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Adrian-Kalchhauser I, Blomberg A, Larsson T, Musilova Z, Peart CR, Pippel M, Solbakken MH, Suurväli J, Walser JC, Wilson JY, Alm Rosenblad M, Burguera D, Gutnik S, Michiels N, Töpel M, Pankov K, Schloissnig S, Winkler S. The round goby genome provides insights into mechanisms that may facilitate biological invasions. BMC Biol 2020; 18:11. [PMID: 31992286 PMCID: PMC6988351 DOI: 10.1186/s12915-019-0731-8] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2019] [Accepted: 12/13/2019] [Indexed: 12/12/2022] Open
Abstract
Background The invasive benthic round goby (Neogobius melanostomus) is the most successful temperate invasive fish and has spread in aquatic ecosystems on both sides of the Atlantic. Invasive species constitute powerful in situ experimental systems to study fast adaptation and directional selection on short ecological timescales and present promising case studies to understand factors involved the impressive ability of some species to colonize novel environments. We seize the unique opportunity presented by the round goby invasion to study genomic substrates potentially involved in colonization success. Results We report a highly contiguous long-read-based genome and analyze gene families that we hypothesize to relate to the ability of these fish to deal with novel environments. The analyses provide novel insights from the large evolutionary scale to the small species-specific scale. We describe expansions in specific cytochrome P450 enzymes, a remarkably diverse innate immune system, an ancient duplication in red light vision accompanied by red skin fluorescence, evolutionary patterns of epigenetic regulators, and the presence of osmoregulatory genes that may have contributed to the round goby’s capacity to invade cold and salty waters. A recurring theme across all analyzed gene families is gene expansions. Conclusions The expanded innate immune system of round goby may potentially contribute to its ability to colonize novel areas. Since other gene families also feature copy number expansions in the round goby, and since other Gobiidae also feature fascinating environmental adaptations and are excellent colonizers, further long-read genome approaches across the goby family may reveal whether gene copy number expansions are more generally related to the ability to conquer new habitats in Gobiidae or in fish. Electronic supplementary material The online version of this article (10.1186/s12915-019-0731-8) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Irene Adrian-Kalchhauser
- Program Man-Society-Environment, Department of Environmental Sciences, University of Basel, Vesalgasse 1, 4051, Basel, Switzerland. .,University of Bern, Institute for Fish and Wildlife Health, Länggassstrasse 122, 3012, Bern, Austria.
| | - Anders Blomberg
- Department of Chemistry and Molecular Biology, University of Gothenburg, Medicinaregatan 9C, 41390, Gothenburg, Sweden
| | - Tomas Larsson
- Department of Marine Sciences, University of Gothenburg, Medicinaregatan 9C, 41390, Gothenburg, Sweden
| | - Zuzana Musilova
- Department of Zoology, Charles University, Vinicna 7, 12844, Prague, Czech Republic
| | - Claire R Peart
- Division of Evolutionary Biology, Faculty of Biology, Ludwig-Maximilians-Universität München, Grosshaderner Strasse 2, 82152 Planegg-, Martinsried, Germany
| | - Martin Pippel
- Max Planck Institute of Molecular Cell Biology and Genetics, Pfotenhauerstrasse 108, 01307, Dresden, Germany
| | - Monica Hongroe Solbakken
- Centre for Ecological and Evolutionary Synthesis, University of Oslo, Blindernveien 31, 0371, Oslo, Norway
| | - Jaanus Suurväli
- Institute for Genetics, University of Cologne, Zülpicher Strasse 47a, 50674, Köln, Germany
| | - Jean-Claude Walser
- Genetic Diversity Centre, ETH, Universitätsstrasse 16, 8092, Zurich, Switzerland
| | - Joanna Yvonne Wilson
- Department of Biology, McMaster University, 1280 Main Street West, Hamilton, ON, Canada
| | - Magnus Alm Rosenblad
- Department of Chemistry and Molecular Biology, University of Gothenburg, Medicinaregatan 9C, 41390, Gothenburg, Sweden.,NBIS Bioinformatics Infrastructure for Life Sciences, University of Gothenburg, Medicinaregatan 9C, 41390, Gothenburg, Sweden
| | - Demian Burguera
- Department of Zoology, Charles University, Vinicna 7, 12844, Prague, Czech Republic
| | - Silvia Gutnik
- Biocenter, University of Basel, Klingelbergstrasse 50/70, 4056, Basel, Switzerland
| | - Nico Michiels
- Institute of Evolution and Ecology, University of Tuebingen, Auf der Morgenstelle 28, 72076, Tübingen, Germany
| | - Mats Töpel
- University of Bern, Institute for Fish and Wildlife Health, Länggassstrasse 122, 3012, Bern, Austria
| | - Kirill Pankov
- Department of Biology, McMaster University, 1280 Main Street West, Hamilton, ON, Canada
| | - Siegfried Schloissnig
- Research Institute of Molecular Pathology (IMP), Vienna BioCenter (VBC), 1030, Vienna, Austria
| | - Sylke Winkler
- Max Planck Institute of Molecular Cell Biology and Genetics, Pfotenhauerstrasse 108, 01307, Dresden, Germany
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Adrian-Kalchhauser I, Walser JC, Schwaiger M, Burkhardt-Holm P. RNA sequencing of early round goby embryos reveals that maternal experiences can shape the maternal RNA contribution in a wild vertebrate. BMC Evol Biol 2018; 18:34. [PMID: 29566669 PMCID: PMC5863367 DOI: 10.1186/s12862-018-1132-2] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2017] [Accepted: 01/29/2018] [Indexed: 01/01/2023] Open
Abstract
Background It has been proposed that non-genetic inheritance could promote species fitness. Non-genetic inheritance could allow offspring to benefit from the experience of their parents, and could advocate pre-adaptation to prevailing and potentially selective conditions. Indeed, adaptive parental effects have been modeled and observed, but the molecular mechanisms behind them are far from understood. Results In the present study, we investigated whether maternal RNA can carry information about environmental conditions experienced by the mother in a wild vertebrate. Maternal RNA directs the development of the early embryo in many non-mammalian vertebrates and invertebrates. However, it is not known whether vertebrate maternal RNA integrates information about the parental environment. We sequenced the maternal RNA contribution from a model that we expected to rely on parental effects: the invasive benthic fish species Neogobius melanostomus (Round Goby). We found that maternal RNA expression levels correlated with the water temperature experienced by the mother before oviposition, and identified temperature-responsive gene groups such as core nucleosome components or the microtubule cytoskeleton. Conclusions Our findings suggest that the maternal RNA contribution may incorporate environmental information. Maternal RNA should therefore be considered a potentially relevant pathway for non-genetic inheritance. Also, the ability of a species to integrate environmental information in the maternal RNA contribution could potentially contribute to species fitness and may also play a role in extraordinary adaptive success stories of invasive species such as the round goby. Electronic supplementary material The online version of this article (10.1186/s12862-018-1132-2) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Irene Adrian-Kalchhauser
- Program Man-Society-Environment, Department of Environmental Sciences, University of Basel, Vesalgasse 1, CH-4051, Basel, Switzerland.
| | - Jean-Claude Walser
- Department of Environmental Systems Science, Genetic Diversity Centre Zurich, ETH Zurich, Universitätstrasse 16, CH-8092, Zurich, Switzerland
| | - Michaela Schwaiger
- Program Man-Society-Environment, Department of Environmental Sciences, University of Basel, Vesalgasse 1, CH-4051, Basel, Switzerland
| | - Patricia Burkhardt-Holm
- Program Man-Society-Environment, Department of Environmental Sciences, University of Basel, Vesalgasse 1, CH-4051, Basel, Switzerland
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Human-mediated and natural dispersal of an invasive fish in the eastern Great Lakes. Heredity (Edinb) 2018; 120:533-546. [PMID: 29317757 DOI: 10.1038/s41437-017-0038-x] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2017] [Revised: 11/11/2017] [Accepted: 11/20/2017] [Indexed: 11/08/2022] Open
Abstract
The globally invasive Round Goby (Neogobius melanostomus) was introduced to the Great Lakes around 1990, spreading widely and becoming the dominant benthic fish in many areas. The speed and scope of this invasion is remarkable and calls into question conventional secondary spread models and scenarios. We utilized nine microsatellites to identify large-scale genetic structure in Round Goby populations in the eastern Great Lakes, and assessed the role of colonization vs. secondary transport and dispersal in developing this structure. We identified three clusters, corresponding with Lake Huron, eastern Lake Erie, and western Lake Erie plus eastern Lake Ontario, along with three highly divergent populations. Bottleneck analysis identified founder effects in two divergent populations. Regression analyses of isolation by distance and allelic richness vs. distance from the initial invasion site were consistent with limited migration. However, some populations in eastern Lake Erie and Lake Ontario showed anomalously low genetic distance from the original site of colonization, consistent with secondary transport of large numbers of individuals via ballast water. We conclude that genetic structure of Round Goby in the Great Lakes principally resulted from long-distance secondary transport via ballast water with additional movement of individual via bait buckets and natural dispersal. The success of Round Gobies represents an interesting model for colonization characterization; however, those same attributes present significant challenges for conservation and fisheries management. Current management likely prevents many new species from arriving in the Great Lakes, but fails to address the transport of species within the lakes after they arrive; this is an issue of clear and pressing importance.
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Snyder MR, Stepien CA. Genetic patterns across an invasion's history: a test of change versus stasis for the Eurasian round goby in North America. Mol Ecol 2017; 26:1075-1090. [PMID: 28029720 DOI: 10.1111/mec.13997] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2016] [Revised: 12/05/2016] [Accepted: 12/12/2016] [Indexed: 01/11/2023]
Abstract
Biological invasions comprise accidental evolutionary experiments, whose genetic compositions underlie relative success, spread and persistence in new habitats. However, little is known about whether, or how, their population genetic patterns change temporally and/or spatially across the invasion's history. Theory predicts that most would undergo founder effect, exhibit low genetic divergence across the new range and gain variation over time via new arriving propagules. To test these predictions, we analyse population genetic diversity and divergence patterns of the Eurasian round goby Neogobius melanostomus across the two decades of its North American invasion in the Laurentian Great Lakes, comparing results from 13 nuclear DNA microsatellite loci and mitochondrial DNA cytochrome b sequences. We test whether 'genetic stasis', 'genetic replacement' and/or 'genetic supplement' scenarios have occurred at the invasion's core and expansion sites, in comparison with its primary native source population in the Dnieper River, Black Sea. Results reveal pronounced genetic divergence across the exotic range, with population areas remaining genetically distinct and statistically consistent across two decades, supporting 'genetic stasis' and 'founder takes most'. The original genotypes continue to predominate, whose high population growth likely outpaced the relative success of later arrivals. The original invasion core has stayed the most similar to the native source. Secondary expansion sites indicate slight allelic composition convergence towards the core population over time, attributable to some early 'genetic supplementation'. The geographic and temporal coverage of this investigation offers a rare opportunity to discern population dynamics over time and space in context of invasion genetic theory vs. reality.
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Affiliation(s)
- Matthew R Snyder
- Great Lakes Genetics/Genomics Laboratory, The Lake Erie Center and Department of Environmental Sciences, The University of Toledo, Toledo, OH, 43606, USA.,NOAA Pacific Marine Environmental Laboratory, 7600 Sand Point Way NE, Seattle, WA, 98115, USA
| | - Carol A Stepien
- Great Lakes Genetics/Genomics Laboratory, The Lake Erie Center and Department of Environmental Sciences, The University of Toledo, Toledo, OH, 43606, USA.,NOAA Pacific Marine Environmental Laboratory, 7600 Sand Point Way NE, Seattle, WA, 98115, USA
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Adrian-Kalchhauser I, Hirsch PE, Behrmann-Godel J, N'Guyen A, Watzlawczyk S, Gertzen S, Borcherding J, Burkhardt-Holm P. The invasive bighead goby Ponticola kessleri displays large-scale genetic similarities and small-scale genetic differentiation in relation to shipping patterns. Mol Ecol 2016; 25:1925-43. [PMID: 26928748 DOI: 10.1111/mec.13595] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2015] [Revised: 02/12/2016] [Accepted: 02/17/2016] [Indexed: 12/11/2022]
Abstract
Colonization events, range expansions and species invasions leave genetic signatures in the genomes of invasive organisms and produce intricate special patterns. Predictions have been made as to how those patterns arise, but only very rarely, genetic processes can be monitored in real time during range expansions. In an attempt to change that, we track a very recently established invasive population of a fish species, the bighead goby Ponticola kessleri, with high temporal and spatial resolution through 2 years to identify patterns over time. We then compare Swiss and German samples of bighead goby along the river Rhine using microsatellites, mitochondrial D-loop sequences and geometric morphometrics to investigate geographic patterns. We detect weak temporal and strong geographic patterns in the data, which are inconsistent with isolation by distance and indicate long range transport. In search of an explanation for our observations, we analyse the vector properties and travel patterns of commercial vessels on the river Rhine. We present evidence that freshwater cargo ships and tankers are plausible vectors for larvae of invasive goby species. We also present indications that cargo ships and tankers act as differential vectors for this species. In summary, we present genetic data at unique temporal resolution from a vertebrate invasion front and substantiate the paramount role of commercial shipping in freshwater fish translocations.
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Affiliation(s)
- I Adrian-Kalchhauser
- Program Man-Society-Environment, Department of Environmental Sciences, University of Basel, Vesalgasse 1, CH-4051, Basel, Switzerland
| | - P E Hirsch
- Program Man-Society-Environment, Department of Environmental Sciences, University of Basel, Vesalgasse 1, CH-4051, Basel, Switzerland.,Research Centre for Sustainable Energy and Water Supply, University of Basel, Peter Merian Weg 6, CH-4002, Basel, Switzerland
| | - J Behrmann-Godel
- Limnological Institute, University of Konstanz, Mainaustrasse 252, D-78457, Konstanz, Germany
| | - A N'Guyen
- Program Man-Society-Environment, Department of Environmental Sciences, University of Basel, Vesalgasse 1, CH-4051, Basel, Switzerland
| | - S Watzlawczyk
- Zoological Institute of the University of Cologne, Department of General Ecology & Limnology, Ecological Field Station Grietherbusch, D-50923, Cologne, Germany
| | - S Gertzen
- Zoological Institute of the University of Cologne, Department of General Ecology & Limnology, Ecological Field Station Grietherbusch, D-50923, Cologne, Germany
| | - J Borcherding
- Zoological Institute of the University of Cologne, Department of General Ecology & Limnology, Ecological Field Station Grietherbusch, D-50923, Cologne, Germany
| | - P Burkhardt-Holm
- Program Man-Society-Environment, Department of Environmental Sciences, University of Basel, Vesalgasse 1, CH-4051, Basel, Switzerland.,Department of Biological Sciences, University of Alberta, 11455 Saskatchewan Drive, Edmonton, AB, Canada
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Neilson ME, Stepien CA. Historic speciation and recent colonization of Eurasian monkey gobies (Neogobius fluviatilis and N. pallasi) revealed by DNA sequences, microsatellites, and morphology. DIVERS DISTRIB 2011. [DOI: 10.1111/j.1472-4642.2011.00762.x] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022] Open
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Bronnenhuber JE, Dufour BA, Higgs DM, Heath DD. Dispersal strategies, secondary range expansion and invasion genetics of the nonindigenous round goby, Neogobius melanostomus, in Great Lakes tributaries. Mol Ecol 2011; 20:1845-59. [PMID: 21492265 DOI: 10.1111/j.1365-294x.2011.05030.x] [Citation(s) in RCA: 72] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Dispersal strategies are important mechanisms underlying the spatial distribution and colonizing ability of all mobile species. In the current study, we use highly polymorphic microsatellite markers to evaluate local dispersal and colonization dynamics of the round goby (Neogobius melanostomus), an aquatic invader expanding its range from lake to river environments in its introduced North American range. Genetic structure, genotype assignment and genetic diversity were compared among 1262 round gobies from 20 river and four lake sites in three Great Lakes tributaries. Our results indicate that a combination of short-distance diffusion and long-distance dispersal, collectively referred to as 'stratified dispersal', is facilitating river colonization. Colonization proceeded upstream yearly (approximately 500 m/year; 2005-2009) in one of two temporal replicates while genetic structure was temporally stable. Contiguous dispersal from the lake was observed in all three rivers with a substantial portion of river fish (7.3%) identified as migrants. Genotype assignment indicated a separate introduction occurred upstream of the invasion front in one river. Genetic diversity was similar and relatively high among lake and recently colonized river populations, indicating that founder effects are mitigated through a dual-dispersal strategy. The remarkable success of round goby as an aquatic invader stresses the need for better diffusion models of secondary range expansion for presumably sessile invasive species.
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Affiliation(s)
- Jennifer E Bronnenhuber
- Great Lakes Institute for Environmental Research, University of Windsor, 401 Sunset Ave. Windsor, ON N9B 3P4, Canada
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Feldheim KA, Willink P, Brown JE, Murphy DJ, Neilson ME, Stepien CA. Microsatellite loci for Ponto-Caspian gobies: markers for assessing exotic invasions. Mol Ecol Resour 2009; 9:639-44. [PMID: 21564715 DOI: 10.1111/j.1755-0998.2008.02495.x] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
We developed and tested eight polymorphic microsatellite loci for Ponto-Caspian 'neogobiin' gobies, many of which are invasive in Eurasia and North America, whose study will aid understanding of the population genetics underlying their success. We tested samples from one to two locations from 12 taxa in the recently revised genera Babka, Benthophilus, Mesogobius, Neogobius = Apollonia, Ponticola and Proterorhinus; including the bighead, Caspian, knout, monkey, racer, round, tadpole and tubenose gobies; and taxa from introduced vs. native populations, those diverging between fresh and marine waters, and those differentiated between the Black and Caspian Seas. Populations conformed to Hardy-Weinberg equilibrium expectations, averaging five to 15 alleles per locus and 0.11 to 0.67 mean heterozygosity. Allelic variation significantly differentiated among all taxa and populations.
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Affiliation(s)
- Kevin A Feldheim
- Field Museum of Natural History, 1400 South Lake Shore Drive, Chicago, IL 60605, USA Lake Erie Center and the Department of Environmental Sciences, The University of Toledo, 6200 Bayshore Road, Toledo, OH 43618, USA
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