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Bohutínská M, Peichel CL. Divergence time shapes gene reuse during repeated adaptation. Trends Ecol Evol 2024; 39:396-407. [PMID: 38155043 DOI: 10.1016/j.tree.2023.11.007] [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: 08/10/2023] [Revised: 11/15/2023] [Accepted: 11/20/2023] [Indexed: 12/30/2023]
Abstract
When diverse lineages repeatedly adapt to similar environmental challenges, the extent to which the same genes are involved (gene reuse) varies across systems. We propose that divergence time among lineages is a key factor driving this variability: as lineages diverge, the extent of gene reuse should decrease due to reductions in allele sharing, functional differentiation among genes, and restructuring of genome architecture. Indeed, we show that many genomic studies of repeated adaptation find that more recently diverged lineages exhibit higher gene reuse during repeated adaptation, but the relationship becomes less clear at older divergence time scales. Thus, future research should explore the factors shaping gene reuse and their interplay across broad divergence time scales for a deeper understanding of evolutionary repeatability.
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Affiliation(s)
- Magdalena Bohutínská
- Division of Evolutionary Ecology, Institute of Ecology and Evolution, University of Bern, Bern, 3012, Switzerland; Department of Botany, Faculty of Science, Charles University, Prague, 12800, Czech Republic.
| | - Catherine L Peichel
- Division of Evolutionary Ecology, Institute of Ecology and Evolution, University of Bern, Bern, 3012, Switzerland
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2
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Lee CE. Genome architecture underlying salinity adaptation in the invasive copepod Eurytemora affinis species complex: A review. iScience 2023; 26:107851. [PMID: 37752947 PMCID: PMC10518491 DOI: 10.1016/j.isci.2023.107851] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 09/28/2023] Open
Abstract
With climate change, habitat salinity is shifting rapidly throughout the globe. In addition, many destructive freshwater invaders are recent immigrants from saline habitats. Recently, populations of the copepod Eurytemora affinis species complex have invaded freshwater habitats multiple times independently from saline estuaries on three continents. This review discusses features of this species complex that could enhance their evolutionary potential during rapid environmental change. Remarkably, across independent freshwater invasions, natural selection has repeatedly favored the same alleles far more than expected. This high degree of parallelism is surprising, given the expectation of nonparallel evolution for polygenic adaptation. Factors such as population structure and the genome architecture underlying critical traits under selection might help drive rapid adaptation and parallel evolution. Given the preponderance of saline-to-freshwater invasions and climate-induced salinity change, the principles found here could provide invaluable insights into mechanisms operating in other systems and the potential for adaptation in a changing planet.
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Affiliation(s)
- Carol Eunmi Lee
- Department of Integrative Biology, University of Wisconsin, 430 Lincoln Drive, Birge Hall, Madison, WI 53706, USA
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3
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Valente S, Moro S, Di Lorenzo M, Milisenda G, Maiorano L, Colloca F. Mediterranean fish communities are struggling to adapt to global warming. Evidence from the western coast of Italy. MARINE ENVIRONMENTAL RESEARCH 2023; 191:106176. [PMID: 37716279 DOI: 10.1016/j.marenvres.2023.106176] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/21/2023] [Revised: 09/08/2023] [Accepted: 09/11/2023] [Indexed: 09/18/2023]
Abstract
Climate change has significant impacts on marine ecosystems, resulting in disruptions in biological interactions, shifts in community composition, and changes in the physiology of fish and other marine organisms. In this study conducted in the central Mediterranean Sea, the mean temperature of the catch (MTC) was employed as an indicator to investigate the climatological factors influencing the fish community. The MTC, which utilizes species-preferred temperatures, was calculated using bottom temperature (BT) data weighted against scientific catches. The estimated MTC increasing rates were 0.01 °C year-1 for the entire community, 0.017 °C year-1 for the shelf break, and 0.004 °C year-1 for the continental slope assemblage. We found that MTC is increasing at a lower rate compared to BT, suggesting a progressive under-adaptation of the fish community that seems not fully able to keep up with the ongoing pace of warming. The study identified sea surface temperature and bottom temperature as key drivers of changes in fish community composition. Notably, the fish community composition exhibited drastic changes over the studied period, and we suggest that the MTC can be a useful index to monitor such changes within the context of the EU's climate change adaptation strategy.
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Affiliation(s)
- Salvatore Valente
- Department of Integrative Marine Ecology, Stazione Zoologica Anton Dohrn, via Po' 25c, 00189, Rome, Italy; Department of Biology and Biotechnologies 'Charles Darwin', Sapienza University of Rome, Rome, Italy.
| | - Stefano Moro
- Department of Integrative Marine Ecology, Stazione Zoologica Anton Dohrn, via Po' 25c, 00189, Rome, Italy
| | - Manfredi Di Lorenzo
- Department of Integrative Marine Ecology, Stazione Zoologica Anton Dohrn, Lungomare Cristoforo Colombo, I-90149, Palermo, Italy
| | - Giacomo Milisenda
- Department of Integrative Marine Ecology, Stazione Zoologica Anton Dohrn, Lungomare Cristoforo Colombo, I-90149, Palermo, Italy
| | - Luigi Maiorano
- Department of Biology and Biotechnologies 'Charles Darwin', Sapienza University of Rome, Rome, Italy
| | - Francesco Colloca
- Department of Integrative Marine Ecology, Stazione Zoologica Anton Dohrn, via Po' 25c, 00189, Rome, Italy
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Tresguerres M, Kwan GT, Weinrauch A. Evolving views of ionic, osmotic and acid-base regulation in aquatic animals. J Exp Biol 2023; 226:jeb245747. [PMID: 37522267 DOI: 10.1242/jeb.245747] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/01/2023]
Abstract
The regulation of ionic, osmotic and acid-base (IOAB) conditions in biological fluids is among the most fundamental functions in all organisms; being surrounded by water uniquely shapes the IOAB regulatory strategies of water-breathing animals. Throughout its centennial history, Journal of Experimental Biology has established itself as a premier venue for publication of comparative, environmental and evolutionary studies on IOAB regulation. This Review provides a synopsis of IOAB regulation in aquatic animals, some of the most significant research milestones in the field, and evolving views about the underlying cellular mechanisms and their evolutionary implications. It also identifies promising areas for future research and proposes ideas for enhancing the impact of aquatic IOAB research.
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Affiliation(s)
- Martin Tresguerres
- Scripps Institution of Oceanography, University of California, San Diego, La Jolla, CA 92037, USA
| | - Garfield T Kwan
- Department of Wildlife, Fish, and Conservation Biology, University of California, Davis, Davis, CA 95616, USA
| | - Alyssa Weinrauch
- Department of Biological Sciences, University of Manitoba, Winnipeg, MB R3T 2M5, Canada
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Snead AA, Tatarenkov A, Avise JC, Taylor DS, Turner BJ, Marson K, Earley RL. Out to sea: ocean currents and patterns of asymmetric gene flow in an intertidal fish species. Front Genet 2023; 14:1206543. [PMID: 37456662 PMCID: PMC10349204 DOI: 10.3389/fgene.2023.1206543] [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: 04/15/2023] [Accepted: 06/14/2023] [Indexed: 07/18/2023] Open
Abstract
Passive dispersal via wind or ocean currents can drive asymmetric gene flow, which influences patterns of genetic variation and the capacity of populations to evolve in response to environmental change. The mangrove rivulus fish (Kryptolebias marmoratus), hereafter "rivulus," is an intertidal fish species restricted to the highly fragmented New World mangrove forests of Central America, the Caribbean, the Bahamas, and Florida. Mangrove patches are biological islands with dramatic differences in both abiotic and biotic conditions compared to adjacent habitat. Over 1,000 individual rivulus across 17 populations throughout its range were genotyped at 32 highly polymorphic microsatellites. Range-wide population genetic structure was evaluated with five complementary approaches that found eight distinct population clusters. However, an analysis of molecular variance indicated significant population genetic structure among regions, populations within regions, sampling locations within populations, and individuals within sampling locations, indicating that rivulus has both broad- and fine-scale genetic differentiation. Integrating range-wide genetic data with biophysical modeling based on 10 years of ocean current data showed that ocean currents and the distance between populations over water drive gene flow patterns on broad scales. Directional migration estimates suggested some significant asymmetries in gene flow that also were mediated by ocean currents and distance. Specifically, populations in the center of the range (Florida Keys) were identified as sinks that received migrants (and alleles) from other populations but failed to export individuals. These populations thus harbor genetic variation, perhaps even from extirpated populations across the range, but ocean currents and complex arrangements of landmasses might prevent the distribution of that genetic variation elsewhere. Hence, the inherent asymmetry of ocean currents shown to impact both genetic differentiation and directional migration rates may be responsible for the complex distribution of genetic variation across the range and observed patterns of metapopulation structure.
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Affiliation(s)
- Anthony A. Snead
- Department of Biological Sciences, University of Alabama, Tuscaloosa, AL, United States
| | - Andrey Tatarenkov
- Department of Ecology and Evolutionary Biology, University of California, Irvine, Irvine, CA, United States
| | - John C. Avise
- Department of Ecology and Evolutionary Biology, University of California, Irvine, Irvine, CA, United States
| | | | - Bruce J. Turner
- Department of Biological Sciences, Virginia Tech, Blacksburg, VA, United States
| | - Kristine Marson
- Department of Biological Sciences, University of Alabama, Tuscaloosa, AL, United States
| | - Ryan L. Earley
- Department of Biological Sciences, University of Alabama, Tuscaloosa, AL, United States
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Nedoluzhko A, Orlova SY, Kurnosov DS, Orlov AM, Galindo-Villegas J, Rastorguev SM. Genomic Signatures of Freshwater Adaptation in Pacific Herring ( Clupea pallasii). Genes (Basel) 2022; 13:genes13101856. [PMID: 36292743 PMCID: PMC9601299 DOI: 10.3390/genes13101856] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2022] [Revised: 10/10/2022] [Accepted: 10/13/2022] [Indexed: 11/04/2022] Open
Abstract
Pacific herring (Clupea pallasii) is an essential target of commercial fishing in the North Pacific Ocean. Previous studies have suggested the existence of marine and lake ecological forms of this species within its range. The lake ecological form of herring has a shortened life cycle, spending the winter and spawning in brackish waters near the shoreline without long migrations for feeding; it also has a relatively smaller body size than the marine form. Genetic-based studies have shown that brackish water Pacific herring not only can be distinguished as a separate lake ecological form but possibly has its genetic legacy. Here, as part of an ongoing study, using ddRAD-sequencing data for marine and lake ecological forms from a total of 54 individuals and methods of comparative bioinformatics, we describe genomic signatures of freshwater adaptivity in Pacific herring. In total, 253 genes containing discriminating SNPs were found, and part of those genes was organized into genome clusters, also known as “genomic islands of divergence”. Moreover, the Tajima’s D test showed that these loci are under directional selection in the lake populations of the Pacific herring. Yet, most discriminating loci between the lake and marine ecological forms of Pacific herring do not intersect (by gene name) with those in other known marine fish species with known freshwater/brackish populations. However, some are associated with the same physiological trait—osmoregulation.
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Affiliation(s)
- Artem Nedoluzhko
- Paleogenomics Laboratory, European University at Saint Petersburg, 191187 Saint Petersburg, Russia
- Limited Liability Company ELGENE, 109029 Moscow, Russia
| | - Svetlana Yu. Orlova
- Laboratory of Molecular Genetics, Russian Federal Research Institute of Fisheries and Oceanography, 107140 Moscow, Russia
- Laboratory of Genetic Basis of Identification, Vavilov Institute of General Genetics of the Russian Academy of Sciences, 119991 Moscow, Russia
- Correspondence: (S.Y.O.); (J.G.-V.); (S.M.R.)
| | - Denis S. Kurnosov
- Research Group of Intraspecific Differentiation, Russian Federal Research Institute of Fisheries and Oceanography, Pacific Branch (TINRO), 690091 Vladivostok, Russia
| | - Alexei M. Orlov
- Laboratory of Oceanic Ichthyofauna, Shirshov Institute of Oceanology of the Russian Academy of Sciences, 117218 Moscow, Russia
- Laboratory of Behavior of Lower Vertebrates, A.N. Severtsov Institute of Ecology and Evolution, Russian Academy of Sciences, 119071 Moscow, Russia
- Department of Ichthyology, Dagestan State University, 367000 Makhachkala, Russia
- Department of Ichthyology and Hydrobiology, Tomsk State University, 634050 Tomsk, Russia
- Laboratory of Marine Biology, Caspian Institute of Biological Resources, Russian Academy of Sciences, 367000 Makhachkala, Russia
| | - Jorge Galindo-Villegas
- Genomics Division, Faculty of Biosciences and Aquaculture, Nord University, 8049 Bodø, Norway
- Correspondence: (S.Y.O.); (J.G.-V.); (S.M.R.)
| | - Sergey M. Rastorguev
- Limited Liability Company ELGENE, 109029 Moscow, Russia
- Kurchatov Center for Genomic Research, National Research Centre “Kurchatov Institute”, 123182 Moscow, Russia
- Correspondence: (S.Y.O.); (J.G.-V.); (S.M.R.)
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Schultz ET, Boush LP. Introduction to "HaloDaSH: The deep and shallow history of aquatic life's passages between marine and freshwater habitats". Integr Comp Biol 2022; 62:288-296. [PMID: 35687014 DOI: 10.1093/icb/icac088] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2022] [Revised: 04/01/2022] [Accepted: 04/08/2022] [Indexed: 11/13/2022] Open
Abstract
This series of papers highlights research into how biological exchanges between salty and freshwater habitats have transformed the biosphere. Life in the ocean and in freshwaters have long been intertwined; multiple major branches of the tree of life originated in the oceans and then adapted to and diversified in freshwaters. Similar exchanges continue to this day, including some species that continually migrate between marine and fresh waters. The series addresses key themes of transitions, transformations, and current threats with a series of questions: When did major colonizations of fresh waters happen? What physiographic changes facilitated transitions? What organismal characteristics facilitate colonization? Once a lineage has colonized freshwater, how frequently is there a return to the sea? Have transitions impelled diversification? How do organisms adapt physiologically to changes in halohabitat, and are such adaptive changes predictable? How do marine and freshwater taxa differ in morphology? How are present-day global changes in the environment influencing halohabitat and how are organisms contending with them? The purpose of the symposium and the papers in this volume is to integrate findings at multiple levels of biological organization and from disparate fields, across biological and geoscience disciplines.
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Affiliation(s)
- Eric T Schultz
- Department of Ecology and Evolutionary Biology, U-3043, University of Connecticut, Storrs CT 06269-3043
| | - Lisa Park Boush
- Department of Geosciences, University of Connecticut, Storrs CT
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