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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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Garcia-Elfring A, Paccard A, Thurman TJ, Wasserman BA, Palkovacs EP, Hendry AP, Barrett RDH. Using seasonal genomic changes to understand historical adaptation to new environments: Parallel selection on stickleback in highly-variable estuaries. Mol Ecol 2021; 30:2054-2064. [PMID: 33713378 DOI: 10.1111/mec.15879] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2020] [Revised: 02/25/2021] [Accepted: 02/26/2021] [Indexed: 12/21/2022]
Abstract
Parallel evolution is considered strong evidence for natural selection. However, few studies have investigated the process of parallel selection as it plays out in real time. The common approach is to study historical signatures of selection in populations already well adapted to different environments. Here, to document selection under natural conditions, we study six populations of threespine stickleback (Gasterosteus aculeatus) inhabiting bar-built estuaries that undergo seasonal cycles of environmental changes. Estuaries are periodically isolated from the ocean due to sandbar formation during dry summer months, with concurrent environmental shifts that resemble the long-term changes associated with postglacial colonization of freshwater habitats by marine populations. We used pooled whole-genome sequencing to track seasonal allele frequency changes in six of these populations and search for signatures of natural selection. We found consistent changes in allele frequency across estuaries, suggesting a potential role for parallel selection. Functional enrichment among candidate genes included transmembrane ion transport and calcium binding, which are important for osmoregulation and ion balance. The genomic changes that occur in threespine stickleback from bar-built estuaries could provide a glimpse into the early stages of adaptation that have occurred in many historical marine to freshwater transitions.
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Affiliation(s)
- Alan Garcia-Elfring
- Department of Biology, Redpath Museum, McGill University, Montreal, QC, Canada
| | - Antoine Paccard
- Department of Biology, Redpath Museum, McGill University, Montreal, QC, Canada.,McGill University Genome Center, McGill University, Montreal, QC, Canada
| | - Timothy J Thurman
- Department of Biology, Redpath Museum, McGill University, Montreal, QC, Canada
| | - Ben A Wasserman
- Department of Ecology and Evolutionary Biology, University of California, Santa Cruz, CA, USA
| | - Eric P Palkovacs
- Department of Ecology and Evolutionary Biology, University of California, Santa Cruz, CA, USA
| | - Andrew P Hendry
- Department of Biology, Redpath Museum, McGill University, Montreal, QC, Canada
| | - Rowan D H Barrett
- Department of Biology, Redpath Museum, McGill University, Montreal, QC, Canada
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Amynthas corticis genome reveals molecular mechanisms behind global distribution. Commun Biol 2021; 4:135. [PMID: 33514865 PMCID: PMC7846840 DOI: 10.1038/s42003-021-01659-4] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2020] [Accepted: 01/05/2021] [Indexed: 01/30/2023] Open
Abstract
Earthworms (Annelida: Crassiclitellata) are widely distributed around the world due to their ancient origination as well as adaptation and invasion after introduction into new habitats over the past few centuries. Herein, we report a 1.2 Gb complete genome assembly of the earthworm Amynthas corticis based on a strategy combining third-generation long-read sequencing and Hi-C mapping. A total of 29,256 protein-coding genes are annotated in this genome. Analysis of resequencing data indicates that this earthworm is a triploid species. Furthermore, gene family evolution analysis shows that comprehensive expansion of gene families in the Amynthas corticis genome has produced more defensive functions compared with other species in Annelida. Quantitative proteomic iTRAQ analysis shows that expression of 147 proteins changed in the body of Amynthas corticis and 16 S rDNA sequencing shows that abundance of 28 microorganisms changed in the gut of Amynthas corticis when the earthworm was incubated with pathogenic Escherichia coli O157:H7. Our genome assembly provides abundant and valuable resources for the earthworm research community, serving as a first step toward uncovering the mysteries of this species, and may provide molecular level indicators of its powerful defensive functions, adaptation to complex environments and invasion ability.
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Erséus C, Williams BW, Horn KM, Halanych KM, Santos SR, James SW, Creuzé des Châtelliers M, Anderson FE. Phylogenomic analyses reveal a Palaeozoic radiation and support a freshwater origin for clitellate annelids. ZOOL SCR 2020. [DOI: 10.1111/zsc.12426] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Affiliation(s)
- Christer Erséus
- Department of Biological and Environmental Sciences University of Gothenburg Göteborg Sweden
| | - Bronwyn W. Williams
- School of Biological Sciences Southern Illinois University Carbondale IL USA
- Research Laboratory North Carolina Museum of Natural Sciences Raleigh NC USA
| | - Kevin M. Horn
- School of Biological Sciences Southern Illinois University Carbondale IL USA
- Division of Natural Sciences and Mathematics Kentucky Wesleyan College Owensboro Kentucky USA
| | - Kenneth M. Halanych
- Molette Biology Laboratory for Environmental and Climate Change Studies Department of Biological Sciences Auburn University Auburn AL USA
| | - Scott R. Santos
- Molette Biology Laboratory for Environmental and Climate Change Studies Department of Biological Sciences Auburn University Auburn AL USA
| | - Samuel W. James
- Sustainable Living Department Maharishi University of Management Fairfield IA USA
| | | | - Frank E. Anderson
- School of Biological Sciences Southern Illinois University Carbondale IL USA
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Horn KM, Anderson FE. Spiralian Genomes Reveal Gene Family Expansions Associated with Adaptation to Freshwater. J Mol Evol 2020; 88:463-472. [PMID: 32388714 DOI: 10.1007/s00239-020-09949-x] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2019] [Accepted: 05/02/2020] [Indexed: 10/24/2022]
Abstract
The colonization of freshwater habitats by marine-adapted organisms represents a major transition that has only occurred a few times in the evolution of animals. Only around half of the extant animal phyla have representatives in both marine and freshwater environments and even within those phyla some major clades are restricted to marine environments. Moving from marine to freshwater environments can create severe osmotic and ionic stresses and the mechanisms that animals have used to adapt to those stresses are still not well understood. In this study, we downloaded amino acid sequence data from 11 spiralian animal genomes (four freshwater taxa representing four different phyla as well as 7 marine taxa) and identified a number of gene family expansions that have occurred exclusively in the freshwater lineages. Further investigation of these gene families and the timing and nature of their expansions will illuminate one of the major evolutionary transitions in the history of life on Earth.
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Affiliation(s)
- Kevin M Horn
- Division of Natural Sciences and Mathematics, Kentucky Wesleyan College, Owensboro, KY, 42301, USA. .,School of Biological Sciences, Southern Illinois University, Carbondale, IL, 62901, USA.
| | - Frank E Anderson
- School of Biological Sciences, Southern Illinois University, Carbondale, IL, 62901, USA
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