the lamina circularis on the second and third pectoral rays occurs in male Bibarba species. The osteology of the two species is illustrated and compared using X-ray microtomography. Bibarba parvoculus has higher vertebral counts, a broader anterior part of the frontal bone at the orbital region and decreased sexual dimorphism when compared with B. bibarba. The coracoid, mesocoracoid and scapula are stouter in males of both species, but the three bones are autogenous in B. parvoculus, while fused with the cleithrum in B. bibarba. Specific differentiation of B. parvoculus is corroborated by both molecular and morphological evidence. The split between the two species is estimated to have occurred in the Early Miocene.
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Affiliation(s)
- You He
- Shanghai Synchrotron Radiation Facility, Shanghai Advanced Research Institute, Chinese Academy of Sciences, Shanghai, China
| | - Yongxia Chen
- Life School, Heibei University, Baoding, Hebei, China
| | - Jian Yang
- Key Laboratory of Beibu Gulf Environment Change and Resources Use, Nanning Normal University, Nanning, Guangxi, China
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Reduced Oxygen as an Environmental Pressure in the Evolution of the Blind Mexican Cavefish. DIVERSITY 2021. [DOI: 10.3390/d13010026] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Extreme environmental features can drive the evolution of extreme phenotypes. Over the course of evolution, certain environmental changes may be so drastic that they lead to extinction. Conversely, if an organism adapts to harsh environmental changes, the adaptations may permit expansion of a novel niche. The interaction between environmental stressors and adaptive changes is well-illustrated by the blind Mexican cavefish, Astyanaxmexicanus, which has recurrently adapted to the stark subterranean environment. The transition from terrestrial rivers and streams (occupied by extant surface morphs of the same species) to the cave has been accompanied by the resorption of eyes, diminished pigmentation and reduced metabolism in cave-dwelling morphs. The principal features of caves most often associated with evolution of these common cave features are the absence of light and limited nutrition. However, a putatively essential cave feature that has received less attention is the frequently low concentration of oxygen within natural karst environments. Here, we review the potential role of limited oxygen as a critical environmental feature of caves in the Sierra de El Abra. Additionally, we review evidence that Astyanax cavefish may have evolved adaptive features enabling them to thrive in lower oxygen compared to their surface-dwelling counterparts.
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Balogh A, Ngo L, Zigler KS, Dixon G. Population genomics in two cave-obligate invertebrates confirms extremely limited dispersal between caves. Sci Rep 2020; 10:17554. [PMID: 33067497 PMCID: PMC7568537 DOI: 10.1038/s41598-020-74508-9] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2020] [Accepted: 09/28/2020] [Indexed: 11/21/2022] Open
Abstract
Caves offer selective pressures that are distinct from the surface. Organisms that have evolved to exist under these pressures typically exhibit a suite of convergent characteristics, including a loss or reduction of eyes and pigmentation. As a result, cave-obligate taxa, termed troglobionts, are no longer viable on the surface. This circumstance has led to an understanding of highly constrained dispersal capabilities, and the prediction that, in the absence of subterranean connections, extreme genetic divergence between cave populations. An effective test of this model would involve (1) common troglobionts from (2) nearby caves in a cave-dense region, (3) good sample sizes per cave, (4) multiple taxa, and (5) genome-wide characterization. With these criteria in mind, we used RAD-seq to genotype an average of ten individuals of the troglobiotic spider Nesticus barri and the troglobiotic beetle Ptomaphagus hatchi, each from four closely located caves (ranging from 3 to 13 km apart) in the cave-rich southern Cumberland Plateau of Tennessee, USA. Consistent with the hypothesis of highly restricted dispersal, we find that populations from separate caves are indeed highly genetically isolated. Our results support the idea of caves as natural laboratories for the study of parallel evolutionary processes.
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Affiliation(s)
- Andras Balogh
- Department of Integrative Biology, University of Texas, PAT Building Room 427, 2401 Speedway, Austin, TX, USA
| | - Lam Ngo
- Department of Biology, University of the South, Sewanee, TN, USA
| | - Kirk S Zigler
- Department of Biology, University of the South, Sewanee, TN, USA
| | - Groves Dixon
- Department of Integrative Biology, University of Texas, PAT Building Room 427, 2401 Speedway, Austin, TX, USA.
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Diversity of Olfactory Responses and Skills in Astyanax Mexicanus Cavefish Populations Inhabiting different Caves. DIVERSITY 2020. [DOI: 10.3390/d12100395] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
Animals in many phyla are adapted to and thrive in the constant darkness of subterranean environments. To do so, cave animals have presumably evolved mechano- and chemosensory compensations to the loss of vision, as is the case for the blind characiform cavefish, Astyanax mexicanus. Here, we systematically assessed the olfactory capacities of cavefish and surface fish of this species in the lab as well as in the wild, in five different caves in northeastern Mexico, using an olfactory setup specially developed to test and record olfactory responses during fieldwork. Overall cavefish showed lower (i.e., better) olfactory detection thresholds than surface fish. However, wild adult cavefish from the Pachón, Sabinos, Tinaja, Chica and Subterráneo caves showed highly variable responses to the three different odorant molecules they were exposed to. Pachón and Subterráneo cavefish showed the highest olfactory capacities, and Chica cavefish showed no response to the odors presented. We discuss these data with regard to the environmental conditions in which these different cavefish populations live. Our experiments in natural settings document the diversity of cave environments inhabited by a single species of cavefish, A. mexicanus, and highlight the complexity of the plastic and genetic mechanisms that underlie cave adaptation.
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Lunghi E, Zhao Y. Do Chinese cavefish show intraspecific variability in morphological traits? Ecol Evol 2020; 10:7723-7730. [PMID: 32760559 PMCID: PMC7391565 DOI: 10.1002/ece3.6495] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2019] [Revised: 04/30/2020] [Accepted: 05/28/2020] [Indexed: 11/18/2022] Open
Abstract
Cavefishes represent one of the most bizarre and intriguing life forms inhabiting groundwater environments. One-third of the known cavefishes worldwide is endemic to China, and almost half of those belongs to a single genus, Sinocyclocheilus (Cypriniformes: Cyprinidae). Analyzing the morphometrics of three Sinocyclocheilus species, we aimed to assess whether variability among conspecific populations exists. We predict that populations inhabiting different subterranean habitats (shallow vs. deep) show divergences in specific morphological traits to better cope with the local ecological conditions. Our results showed that the populations showing bigger eyes and reduced humpback were those occurring close to the cave entrance (habitats with light and high food availability), while specimens with smaller eyes and increased humpback were collected from deeper groundwater areas (habitats laying in darkness with food scarcity). This explorative study paves the way for further researches aiming to collect novel data on Chinese cavefishes and highlights the usefulness of these species in evolutionary studies.
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Affiliation(s)
- Enrico Lunghi
- Key Laboratory of the Zoological Systematics and EvolutionInstitute of ZoologyChinese Academy of SciencesBeijingChina
- Museo di Storia Naturale dell'Università degli Studi di FirenzeMuseo “La Specola”FirenzeItalia
| | - Yahui Zhao
- Key Laboratory of the Zoological Systematics and EvolutionInstitute of ZoologyChinese Academy of SciencesBeijingChina
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28
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Exploration of space to achieve scientific breakthroughs. Biotechnol Adv 2020; 43:107572. [PMID: 32540473 DOI: 10.1016/j.biotechadv.2020.107572] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2020] [Revised: 05/05/2020] [Accepted: 05/29/2020] [Indexed: 12/13/2022]
Abstract
Living organisms adapt to changing environments using their amazing flexibility to remodel themselves by a process called evolution. Environmental stress causes selective pressure and is associated with genetic and phenotypic shifts for better modifications, maintenance, and functioning of organismal systems. The natural evolution process can be used in complement to rational strain engineering for the development of desired traits or phenotypes as well as for the production of novel biomaterials through the imposition of one or more selective pressures. Space provides a unique environment of stressors (e.g., weightlessness and high radiation) that organisms have never experienced on Earth. Cells in the outer space reorganize and develop or activate a range of molecular responses that lead to changes in cellular properties. Exposure of cells to the outer space will lead to the development of novel variants more efficiently than on Earth. For instance, natural crop varieties can be generated with higher nutrition value, yield, and improved features, such as resistance against high and low temperatures, salt stress, and microbial and pest attacks. The review summarizes the literature on the parameters of outer space that affect the growth and behavior of cells and organisms as well as complex colloidal systems. We illustrate an understanding of gravity-related basic biological mechanisms and enlighten the possibility to explore the outer space environment for application-oriented aspects. This will stimulate biological research in the pursuit of innovative approaches for the future of agriculture and health on Earth.
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Abstract
The discipline of subterranean biology has provided us incredible information on the diversity, ecology and evolution of species living in different typologies of subterranean habitats. However, a general lack of information on the relationships between cave species still exists, leaving uncertainty regarding the dynamics that hold together cave communities and the roles of specific organisms (from the least to the most adapted species) for the community, as well as the entire ecosystem. This Special Issue aims to stimulate and gather studies which are focusing on cave communities belonging to all different typologies of subterranean habitats, with the overarching goal to corroborate the key role of the subterranean biology in ecological and evolutionary studies.
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Karaoglan M, Er HC, Aytaç EH, Keskin M. The trade-off between the olfactory bulb and eyeball volume in precocious puberty. J Pediatr Endocrinol Metab 2020; 33:271-277. [PMID: 31926097 DOI: 10.1515/jpem-2019-0450] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/29/2019] [Accepted: 11/15/2019] [Indexed: 11/15/2022]
Abstract
Background The olfactory bulb (OB) and eyeball size change depending on age and puberty. There is a well-established trade-off between sensory structures of the brain such as the eye and the olfactory bulb that depend on environmental circumstances in the evolutionary history of animals. The aim of this study was to developmentally investigate the potential reciprocal changes between OB and eyeball volumes (EV) in girls with precocious puberty (PP). Methods A total of 148 girls aged between 5 and 8 years (63 PP, 85 healthy) were included in the study. Exclusion criteria: Cases of anosmia/hyposmia, neurodegenerative disorder, refractive errors and trauma. The pituitary height (PH), EV and OB volumes were measured on segmentation of a magnetic resonance image (MRI) slice using manual countering. The corrected measurements by body surface were used in all statistical analyses. Results In girls with PP, the means of the OB volume and PH were larger (71.11 ± 20.64 mL) and higher (4.62 ± 1.18 mm), respectively, while the mean of EVs was smaller (11.24 ± 2.62 cm3) (p = 0.000). Cut-off values were 62.27 mL, 10.7 cm3 and 4.71 mm for OB volume, EV and PH, respectively. While negative correlations were found between OB volume-EV and EV-PH (r63 = -0.224, p = 0.001 and r63 = -0.116, p = 0.001, respectively), OB volume was positively correlated with PH (r63 = 0.578, p = 0.001). Conclusions The present study demonstrates that girls with PP have significantly larger OB volume, but smaller EV, and there is negative correlation between the two structures. These results indicate that there is trade-off between anatomical dimensions of OB and eyeball in favor of OB in PP girls.
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Affiliation(s)
- Murat Karaoglan
- Department of Pediatric Endocrinology, Gaziantep University Faculty of Medicine, 27070 Gaziantep, Turkey
| | - Hale Colakoğlu Er
- Department of Radiology, Gaziantep University Faculty of Medicine, Gaziantep, Turkey
| | - Emel Hatun Aytaç
- Department of Pediatric Endocrinology, Gaziantep University Faculty of Medicine, 27070 Gaziantep, Turkey
| | - Mehmet Keskin
- Department of Pediatric Endocrinology, Gaziantep University Faculty of Medicine, 27070 Gaziantep, Turkey
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Zhao Q, Zhang R, Xiao Y, Niu Y, Shao F, Li Y, Peng Z. Comparative Transcriptome Profiling of the Loaches Triplophysa bleekeri and Triplophysa rosa Reveals Potential Mechanisms of Eye Degeneration. Front Genet 2020; 10:1334. [PMID: 32010191 PMCID: PMC6977438 DOI: 10.3389/fgene.2019.01334] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2019] [Accepted: 12/06/2019] [Indexed: 12/30/2022] Open
Abstract
Eye degeneration is one of the most obvious characteristics of organisms restricted to subterranean habitats. In cavefish, eye degeneration has evolved independently numerous times and each process is associated with different genetic mechanisms. To gain a better understanding of these mechanisms, we compared the eyes of adult individuals of the cave loach Triplophysa rosa and surface loach Triplophysa bleekeri. Compared with the normal eyes of the surface loach, those of the cave loach were found to possess a small abnormal lens and a defective retina containing photoreceptor cells that lack outer segments. Sequencing of the transcriptomes of both species to identify differentially expressed genes (DEGs) and genes under positive selection revealed 4,802 DEGs and 50 genes under positive selection (dN/dS > 1, FDR < 0.1). For cave loaches, we identified one Gene Ontology category related to vision that was significantly enriched in downregulated genes. Specifically, we found that many of the downregulated genes, including pitx3, lim2, crx, gnat2, rx1, rho, prph2, and β|γ-crystallin are associated with lens/retinal development and maintenance. However, compared with those in the surface loach, the lower dS rates but higher dN rates of the protein-coding sequences in T. rosa indicate that changes in amino acid sequences might be involved in the adaptation and visual degeneration of cave loaches. We also found that genes associated with light perception and light-stimulated vision have evolved at higher rates (some genes dN/dS > 1 but FDR > 0.1). Collectively, the findings of this study indicate that the degradation of cavefish vision is probably associated with both gene expression and amino acid changes and provide new insights into the mechanisms underlying the degeneration of cavefish eyes.
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Affiliation(s)
- Qingyuan Zhao
- Key Laboratory of Freshwater Fish Reproduction and Development (Ministry of Education), Southwest University School of Life Sciences, Chongqing, China
| | - Renyi Zhang
- School of Life Sciences, Guizhou Normal University, Guiyang, China
| | - Yingqi Xiao
- Key Laboratory of Freshwater Fish Reproduction and Development (Ministry of Education), Southwest University School of Life Sciences, Chongqing, China
| | - Yabing Niu
- Key Laboratory of Freshwater Fish Reproduction and Development (Ministry of Education), Southwest University School of Life Sciences, Chongqing, China
| | - Feng Shao
- Key Laboratory of Freshwater Fish Reproduction and Development (Ministry of Education), Southwest University School of Life Sciences, Chongqing, China
| | - Yanping Li
- Key Laboratory of Freshwater Fish Reproduction and Development (Ministry of Education), Southwest University School of Life Sciences, Chongqing, China
| | - Zuogang Peng
- Key Laboratory of Freshwater Fish Reproduction and Development (Ministry of Education), Southwest University School of Life Sciences, Chongqing, China
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Huntsman BM, Venarsky MP, Abadi F, Huryn AD, Kuhajda BR, Cox CL, Benstead JP. Evolutionary history and sex are significant drivers of crayfish demography in resource-limited cave ecosystems. Evol Ecol 2019. [DOI: 10.1007/s10682-019-10029-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
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Jossart Q, Terrana L, De Ridder C, Eeckhaut I, Monteyne D, Caulier G. To see or to smell: the role of vision in host-recognition by an ectoparasitic crab. Symbiosis 2019. [DOI: 10.1007/s13199-019-00657-9] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
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Sumner-Rooney L, Kenny NJ, Ahmed F, Williams ST. The utility of micro-computed tomography for the non-destructive study of eye microstructure in snails. Sci Rep 2019; 9:15411. [PMID: 31659206 PMCID: PMC6817935 DOI: 10.1038/s41598-019-51909-z] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2019] [Accepted: 10/09/2019] [Indexed: 02/02/2023] Open
Abstract
Molluscan eyes exhibit an enormous range of morphological variation, ranging from tiny pigment-cup eyes in limpets, compound eyes in ark clams and pinhole eyes in Nautilus, through to concave mirror eyes in scallops and the large camera-type eyes of the more derived cephalopods. Here we assess the potential of non-destructive micro-computed tomography (µ-CT) for investigating the anatomy of molluscan eyes in three species of the family Solariellidae, a group of small, deep-sea gastropods. We compare our results directly with those from traditional histological methods applied to the same specimens, and show not only that eye microstructure can be visualised in sufficient detail for meaningful comparison even in very small animals, but also that μ-CT can provide additional insight into gross neuroanatomy without damaging rare and precious specimens. Data from μ-CT scans also show that neurological innervation of eyes is reduced in dark-adapted snails when compared with the innervation of cephalic tentacles, which are involved in mechanoreception and possibly chemoreception. Molecular tests also show that the use of µ-CT and phosphotungstic acid stain do not prevent successful downstream DNA extraction, PCR amplification or sequencing. The use of µ-CT methods is therefore highly recommended for the investigation of difficult-to-collect or unique specimens.
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Affiliation(s)
| | | | - Farah Ahmed
- Natural History Museum, Cromwell Road, London, UK
- Exponent International Ltd, London, UK
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35
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Makhrov AA. Decreased Evolutionary Plasticity as a Result of Phylogenetic Immobilization and Its Ecological Significance. CONTEMP PROBL ECOL+ 2019. [DOI: 10.1134/s199542551905007x] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
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36
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Evolution of acoustic communication in blind cavefish. Nat Commun 2019; 10:4231. [PMID: 31530801 PMCID: PMC6748933 DOI: 10.1038/s41467-019-12078-9] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2018] [Accepted: 08/13/2019] [Indexed: 12/31/2022] Open
Abstract
Acoustic communication allows the exchange of information within specific contexts and during specific behaviors. The blind, cave-adapted and the sighted, river-dwelling morphs of the species Astyanax mexicanus have evolved in markedly different environments. During their evolution in darkness, cavefish underwent a series of morphological, physiological and behavioral changes, allowing the study of adaptation to drastic environmental change. Here we discover that Astyanax is a sonic species, in the laboratory and in the wild, with sound production depending on the social contexts and the type of morph. We characterize one sound, the "Sharp Click", as a visually-triggered sound produced by dominant surface fish during agonistic behaviors and as a chemosensory-, food odor-triggered sound produced by cavefish during foraging. Sharp Clicks also elicit different reactions in the two morphs in play-back experiments. Our results demonstrate that acoustic communication does exist and has evolved in cavefish, accompanying the evolution of its behaviors.
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Ramaekers A, Claeys A, Kapun M, Mouchel-Vielh E, Potier D, Weinberger S, Grillenzoni N, Dardalhon-Cuménal D, Yan J, Wolf R, Flatt T, Buchner E, Hassan BA. Altering the Temporal Regulation of One Transcription Factor Drives Evolutionary Trade-Offs between Head Sensory Organs. Dev Cell 2019; 50:780-792.e7. [PMID: 31447264 DOI: 10.1016/j.devcel.2019.07.027] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2018] [Revised: 04/24/2019] [Accepted: 07/25/2019] [Indexed: 12/30/2022]
Abstract
Size trade-offs of visual versus olfactory organs is a pervasive feature of animal evolution. This could result from genetic or functional constraints. We demonstrate that head sensory organ size trade-offs in Drosophila are genetically encoded and arise through differential subdivision of the head primordium into visual versus non-visual fields. We discover that changes in the temporal regulation of the highly conserved eyeless/Pax6 gene expression during development is a conserved mechanism for sensory trade-offs within and between Drosophila species. We identify a natural single nucleotide polymorphism in the cis-regulatory region of eyeless in a binding site of its repressor Cut that is sufficient to alter its temporal regulation and eye size. Because eyeless/Pax6 is a conserved regulator of head sensory placode subdivision, we propose that its temporal regulation is key to define the relative size of head sensory organs.
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Affiliation(s)
- Ariane Ramaekers
- Institut du Cerveau et de la Moelle Epinière (ICM) - Hôpital Pitié-Salpêtrière, Sorbonne Université, Inserm, CNRS, Paris, France.
| | - Annelies Claeys
- VIB Center for Brain and Disease, VIB, Leuven, Belgium; Center for Human Genetics, University of Leuven School of Medicine, Leuven, Belgium
| | - Martin Kapun
- Department of Biology, University of Fribourg, Fribourg, Switzerland
| | - Emmanuèle Mouchel-Vielh
- Sorbonne Université, CNRS, Laboratoire de Biologie du Développement, Institut de Biologie Paris Seine, LBD-IBPS), Paris, France
| | - Delphine Potier
- Aix-Marseille Université, CNRS, INSERM, CIML, Marseille, France
| | - Simon Weinberger
- VIB Center for Brain and Disease, VIB, Leuven, Belgium; Center for Human Genetics, University of Leuven School of Medicine, Leuven, Belgium
| | - Nicola Grillenzoni
- Institut du Cerveau et de la Moelle Epinière (ICM) - Hôpital Pitié-Salpêtrière, Sorbonne Université, Inserm, CNRS, Paris, France
| | - Delphine Dardalhon-Cuménal
- Sorbonne Université, CNRS, Laboratoire de Biologie du Développement, Institut de Biologie Paris Seine, LBD-IBPS), Paris, France
| | - Jiekun Yan
- VIB Center for Brain and Disease, VIB, Leuven, Belgium; Center for Human Genetics, University of Leuven School of Medicine, Leuven, Belgium
| | - Reinhard Wolf
- Rudolf Virchow Center for Experimental Biomedicine, University of Würzburg, Würzburg, Germany
| | - Thomas Flatt
- Department of Biology, University of Fribourg, Fribourg, Switzerland
| | - Erich Buchner
- Institute for Clinical Neurobiology, University Hospital Würzburg, Würzburg, Germany
| | - Bassem A Hassan
- Institut du Cerveau et de la Moelle Epinière (ICM) - Hôpital Pitié-Salpêtrière, Sorbonne Université, Inserm, CNRS, Paris, France.
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Torres-Paz J, Hyacinthe C, Pierre C, Rétaux S. Towards an integrated approach to understand Mexican cavefish evolution. Biol Lett 2019; 14:rsbl.2018.0101. [PMID: 30089659 DOI: 10.1098/rsbl.2018.0101] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2018] [Accepted: 07/16/2018] [Indexed: 12/14/2022] Open
Abstract
The Mexican tetra, Astyanax mexicanus, comes in two forms: a classical river-dwelling fish and a blind and depigmented cave-dwelling fish. The two morphotypes are used as models for evolutionary biology, to decipher mechanisms of morphological and behavioural evolution in response to environmental change. Over the past 40 years, insights have been obtained from genetics, developmental biology, physiology and metabolism, neuroscience, genomics, population biology and ecology. Here, we promote the idea that A. mexicanus, as a model, has reached a stage where an integrated approach or a multi-disciplinary method of analysis, whereby a phenomenon is examined from several angles, is a powerful tool that can be applied to understand general evolutionary processes. Mexican cavefish have undergone considerable selective pressure and extreme morphological evolution, an obvious advantage to contribute to our understanding of evolution through comparative analyses and to pinpoint the specific traits that may have helped their ancestors to colonize caves.
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Affiliation(s)
- Jorge Torres-Paz
- Paris-Saclay Institute of Neuroscience, CNRS UMR9197, Université Paris-Sud, Université Paris-Saclay, Avenue de la terrasse, 91198 Gif-sur-Yvette, France
| | - Carole Hyacinthe
- Paris-Saclay Institute of Neuroscience, CNRS UMR9197, Université Paris-Sud, Université Paris-Saclay, Avenue de la terrasse, 91198 Gif-sur-Yvette, France
| | - Constance Pierre
- Paris-Saclay Institute of Neuroscience, CNRS UMR9197, Université Paris-Sud, Université Paris-Saclay, Avenue de la terrasse, 91198 Gif-sur-Yvette, France
| | - Sylvie Rétaux
- Paris-Saclay Institute of Neuroscience, CNRS UMR9197, Université Paris-Sud, Université Paris-Saclay, Avenue de la terrasse, 91198 Gif-sur-Yvette, France
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Canino-Koning R, Wiser MJ, Ofria C. Fluctuating environments select for short-term phenotypic variation leading to long-term exploration. PLoS Comput Biol 2019; 15:e1006445. [PMID: 31002665 PMCID: PMC6474582 DOI: 10.1371/journal.pcbi.1006445] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2018] [Accepted: 01/15/2019] [Indexed: 11/19/2022] Open
Abstract
Genetic spaces are often described in terms of fitness landscapes or genotype-to-phenotype maps, where each genetic sequence is associated with phenotypic properties and linked to other genotypes that are a single mutational step away. The positions close to a genotype make up its "mutational landscape" and, in aggregate, determine the short-term evolutionary potential of a population. Populations with wider ranges of phenotypes in their mutational neighborhood are known to be more evolvable. Likewise, those with fewer phenotypic changes available in their local neighborhoods are more mutationally robust. Here, we examine whether forces that change the distribution of phenotypes available by mutation profoundly alter subsequent evolutionary dynamics. We compare evolved populations of digital organisms that were subject to either static or cyclically-changing environments. For each of these, we examine diversity of the phenotypes that are produced through mutations in order to characterize the local genotype-phenotype map. We demonstrate that environmental change can push populations toward more evolvable mutational landscapes where many alternate phenotypes are available, though purely deleterious mutations remain suppressed. Further, we show that populations in environments with harsh changes switch phenotypes more readily than those in environments with more benign changes. We trace this effect to repeated population bottlenecks in the harsh environments, which result in shorter coalescence times and keep populations in regions of the mutational landscape where the phenotypic shifts in question are more likely to occur. Typically, static environments select solely for immediate optimization, at the expensive of long-term evolvability. In contrast, we show that with changing environments, short-term pressures to deal with immediate challenges can align with long-term pressures to explore a more productive portion of the mutational landscape.
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Affiliation(s)
- Rosangela Canino-Koning
- Department of Computer Science and Engineering, Michigan State University, East Lansing, MI, USA
- BEACON Center for the Study of Evolution in Action, Michigan State University, East Lansing, MI, USA
- Ecology, Evolutionary Biology, and Behavior, Michigan State University, East Lansing, MI, USA
| | - Michael J. Wiser
- BEACON Center for the Study of Evolution in Action, Michigan State University, East Lansing, MI, USA
- Ecology, Evolutionary Biology, and Behavior, Michigan State University, East Lansing, MI, USA
| | - Charles Ofria
- Department of Computer Science and Engineering, Michigan State University, East Lansing, MI, USA
- BEACON Center for the Study of Evolution in Action, Michigan State University, East Lansing, MI, USA
- Ecology, Evolutionary Biology, and Behavior, Michigan State University, East Lansing, MI, USA
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Sumner-Rooney L. The Kingdom of the Blind: Disentangling Fundamental Drivers in the Evolution of Eye Loss. Integr Comp Biol 2019; 58:372-385. [PMID: 29873729 DOI: 10.1093/icb/icy047] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
Abstract
Light is a fundamentally important biological cue used by almost every animal on earth, to maintain daily rhythms, navigate, forage, find mates, or avoid predators. But an enormous number of species live in darkness: in subterranean caves, deep oceans, underground burrows, and within parasitic host bodies, and the loss of eyes appears consistently across these ecosystems. However, the evolutionary mechanisms that lead to the reduction of the visual system remain the subject of great interest and debate more than 150 years after Darwin tackled the issue. Studies of model taxa have discovered significant roles for natural selection, neutral evolution, and pleiotropy, but the interplay between them remains unclear. To nail down unifying concepts surrounding the evolution of eye loss, we must embrace the enormous range of affected animals and habitats. The fine developmental details of model systems such as the Mexican cave tetra Astyanax mexicanus have transformed and enriched the field, but these should be complemented by wider studies to identify truly overarching patterns that apply throughout animals. Here, the major evolutionary drivers are placed within a conceptual cost-benefit framework that incorporates the fundamental constraints and forces that influence evolution in the dark. Major physiological, ecological, and environmental factors are considered within the context of this framework, which appears faithful to observed patterns in deep-sea and cavernicolous animals. To test evolutionary hypotheses, a comparative phylogenetic approach is recommended, with the goal of studying large groups exhibiting repeated reduction, and then comparing these across habitats, taxa, and lifestyles. Currently, developmental and physiological methods cannot feasibly be used on such large scales, but penetrative imaging techniques could provide detailed morphological data non-invasively and economically for large numbers of species. Comprehensive structural datasets can then be contextualized phylogenetically to examine recurrent trends and associations, and to reconstruct character histories through multiple independent transitions into darkness. By assessing these evolutionary trajectories within an energetic cost-benefit framework, the relationships between fundamental influences can be inferred and compared across different biological and physical parameters. However, substantial numbers of biological and environmental factors affect the evolutionary trajectory of loss, and it is critical that researchers make fair and reasonable comparisons between objectively similar groups.
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Vörös J, Ursenbacher S, Jelić D. Population Genetic Analyses Using 10 New Polymorphic Microsatellite Loci Confirms Genetic Subdivision within the Olm, Proteus anguinus. J Hered 2019; 110:211-218. [PMID: 30576453 DOI: 10.1093/jhered/esy067] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2018] [Accepted: 12/19/2018] [Indexed: 11/13/2022] Open
Abstract
We provide a comparative population genetic study of the elusive amphibian, Proteus anguinus, by comparing the genetic diversity and divergence among 4 cave populations (96 individuals) sampled in the Dinaric Karst of Croatia. We developed 10 variable microsatellite markers using pyrosequencing and applied them to the 4 selected populations belonging to 4 different cave systems. The results showed strong genetic differentiation between the 4 caves corroborating with previous findings suggesting that Proteus might comprise several unrecognized taxa. Our results confirmed that gene flow should be high within the caves, whereas it is low between hydrographic systems since geological periods. Finally, we conclude that the high genetic subdivision suggests the necessity of treating the 4 studied Proteus populations as evolutionary significant units.
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Affiliation(s)
- Judit Vörös
- Department of Zoology, Hungarian Natural History Museum, Baross u., Hungary.,Laboratory for Molecular Taxonomy, Hungarian Natural History Museum, Ludovika-tér 2-6, Hungary
| | - Sylvain Ursenbacher
- Department of Environmental Science Section of Conservation Biology, University of Basel, Basel, Switzerland.,The info fauna, UniMail-Bâtiment G, Bellevaux, Neuchâtel, Switzerland
| | - Dušan Jelić
- The Croatian Institute for Biodiversity, BIOTA j.d.o.o., Zagreb, Maksimirska cesta, Croatia
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New ecosystems in the deep subsurface follow the flow of water driven by geological activity. Sci Rep 2019; 9:3310. [PMID: 30824745 PMCID: PMC6397172 DOI: 10.1038/s41598-019-39699-w] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2018] [Accepted: 01/30/2019] [Indexed: 11/17/2022] Open
Abstract
Eukarya have been discovered in the deep subsurface at several locations in South Africa, but how organisms reach the subsurface remains unknown. We studied river-subsurface fissure water systems and identified Eukarya from a river that are genetically identical for 18S rDNA. To further confirm that these are identical species one metazoan species recovered from the overlying river interbred successfully with specimen recovered from an underlying mine at −1.4 km. In situ seismic simulation experiments were carried out and show seismic activity to be a major force increasing the hydraulic conductivity in faults allowing organisms to create ecosystems in the deep subsurface. As seismic activity is a non-selective force we recovered specimen of algae and Insecta that defy any obvious other explanation at a depth of −3.4 km. Our results show there is a steady flow of surface organisms to the deep subsurface where some survive and adapt and others perish. As seismic activity is also present on other planets and moons in our solar system the mechanism elucidated here may be relevant for future search and selection of landing sites in planetary exploration.
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Evolutionary Tinkering of the Mandibular Canal Linked to Convergent Regression of Teeth in Placental Mammals. Curr Biol 2019; 29:468-475.e3. [PMID: 30661801 DOI: 10.1016/j.cub.2018.12.023] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2018] [Revised: 11/07/2018] [Accepted: 12/13/2018] [Indexed: 11/22/2022]
Abstract
Loss or reduction of teeth has occurred independently in all major clades of mammals [1]. This process is associated with specialized diets, such as myrmecophagy and filter feeding [2, 3], and led to an extensive rearrangement of the mandibular anatomy. The mandibular canal enables lower jaw innervation through the passage of the inferior alveolar nerve (IAN) [4, 5]. In order to innervate teeth, the IAN projects ascending branches directly through tooth roots [5, 6], bone trabeculae [6], or bone canaliculi (i.e., dorsal canaliculi) [7]. Here, we used micro-computed tomography (μ-CT) scans of mandibles, from eight myrmecophagous species with reduced dentition and 21 non-myrmecophages, to investigate the evolutionary fate of dental innervation structures following convergent tooth regression in mammals. Our observations provide strong evidence for a link between the presence of tooth loci and the development of dorsal canaliculi. Interestingly, toothless anteaters present dorsal canaliculi and preserve intact tooth innervation, while equally toothless pangolins do not. We show that the internal mandibular morphology of anteaters has a closer resemblance to that of baleen whales [7] than to pangolins. This is despite masticatory apparatus resemblances that have made anteaters and pangolins a textbook example of convergent evolution. Our results suggest that early tooth loci innervation [8] is required for maintaining the dorsal innervation of the mandible and underlines the dorsal canaliculi sensorial role in the context of mediolateral mandibular movements. This study presents a unique example of convergent redeployment of the tooth developmental pathway to a strictly sensorial function following tooth regression in anteaters and baleen whales.
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44
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Soares D, Niemiller ML. Extreme Adaptation in Caves. Anat Rec (Hoboken) 2018; 303:15-23. [PMID: 30537183 DOI: 10.1002/ar.24044] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2017] [Revised: 04/17/2018] [Accepted: 05/03/2018] [Indexed: 12/31/2022]
Abstract
Cave adaptation leads to unique anatomical specializations in many taxonomic groups. As the role of vision is reduced or disappears in a subterranean environment, other specializations arise to allow the organism to successfully detect and interact with their environment. A suite of unique, convergent phenotypes associated with subterranean adaptation has emerged (termed troglomorphy), with reduction or loss of pigmentation and eyes being the most conspicuous. Two vertebrate groups that have successfully colonized and adapted to subterranean environments are cavefishes and cave salamanders. There are many shared troglomorphic anatomical characters shared between these two groups, and we describe herein the morphological traits that are unique to fishes and salamanders that are adapted to caves and other subterranean habitats. Troglobionts, animals strictly bound and adapted to underground habitats, are outcomes of not just regressive evolution, but also constructive adaptation. There are skeletal changes, such as broadening and flattening of the head, as well as hypertrophy of non-visual modalities. Cavefishes and salamanders have lost eyes and pigmentation, but also enhanced mechanosenzation, chemosenzation and, in some cases, electroreception. Both cavefishes and cave salamanders have become important models in the study of the ecology, behavior, and evolution of subterranean colonization and adaptation. However, our knowledge is primarily limited to a few taxa and many questions remain to be studied. Anat Rec, 2018. © 2018 American Association for Anatomy.
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Affiliation(s)
- Daphne Soares
- Department of Biological Sciences, New Jersey Institute of Technology, Newark, New Jersey
| | - Matthew L Niemiller
- Department of Biological Sciences, The University of Alabama in Huntsville, Huntsville, Alabama
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Arribas P, Gutiérrez-Cánovas C, Botella-Cruz M, Cañedo-Argüelles M, Antonio Carbonell J, Millán A, Pallarés S, Velasco J, Sánchez-Fernández D. Insect communities in saline waters consist of realized but not fundamental niche specialists. Philos Trans R Soc Lond B Biol Sci 2018; 374:rstb.2018.0008. [PMID: 30509910 DOI: 10.1098/rstb.2018.0008] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 10/23/2018] [Indexed: 12/16/2022] Open
Abstract
Considering how organisms adapt to stress is essential if we are to anticipate biological responses to global change in ecosystems. Communities in stressful environments can potentially be assembled by specialists (i.e. species that only occur in a limited range of environmental conditions) and/or generalist species with wider environmental tolerances. We review the existing literature on the salinity tolerance of aquatic insects previously identified as saline specialists because they were exclusively found in saline habitats, and explore if these saline realized niche specialists are also specialists in their fundamental niches or on the contrary are fundamental niche generalist species confined to the highest salinities they can tolerate. The results suggest that species inhabiting saline waters are generalists in their fundamental niches, with a predominant pattern of high survival in freshwater-low salinity conditions, where their fitness tends to be similar or even higher than in saline waters. Additionally, their performance in freshwater tends to be similar to related strictly freshwater species, so no apparent trade-off of generalization is shown. These results are discussed in the framework of the ecological and evolutionary processes driving community assembly across the osmotic stress gradient, and their potential implications for predicting impacts from saline dilution and freshwater salinization.This article is part of the theme issue 'Salt in freshwaters: causes, ecological consequences and future prospects'.
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Affiliation(s)
- Paula Arribas
- Island Ecology and Evolution Research Group, Instituto de Productos Naturales y Agrobiología (IPNA-CSIC), 38206 La Laguna, Canary Islands, Spain
| | - Cayetano Gutiérrez-Cánovas
- Grup de Recerca Freshwater Ecology and Management (FEM), Departament de Biologia Evolutiva, Ecologia i Ciències Ambientals, Facultat de Biologia, Institut de Recerca de la Biodiversitat (IRBio), Universitat de Barcelona (UB), 08028 Barcelona, Catalonia, Spain
| | - María Botella-Cruz
- Department of Ecology and Hydrology, University of Murcia, 30100 Murcia, Spain
| | - Miguel Cañedo-Argüelles
- Grup de Recerca Freshwater Ecology, Hydrology and Management (FEHM-LAB), Departament de Biologia Evolutiva, Ecologia i Ciències Ambientals, Facultat de Biologia, Institut de Recerca de l'Aigua (IdRA), Universitat de Barcelona (UB), 08028 Barcelona, Catalonia, Spain
| | | | - Andrés Millán
- Department of Ecology and Hydrology, University of Murcia, 30100 Murcia, Spain
| | - Susana Pallarés
- Instituto de Ciencias Ambientales (ICAM), Universidad de Castilla-La Mancha, Toledo, Spain
| | - Josefa Velasco
- Department of Ecology and Hydrology, University of Murcia, 30100 Murcia, Spain
| | - David Sánchez-Fernández
- Department of Ecology and Hydrology, University of Murcia, 30100 Murcia, Spain .,Instituto de Ciencias Ambientales (ICAM), Universidad de Castilla-La Mancha, Toledo, Spain
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Østbye K, Østbye E, Lien AM, Lee LR, Lauritzen SE, Carlini DB. Morphology and life history divergence in cave and surface populations of Gammarus lacustris (L.). PLoS One 2018; 13:e0205556. [PMID: 30359400 PMCID: PMC6201897 DOI: 10.1371/journal.pone.0205556] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2017] [Accepted: 09/27/2018] [Indexed: 01/15/2023] Open
Abstract
Cave animals provide a unique opportunity to study contrasts in phenotype and life history in strikingly different environments when compared to surface populations, potentially related to natural selection. As such, we compared a permanent cave-living Gammarus lacustris (L.) population with two lake-resident surface populations analyzing morphology (eye- and antennal characters) and life-history (size at maturity, fecundity and egg-size). A part of the cytochrome c oxidase subunit I gene in the mitochondrion (COI) was analyzed to contrast genetic relationship of populations and was compared to sequences in GenBank to assess phylogeography and colonization scenarios. In the cave, a longer life cycle was implied, while surface populations seemed to have a shorter life cycle. Egg size, and size at maturity for both sexes, were larger in the cave than in surface populations, while fecundity was lower in the cave than in surface populations. The cave population had longer first- and second antennae with more articles, longer first- and second peduncles, and fewer ommatidia than surface populations. The cold low-productive cave environment may facilitate different phenotypic and life-history traits than in the warmer and more productive surface lake environments. The trait divergences among cave and surface populations resembles other cave-surface organism comparisons and may support a hypothesis of selection on sensory traits. The cave and Lake Ulvenvann populations grouped together with a sequence from Slovenia (comprising one genetic cluster), while Lake Lille Lauarvann grouped with a sequence from Ukraine (comprising another cluster), which are already recognized phylogenetic clusters. One evolutionary scenario is that the cave and surface populations were colonized postglacially around 9 000–10 000 years ago. We evaluate that an alternative scenario is that the cave was colonized during an interstadial during the last glaciation or earlier during the warm period before onset of the last glaciation.
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Affiliation(s)
- Kjartan Østbye
- Inland Norway University of Applied Sciences, Department of Forestry and Wildlife Management, Campus Evenstad, Koppang, Norway
- Center for Ecological and Evolutionary Synthesis (CEES), Department of Biosciences, University of Oslo, Oslo, Norway
- * E-mail:
| | - Eivind Østbye
- Center for Ecological and Evolutionary Synthesis (CEES), Department of Biosciences, University of Oslo, Oslo, Norway
| | | | - Laura R. Lee
- Department of Biology, Stanford University, Stanford, CA, United States of America
| | | | - David B. Carlini
- Department of Biology, American University, Washington, D.C., United States of America
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Pérez-Moreno JL, Balázs G, Bracken-Grissom HD. Transcriptomic Insights into the Loss of Vision in Molnár János Cave’s Crustaceans. Integr Comp Biol 2018; 58:452-464. [DOI: 10.1093/icb/icy071] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023] Open
Affiliation(s)
- Jorge L Pérez-Moreno
- Department of Biological Sciences, Florida International University—Biscayne Bay Campus, North Miami, FL 33181, USA
| | - Gergely Balázs
- Department of Systematic Zoology and Ecology, Eötvös Loránd University, Budapest, 1117, Hungary
| | - Heather D Bracken-Grissom
- Department of Biological Sciences, Florida International University—Biscayne Bay Campus, North Miami, FL 33181, USA
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48
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Fernandes VFL, Macaspac C, Lu L, Yoshizawa M. Evolution of the developmental plasticity and a coupling between left mechanosensory neuromasts and an adaptive foraging behavior. Dev Biol 2018; 441:262-271. [PMID: 29782817 DOI: 10.1016/j.ydbio.2018.05.012] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2018] [Revised: 05/10/2018] [Accepted: 05/15/2018] [Indexed: 11/30/2022]
Abstract
Many animal species exhibit laterality in sensation and behavioral responses, namely, the preference for using either the left or right side of the sensory system. For example, some fish use their left eye when observing social stimuli, whereas they use their right eye to observe novel objects. However, it is largely unknown whether such laterality in sensory-behavior coupling evolves during rapid adaptation processes. Here, in the Mexican tetra, Astyanax mexicanus, we investigate the laterality in the relationship between an evolved adaptive behavior, vibration attraction behavior (VAB), and its main sensors, mechanosensory neuromasts. A. mexicanus has a surface-dwelling form and cave-dwelling forms (cavefish), whereby a surface fish ancestor colonized the new environment of a cave, eventually evolving cave-type morphologies such as increased numbers of neuromasts at the cranium. These neuromasts are known to regulate VAB, and it is known that, in teleosts, the budding (increasing) process of neuromasts is accompanied with dermal bone formation. This bone formation is largely regulated by endothelin signaling. To assess the evolutionary relationship between bone formation, neuromast budding, and VAB, we treated 1-3 month old juvenile fish with endothelin receptor antagonists. This treatment significantly increased cranial neuromasts in both surface and cavefish, and the effect was significantly more pronounced in cavefish. Antagonist treatment also increased the size of dermal bones in cavefish, but neuromast enhancement was observed earlier than dermal bone formation, suggesting that endothelin signaling may independently regulate neuromast development and bone formation. In addition, although we did not detect a major change in VAB level under this antagonist treatment, cavefish did show a positive correlation of VAB with the number of neuromasts on their left side but not their right. This laterality in correlation was observed when VAB emerged during cavefish development, but it was not seen in surface fish under any conditions tested, suggesting this laterality emerged through an evolutionary process. Above all, cavefish showed higher developmental plasticity in neuromast number and bone formation, and they showed an asymmetric correlation between the number of left-right neuromasts and VAB.
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Affiliation(s)
| | - Christian Macaspac
- Department of Biology, University of Hawai'i at Mānoa, Honolulu, HI 96822, USA
| | - Louise Lu
- Department of Biology, University of Hawai'i at Mānoa, Honolulu, HI 96822, USA
| | - Masato Yoshizawa
- Department of Biology, University of Hawai'i at Mānoa, Honolulu, HI 96822, USA.
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Fumey J, Hinaux H, Noirot C, Thermes C, Rétaux S, Casane D. Evidence for late Pleistocene origin of Astyanax mexicanus cavefish. BMC Evol Biol 2018; 18:43. [PMID: 29665771 PMCID: PMC5905186 DOI: 10.1186/s12862-018-1156-7] [Citation(s) in RCA: 68] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2017] [Accepted: 03/19/2018] [Indexed: 12/18/2022] Open
Abstract
BACKGROUND Cavefish populations belonging to the Mexican tetra species Astyanax mexicanus are outstanding models to study the tempo and mode of adaptation to a radical environmental change. They are currently assigned to two main groups, the so-called "old" and "new" lineages, which would have populated several caves independently and at different times. However, we do not have yet accurate estimations of the time frames of evolution of these populations. RESULTS We reanalyzed the geographic distribution of mitochondrial and nuclear DNA polymorphisms and we found that these data do not support the existence of two cavefish lineages. Using IMa2, a program that allows dating population divergence in addition to demographic parameters, we found that microsatellite polymorphism strongly supports a very recent origin of cave populations (< 20,000 years). We identified a large number of single-nucleotide polymorphisms (SNPs) in transcript sequences of pools of embryos (Pool-seq) belonging to Pachón cave population and a surface population from Texas. Based on summary statistics that can be computed with this SNP data set together with simulations of evolution of SNP polymorphisms in two recently isolated populations, we looked for sets of demographic parameters that allow the computation of summary statistics with simulated populations that are similar to the ones with the sampled populations. In most simulations for which we could find a good fit between the summary statistics of observed and simulated data, the best fit occurred when the divergence between simulated populations was less than 30,000 years. CONCLUSIONS Although it is often assumed that some cave populations have a very ancient origin, a recent origin of these populations is strongly supported by our analyses of independent sets of nuclear DNA polymorphism. Moreover, the observation of two divergent haplogroups of mitochondrial and nuclear genes with different geographic distributions support a recent admixture of two divergent surface populations, before the isolation of cave populations. If cave populations are indeed only several thousand years old, many phenotypic changes observed in cavefish would thus have mainly involved the fixation of genetic variants present in surface fish populations and within a very short period of time.
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Affiliation(s)
- Julien Fumey
- Évolution, Génomes, Comportement, Écologie, CNRS, IRD, Univ Paris-Sud. Université Paris-Saclay, F-91198, Gif-sur-Yvette, France.,Institute for Integrative Biology of the Cell (I2BC), CEA, CNRS, Université Paris-Sud, UMR 9198, FRC 3115, Avenue de la Terrasse, Bâtiment 24, Gif-sur-Yvette, F-91198, Paris, France
| | - Hélène Hinaux
- DECA group, Paris-Saclay Institute of Neuroscience, UMR 9197, CNRS, Gif sur Yvette, France
| | - Céline Noirot
- Plateforme Bioinformatique Toulouse, Midi-Pyrénées, UBIA, INRA, Auzeville Castanet-Tolosan, France
| | - Claude Thermes
- Institute for Integrative Biology of the Cell (I2BC), CEA, CNRS, Université Paris-Sud, UMR 9198, FRC 3115, Avenue de la Terrasse, Bâtiment 24, Gif-sur-Yvette, F-91198, Paris, France
| | - Sylvie Rétaux
- DECA group, Paris-Saclay Institute of Neuroscience, UMR 9197, CNRS, Gif sur Yvette, France
| | - Didier Casane
- Évolution, Génomes, Comportement, Écologie, CNRS, IRD, Univ Paris-Sud. Université Paris-Saclay, F-91198, Gif-sur-Yvette, France. .,Université Paris Diderot, Sorbonne Paris Cité, Paris, France.
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50
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Yohe LR, Dávalos LM. Strength of selection on the Trpc2 gene predicts accessory olfactory bulb form in bat vomeronasal evolution. Biol J Linn Soc Lond 2018. [DOI: 10.1093/biolinnean/bly015] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022]
Affiliation(s)
- Laurel R Yohe
- Department of Ecology and Evolution, Stony Brook University, Stony Brook, NY, USA
| | - Liliana M Dávalos
- Department of Ecology and Evolution, Stony Brook University, Stony Brook, NY, USA
- Consortium for Inter-Disciplinary Environmental Research, Stony Brook University, Stony Brook, NY, USA
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