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Kurata NP, Stiassny MLJ, Hickerson MJ, Alter SE. Impacts of Quaternary Climatic Changes on the Diversification of Riverine Cichlids in the Lower Congo River. Integr Comp Biol 2024; 64:520-532. [PMID: 38641423 DOI: 10.1093/icb/icae021] [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: 02/02/2024] [Revised: 04/14/2024] [Accepted: 04/16/2024] [Indexed: 04/21/2024] Open
Abstract
Climatic and geomorphological changes during the Quaternary period impacted global patterns of speciation and diversification across a wide range of taxa, but few studies have examined these effects on African riverine fish. The lower Congo River is an excellent natural laboratory for understanding complex speciation and population diversification processes, as it is hydrologically extremely dynamic and recognized as a continental hotspot of diversity harboring many narrowly endemic species. A previous study using genome-wide SNP data highlighted the importance of dynamic hydrological regimes to the diversification and speciation in lower Congo River cichlids. However, historical climate and hydrological changes (e.g., reduced river discharge during extended dry periods) have likely also influenced ichthyofaunal diversification processes in this system. The lower Congo River offers a unique opportunity to study climate-driven changes in river discharge, given the massive volume of water from the entire Congo basin flowing through this short stretch of the river. Here, we, for the first time, investigate the impacts of paleoclimatic factors on ichthyofaunal diversification in this system by inferring divergence times and modeling patterns of gene flow in four endemic lamprologine cichlids, including the blind cichlid, Lamprologus lethops. Our results suggest that Quaternary climate changes associated with river discharge fluctuations may have impacted the diversification of species along the system and the emergence of cryptophthalmic phenotype in some endemic species. Our study, using reduced representation sequencing (2RADseq), indicates that the lower Congo River lamprologines emerged during the Early-Middle Pleistocene transition, characterized as one of the earth's major climatic transformation periods. Modeling results suggest that gene flow across populations and between species was not constant but occurred in temporally constrained pulses. We show that these results correlate with glacial-interglacial fluctuations. The current hyper-diverse fish assemblages of the lower Congo River riverscape likely reflect the synergistic effects of multiple drivers fueling complex evolutionary processes through time.
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Affiliation(s)
- Naoko P Kurata
- Department of Ichthyology, American Museum of Natural History, 79th Street and Central Park West, NY 10024, USA
- Department of Natural Resources and the Environment, Cornell University, Ithaca, NY 14853, USA
- The Graduate Center of the City University of New York, 365 Fifth Avenue, NY 10016, USA
| | - Melanie L J Stiassny
- Department of Ichthyology, American Museum of Natural History, 79th Street and Central Park West, NY 10024, USA
- The Sackler Institute for Comparative Genomics, American Museum of Natural History, 79th Street and Central Park West, NY 10024, USA
| | - Michael J Hickerson
- The Graduate Center of the City University of New York, 365 Fifth Avenue, NY 10016, USA
- The City College of New York, 160 Convent Ave, NY 10031, USA
- Division of Invertebrate Zoology, American Museum of Natural History, 79th Street and Central Park West, NY 10024, USA
| | - S Elizabeth Alter
- Department of Ichthyology, American Museum of Natural History, 79th Street and Central Park West, NY 10024, USA
- Department of Biology and Chemistry, California State University Monterey Bay, Seaside, CA 93955, USA
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Drabeck DH, Wiese J, Gilbertson E, Arroyave J, Stiassny MLJ, Alter SE, Borowsky R, Hendrickson DA, Arcila D, McGaugh SE. Gene loss and relaxed selection of plaat1 in vertebrates adapted to low-light environments. Proc Biol Sci 2024; 291:20232847. [PMID: 38864338 DOI: 10.1098/rspb.2023.2847] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2023] [Accepted: 05/03/2024] [Indexed: 06/13/2024] Open
Abstract
Gene loss is an important mechanism for evolution in low-light or cave environments where visual adaptations often involve a reduction or loss of eyesight. The plaat gene family encodes phospholipases essential for the degradation of organelles in the lens of the eye. These phospholipases translocate to damaged organelle membranes, inducing them to rupture. This rupture is required for lens transparency and is essential for developing a functioning eye. Plaat3 is thought to be responsible for this role in mammals, while plaat1 is thought to be responsible in other vertebrates. We used a macroevolutionary approach and comparative genomics to examine the origin, loss, synteny and selection of plaat1 across bony fishes and tetrapods. We showed that plaat1 (probably ancestral to all bony fish + tetrapods) has been lost in squamates and is significantly degraded in lineages of low-visual-acuity and blind mammals and fishes. Our findings suggest that plaat1 is important for visual acuity across bony vertebrates, and that its loss through relaxed selection and pseudogenization may have played a role in the repeated evolution of visual systems in low-light environments. Our study sheds light on the importance of gene-loss in trait evolution and provides insights into the mechanisms underlying visual acuity in low-light environments.
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Affiliation(s)
- Danielle H Drabeck
- Department of Ecology, Evolution and Behavior, University of Minnesota Twin Cities, 1475 Gortner Ave, St, Paul, MN 55108, USA
| | - Jonathan Wiese
- Department of Ecology, Evolution and Behavior, University of Minnesota Twin Cities, 1475 Gortner Ave, St, Paul, MN 55108, USA
| | - Erin Gilbertson
- Department of Epidemiology and Biostatistics, University of San Francisco, University of California, San Francisco, CA, USA
| | - Jairo Arroyave
- Instituto de Biología, Universidad Nacional Autónoma de México (UNAM), Ciudad de México, México
| | - Melanie L J Stiassny
- Department of Ichthyology, American Museum of Natural History, New York, NY 10024, USA
| | - S Elizabeth Alter
- Biology and Chemistry Department, California State University Monterey Bay, Chapman Academic Science Center, Seaside, CA, USA
| | - Richard Borowsky
- Department of Biology, New York University, Washington Square, New York, NY 10003, USA
| | - Dean A Hendrickson
- Biodiversity Center, Texas Natural History Collections, University of Texas at Austin, Austin, TX 78758, USA
| | - Dahiana Arcila
- Scripps Institution of Oceanography, University of California San Diego, La Jolla, CA 92093, USA
| | - Suzanne E McGaugh
- Department of Ecology, Evolution and Behavior, University of Minnesota Twin Cities, 1475 Gortner Ave, St, Paul, MN 55108, USA
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Drabeck DH, Wiese J, Gilbertson E, Arroyave J, Arcila D, Alter SE, Borowsky R, Hendrickson D, Stiassny M, McGaugh SE. Gene loss and relaxed selection of plaat1 in vertebrates adapted to low-light environments. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.12.12.571336. [PMID: 38168154 PMCID: PMC10760033 DOI: 10.1101/2023.12.12.571336] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/05/2024]
Abstract
Gene loss is an important mechanism for evolution in low-light or cave environments where visual adaptations often involve a reduction or loss of eyesight. The plaat gene family are phospholipases essential for the degradation of organelles in the lens of the eye. They translocate to damaged organelle membranes, inducing them to rupture. This rupture is required for lens transparency and is essential for developing a functioning eye. Plaat3 is thought to be responsible for this role in mammals, while plaat1 is thought to be responsible in other vertebrates. We used a macroevolutionary approach and comparative genomics to examine the origin, loss, synteny, and selection of plaat1 across bony fishes and tetrapods. We show that plaat1 (likely ancestral to all bony fish + tetrapods) has been lost in squamates and is significantly degraded in lineages of low-visual acuity and blind mammals and fish. Our findings suggest that plaat1 is important for visual acuity across bony vertebrates, and that its loss through relaxed selection and pseudogenization may have played a role in the repeated evolution of visual systems in low-light-environments. Our study sheds light on the importance of gene-loss in trait evolution and provides insights into the mechanisms underlying visual acuity in low-light environments.
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Affiliation(s)
- Danielle H Drabeck
- Department of Ecology, Evolution and Behavior, University of Minnesota Twin Cities, 1475 Gortner Ave, St. Paul, MN 55108
| | - Jonathan Wiese
- Department of Ecology, Evolution and Behavior, University of Minnesota Twin Cities, 1475 Gortner Ave, St. Paul, MN 55108
| | - Erin Gilbertson
- University of San Francisco, Department of Epidemiology and Biostatistics, University of California, San Francisco, CA
| | - Jairo Arroyave
- Instituto de Biología, Universidad Nacional Autónoma de México (UNAM), Ciudad de México, México
| | - Dahiana Arcila
- Marine Vertebrate Collection, Scripps Institution of Oceanography, University of California San Diego, La Jolla, California, 92093, USA
| | - S Elizabeth Alter
- California State University Monterey Bay, Biology and Chemistry Department, Chapman Academic Science Center, Seaside, CA
| | - Richard Borowsky
- Department of Biology, New York University, Washington Square, New York, NY, 10003, USA
| | - Dean Hendrickson
- Biodiversity Center, Texas Natural History Collections, University of Texas at Austin, Austin, TX 78758, United States
| | - Melanie Stiassny
- Department of Ichthyology, American Museum of Natural History, New York, NY 10024, USA
| | - Suzanne E McGaugh
- Department of Ecology, Evolution and Behavior, University of Minnesota Twin Cities, 1475 Gortner Ave, St. Paul, MN 55108
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Costa FP, Schrago CG, Mello B. Assessing the relative performance of fast molecular dating methods for phylogenomic data. BMC Genomics 2022; 23:798. [PMID: 36460948 PMCID: PMC9719170 DOI: 10.1186/s12864-022-09030-5] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2022] [Accepted: 11/21/2022] [Indexed: 12/05/2022] Open
Abstract
Advances in genome sequencing techniques produced a significant growth of phylogenomic datasets. This massive amount of data represents a computational challenge for molecular dating with Bayesian approaches. Rapid molecular dating methods have been proposed over the last few decades to overcome these issues. However, a comparative evaluation of their relative performance on empirical data sets is lacking. We analyzed 23 empirical phylogenomic datasets to investigate the performance of two commonly employed fast dating methodologies: penalized likelihood (PL), implemented in treePL, and the relative rate framework (RRF), implemented in RelTime. They were compared to Bayesian analyses using the closest possible substitution models and calibration settings. We found that RRF was computationally faster and generally provided node age estimates statistically equivalent to Bayesian divergence times. PL time estimates consistently exhibited low levels of uncertainty. Overall, to approximate Bayesian approaches, RelTime is an efficient method with significantly lower computational demand, being more than 100 times faster than treePL. Thus, to alleviate the computational burden of Bayesian divergence time inference in the era of massive genomic data, molecular dating can be facilitated using the RRF, allowing evolutionary hypotheses to be tested more quickly and efficiently.
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Affiliation(s)
- Fernanda P. Costa
- grid.8536.80000 0001 2294 473XDepartment of Genetics, Federal University of Rio de Janeiro, Rio de Janeiro, RJ 21941-617 Brazil
| | - Carlos G. Schrago
- grid.8536.80000 0001 2294 473XDepartment of Genetics, Federal University of Rio de Janeiro, Rio de Janeiro, RJ 21941-617 Brazil
| | - Beatriz Mello
- grid.8536.80000 0001 2294 473XDepartment of Genetics, Federal University of Rio de Janeiro, Rio de Janeiro, RJ 21941-617 Brazil
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Kurata NP, Hickerson MJ, Hoffberg SL, Gardiner N, Stiassny MLJ, Alter SE. Riverscape genomics of cichlid fishes in the lower Congo: Uncovering mechanisms of diversification in an extreme hydrological regime. Mol Ecol 2022; 31:3516-3532. [PMID: 35532943 DOI: 10.1111/mec.16495] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2021] [Revised: 04/10/2022] [Accepted: 05/04/2022] [Indexed: 11/28/2022]
Abstract
Freshwater fishes are notably diverse, given that freshwater habitat represents a tiny fraction of the earth's surface, but the mechanisms generating this diversity remain poorly understood. Rivers provide excellent models to understand how freshwater diversity is generated and maintained across heterogeneous habitats. In particular, the lower Congo River (LCR) consists of a dynamic hydroscape exhibiting extraordinary aquatic biodiversity, endemicity, morphological and ecological specialization. Previous studies have suggested that the numerous high-energy rapids throughout the LCR form physical barriers to gene flow, thus facilitating diversification and speciation, generating ichthyofaunal diversity. However, this hypothesis has not been fully explored using genome-wide SNPs for fish species distributed across the LCR. Here, we examined four lamprologine cichlids endemic to the LCR that are distributed along the river without range overlap. Using genome-wide SNP data, we tested the hypotheses that high-energy rapids serve as physical barriers to gene flow that generate genetic divergence at inter- and intraspecific levels, and that gene flow occurs primarily in a downstream direction. Our results are consistent with the prediction that powerful rapids sometimes act as a barrier to gene flow but also suggest that, at certain temporal and spatial scales, they may provide multidirectional dispersal opportunities for riverine rheophilic cichlid fishes. These results highlight the complexity of diversification processes in rivers and the importance of assessing such processes across different riverscapes.
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Affiliation(s)
- Naoko P Kurata
- The Graduate Center of the City University of New York, 365 Fifth Avenue, New York, NY, 10016, USA.,Department of Ichthyology, American Museum of Natural History, 79th Street and Central Park West, New York, NY, 10024, USA
| | - Michael J Hickerson
- The Graduate Center of the City University of New York, 365 Fifth Avenue, New York, NY, 10016, USA.,The City College of New York, 160 Convent Ave, New York, NY, 10031, USA.,Division of Invertebrate Zoology, American Museum of Natural History, 79th Street and Central Park West, New York, NY, 10024, USA
| | - Sandra L Hoffberg
- Department of Ecology, Evolution and Environmental Biology, Columbia University, New York, NY, 10027, USA
| | - Ned Gardiner
- Department of Geography, University of Georgia, 210 Field St #204, Athens, Georgia, GA, 30602, USA
| | - Melanie L J Stiassny
- Department of Ichthyology, American Museum of Natural History, 79th Street and Central Park West, New York, NY, 10024, USA.,The Sackler Institute for Comparative Genomics, American Museum of Natural History, 79th Street and Central Park West, New York, NY, 10024, USA
| | - S Elizabeth Alter
- Department of Ichthyology, American Museum of Natural History, 79th Street and Central Park West, New York, NY, 10024, USA.,Department of Biology and Chemistry, California State University Monterey Bay, Seaside, California, CA, 93955, USA
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Musilova Z, Salzburger W, Cortesi F. The Visual Opsin Gene Repertoires of Teleost Fishes: Evolution, Ecology, and Function. Annu Rev Cell Dev Biol 2021; 37:441-468. [PMID: 34351785 DOI: 10.1146/annurev-cellbio-120219-024915] [Citation(s) in RCA: 45] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Visual opsin genes expressed in the rod and cone photoreceptor cells of the retina are core components of the visual sensory system of vertebrates. Here, we provide an overview of the dynamic evolution of visual opsin genes in the most species-rich group of vertebrates, teleost fishes. The examination of the rich genomic resources now available for this group reveals that fish genomes contain more copies of visual opsin genes than are present in the genomes of amphibians, reptiles, birds, and mammals. The expansion of opsin genes in fishes is due primarily to a combination of ancestral and lineage-specific gene duplications. Following their duplication, the visual opsin genes of fishes repeatedly diversified at the same key spectral-tuning sites, generating arrays of visual pigments sensitive from the ultraviolet to the red spectrum of the light. Species-specific opsin gene repertoires correlate strongly with underwater light habitats, ecology, and color-based sexual selection. Expected final online publication date for the Annual Review of Cell and Developmental Biology, Volume 37 is October 2021. Please see http://www.annualreviews.org/page/journal/pubdates for revised estimates.
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Affiliation(s)
- Zuzana Musilova
- Department of Zoology, Charles University, Prague 128 44, Czech Republic;
| | | | - Fabio Cortesi
- Queensland Brain Institute, The University of Queensland, Brisbane 4072, Queensland, Australia;
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Parichy DM. Evolution of pigment cells and patterns: recent insights from teleost fishes. Curr Opin Genet Dev 2021; 69:88-96. [PMID: 33743392 DOI: 10.1016/j.gde.2021.02.006] [Citation(s) in RCA: 21] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2021] [Revised: 02/04/2021] [Accepted: 02/09/2021] [Indexed: 01/08/2023]
Abstract
Skin pigment patterns of vertebrates are stunningly diverse, and nowhere more so than in teleost fishes. Several species, including relatives of zebrafish, recently evolved cichlid fishes of East Africa, clownfishes, deep sea fishes, and others are providing insights into pigment pattern evolution. This overview describes recent advances in understanding periodic patterns, like stripes and spots, the loss of patterns, and the role of cell-type diversification in generating pigmentation phenotypes. Advances in this area are being facilitated by the application of modern methods of gene editing, genomics, computational analysis, and other approaches to non-traditional model organisms having interesting pigmentary phenotypes. Several topics worthy of future attention are outlined as well.
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Affiliation(s)
- David M Parichy
- Department of Biology, Department of Cell Biology, University of Virginia, Charlottesville, VA 22903, United States.
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