1
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Luo M, Hu J. Alternative splicing in parallel evolution and the evolutionary potential in sticklebacks. J Anim Ecol 2024. [PMID: 39056271 DOI: 10.1111/1365-2656.14157] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2023] [Accepted: 06/28/2024] [Indexed: 07/28/2024]
Abstract
Repeatability of adaptation to similar environments provides opportunity to evaluate the predictability of natural selection. While many studies have investigated gene expression differences between populations adapted to contrasting environments, the role of post-transcriptional processes such as alternative splicing has rarely been evaluated in the context of parallel adaptation. To address the aforementioned knowledge gap, we reanalysed transcriptomic data from three pairs of threespine stickleback (Gasterosteus aculeatus) ecotypes adapted to marine or freshwater environment. First, we identified genes with repeated expression or splicing divergence across ecotype pairs, and compared the genetic architecture and biological processes between parallelly expressed and parallelly spliced loci. Second, we analysed the extent to which parallel adaptation was reflected at gene expression and alternative splicing levels. Finally, we tested how the two axes of transcriptional variation differed in their potential for evolutionary change. Although both repeated differential splicing and differential expression across ecotype pairs showed tendency for parallel divergence, the degree of parallelism was lower for splicing than expression. Furthermore, parallel divergences in splicing and expression were likely to be associated with distinct cis-regulatory genetic variants and functionally unique set of genes. Finally, we found that parallelly spliced genes showed higher nucleotide diversity than parallelly expressed genes, indicating splicing is less susceptible to genetic variation erosion during parallel adaptation. Our results provide novel insight into the role of splicing in parallel adaptation, and underscore the contribution of splicing to the evolutionary potential of wild populations under environmental change.
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Affiliation(s)
- Man Luo
- Ministry of Education Key Laboratory for Biodiversity Science and Ecological Engineering, Institute of Biodiversity Science, Center for Evolutionary Biology, School of Life Sciences, Fudan University, Shanghai, China
| | - Juntao Hu
- Ministry of Education Key Laboratory for Biodiversity Science and Ecological Engineering, Institute of Biodiversity Science, Center for Evolutionary Biology, School of Life Sciences, Fudan University, Shanghai, China
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2
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Gutiérrez-Guerrero YT, Phifer-Rixey M, Nachman MW. Across two continents: The genomic basis of environmental adaptation in house mice (Mus musculus domesticus) from the Americas. PLoS Genet 2024; 20:e1011036. [PMID: 38968323 PMCID: PMC11253941 DOI: 10.1371/journal.pgen.1011036] [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: 10/27/2023] [Revised: 07/17/2024] [Accepted: 06/10/2024] [Indexed: 07/07/2024] Open
Abstract
Replicated clines across environmental gradients can be strong evidence of adaptation. House mice (Mus musculus domesticus) were introduced to the Americas by European colonizers and are now widely distributed from Tierra del Fuego to Alaska. Multiple aspects of climate, such as temperature, vary predictably across latitude in the Americas. Past studies of North American populations across latitudinal gradients provided evidence of environmental adaptation in traits related to body size, metabolism, and behavior and identified candidate genes using selection scans. Here, we investigate genomic signals of environmental adaptation on a second continent, South America, and ask whether there is evidence of parallel adaptation across multiple latitudinal transects in the Americas. We first identified loci across the genome showing signatures of selection related to climatic variation in mice sampled across a latitudinal transect in South America, accounting for neutral population structure. Consistent with previous results, most candidate SNPs were in putatively regulatory regions. Genes that contained the most extreme outliers relate to traits such as body weight or size, metabolism, immunity, fat, eye function, and the cardiovascular system. We then compared these results with the results of analyses of published data from two transects in North America. While most candidate genes were unique to individual transects, we found significant overlap among candidate genes identified independently in the three transects. These genes are diverse, with functions relating to metabolism, immunity, cardiac function, and circadian rhythm, among others. We also found parallel shifts in allele frequency in candidate genes across latitudinal gradients. Finally, combining data from all three transects, we identified several genes associated with variation in body weight. Overall, our results provide strong evidence of shared responses to selection and identify genes that likely underlie recent environmental adaptation in house mice across North and South America.
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Affiliation(s)
- Yocelyn T. Gutiérrez-Guerrero
- Department of Integrative Biology and Museum of Vertebrate Zoology, University of California, Berkeley, California, United States of America
| | - Megan Phifer-Rixey
- Department of Integrative Biology and Museum of Vertebrate Zoology, University of California, Berkeley, California, United States of America
- Department of Biology, Drexel University, Philadelphia, Pennsylvania, United States of America
| | - Michael W. Nachman
- Department of Integrative Biology and Museum of Vertebrate Zoology, University of California, Berkeley, California, United States of America
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3
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Efstratiou A, Gaigher A, Künzel S, Teles A, Lenz TL. Template-specific optimization of NGS genotyping pipelines reveals allele-specific variation in MHC gene expression. Mol Ecol Resour 2024; 24:e13935. [PMID: 38332480 DOI: 10.1111/1755-0998.13935] [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: 06/02/2023] [Revised: 01/19/2024] [Accepted: 01/25/2024] [Indexed: 02/10/2024]
Abstract
Using high-throughput sequencing for precise genotyping of multi-locus gene families, such as the major histocompatibility complex (MHC), remains challenging, due to the complexity of the data and difficulties in distinguishing genuine from erroneous variants. Several dedicated genotyping pipelines for data from high-throughput sequencing, such as next-generation sequencing (NGS), have been developed to tackle the ensuing risk of artificially inflated diversity. Here, we thoroughly assess three such multi-locus genotyping pipelines for NGS data, the DOC method, AmpliSAS and ACACIA, using MHC class IIβ data sets of three-spined stickleback gDNA, cDNA and "artificial" plasmid samples with known allelic diversity. We show that genotyping of gDNA and plasmid samples at optimal pipeline parameters was highly accurate and reproducible across methods. However, for cDNA data, the gDNA-optimal parameter configuration yielded decreased overall genotyping precision and consistency between pipelines. Further adjustments of key clustering parameters were required tο account for higher error rates and larger variation in sequencing depth per allele, highlighting the importance of template-specific pipeline optimization for reliable genotyping of multi-locus gene families. Through accurate paired gDNA-cDNA typing and MHC-II haplotype inference, we show that MHC-II allele-specific expression levels correlate negatively with allele number across haplotypes. Lastly, sibship-assisted cDNA-typing of MHC-I revealed novel variants linked in haplotype blocks, and a higher-than-previously-reported individual MHC-I allelic diversity. In conclusion, we provide novel genotyping protocols for the three-spined stickleback MHC-I and -II genes, and evaluate the performance of popular NGS-genotyping pipelines. We also show that fine-tuned genotyping of paired gDNA-cDNA samples facilitates amplification bias-corrected MHC allele expression analysis.
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Affiliation(s)
- Artemis Efstratiou
- Research Unit for Evolutionary Immunogenomics, Department of Biology, University of Hamburg, Hamburg, Germany
- Research Group for Evolutionary Immunogenomics, Max Planck Institute for Evolutionary Biology, Plön, Germany
| | - Arnaud Gaigher
- Research Unit for Evolutionary Immunogenomics, Department of Biology, University of Hamburg, Hamburg, Germany
- Research Group for Evolutionary Immunogenomics, Max Planck Institute for Evolutionary Biology, Plön, Germany
- CIBIO-InBIO, Research Center in Biodiversity and Genetic Resources, University of Porto, Vairão, Portugal
| | - Sven Künzel
- Department of Evolutionary Genetics, Max Planck Institute for Evolutionary Biology, Plön, Germany
| | - Ana Teles
- Research Unit for Evolutionary Immunogenomics, Department of Biology, University of Hamburg, Hamburg, Germany
- Research Group for Evolutionary Immunogenomics, Max Planck Institute for Evolutionary Biology, Plön, Germany
- Department of Evolutionary Ecology, Max Planck Institute for Evolutionary Biology, Plön, Germany
| | - Tobias L Lenz
- Research Unit for Evolutionary Immunogenomics, Department of Biology, University of Hamburg, Hamburg, Germany
- Research Group for Evolutionary Immunogenomics, Max Planck Institute for Evolutionary Biology, Plön, Germany
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4
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Coll-Costa C, Dahms C, Kemppainen P, Alexandre CM, Ribeiro F, Zanella D, Zanella L, Merilä J, Momigliano P. Parallel evolution despite low genetic diversity in three-spined sticklebacks. Proc Biol Sci 2024; 291:20232617. [PMID: 38593844 PMCID: PMC11003780 DOI: 10.1098/rspb.2023.2617] [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: 11/20/2023] [Accepted: 03/08/2024] [Indexed: 04/11/2024] Open
Abstract
When populations repeatedly adapt to similar environments they can evolve similar phenotypes based on shared genetic mechanisms (parallel evolution). The likelihood of parallel evolution is affected by demographic history, as it depends on the standing genetic variation of the source population. The three-spined stickleback (Gasterosteus aculeatus) repeatedly colonized and adapted to brackish and freshwater. Most parallel evolution studies in G. aculeatus were conducted at high latitudes, where freshwater populations maintain connectivity to the source marine populations. Here, we analysed southern and northern European marine and freshwater populations to test two hypotheses. First, that southern European freshwater populations (which currently lack connection to marine populations) lost genetic diversity due to bottlenecks and inbreeding compared to their northern counterparts. Second, that the degree of genetic parallelism is higher among northern than southern European freshwater populations, as the latter have been subjected to strong drift due to isolation. The results show that southern populations exhibit lower genetic diversity but a higher degree of genetic parallelism than northern populations. Hence, they confirm the hypothesis that southern populations have lost genetic diversity, but this loss probably happened after they had already adapted to freshwater conditions, explaining the high degree of genetic parallelism in the south.
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Affiliation(s)
- Carla Coll-Costa
- Ecological Genetics Research Unit, Organismal and Evolutionary Biology Research Programme, Faculty of Biological and Environmental Sciences, University of Helsinki, Helsinki, FI-00014, Finland
| | - Carolin Dahms
- School of Biological Sciences, Faculty of Science, The University of Hong Kong, Hong Kong SAR, People's Republic of China
- Swire Institute of Marine Science, Faculty of Science, The University of Hong Kong, Hong Kong SAR, People's Republic of China
| | - Petri Kemppainen
- School of Biological Sciences, Faculty of Science, The University of Hong Kong, Hong Kong SAR, People's Republic of China
- Swire Institute of Marine Science, Faculty of Science, The University of Hong Kong, Hong Kong SAR, People's Republic of China
| | - Carlos M. Alexandre
- MARE—Marine and Environmental Sciences Centre, Universidade de Évora, Évora, 7004-516, Portugal
| | - Filipe Ribeiro
- MARE—Marine and Environmental Sciences Centre, Faculdade de Ciências, Universidade de Lisboa, Campo Grande, 1749-016, Lisboa, Portugal
| | - Davor Zanella
- Department of Biology, Faculty of Science, University of Zagreb, Rooseveltov trg 6, Zagreb, 10000, Croatia
| | - Linda Zanella
- Department of Biology, Faculty of Science, University of Zagreb, Rooseveltov trg 6, Zagreb, 10000, Croatia
| | - Juha Merilä
- Ecological Genetics Research Unit, Organismal and Evolutionary Biology Research Programme, Faculty of Biological and Environmental Sciences, University of Helsinki, Helsinki, FI-00014, Finland
- School of Biological Sciences, Faculty of Science, The University of Hong Kong, Hong Kong SAR, People's Republic of China
| | - Paolo Momigliano
- School of Biological Sciences, Faculty of Science, The University of Hong Kong, Hong Kong SAR, People's Republic of China
- Swire Institute of Marine Science, Faculty of Science, The University of Hong Kong, Hong Kong SAR, People's Republic of China
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5
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Thorburn DMJ, Sagonas K, Binzer-Panchal M, Chain FJJ, Feulner PGD, Bornberg-Bauer E, Reusch TBH, Samonte-Padilla IE, Milinski M, Lenz TL, Eizaguirre C. Origin matters: Using a local reference genome improves measures in population genomics. Mol Ecol Resour 2023; 23:1706-1723. [PMID: 37489282 DOI: 10.1111/1755-0998.13838] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2023] [Revised: 05/10/2023] [Accepted: 06/02/2023] [Indexed: 07/26/2023]
Abstract
Genome sequencing enables answering fundamental questions about the genetic basis of adaptation, population structure and epigenetic mechanisms. Yet, we usually need a suitable reference genome for mapping population-level resequencing data. In some model systems, multiple reference genomes are available, giving the challenging task of determining which reference genome best suits the data. Here, we compared the use of two different reference genomes for the three-spined stickleback (Gasterosteus aculeatus), one novel genome derived from a European gynogenetic individual and the published reference genome of a North American individual. Specifically, we investigated the impact of using a local reference versus one generated from a distinct lineage on several common population genomics analyses. Through mapping genome resequencing data of 60 sticklebacks from across Europe and North America, we demonstrate that genetic distance among samples and the reference genomes impacts downstream analyses. Using a local reference genome increased mapping efficiency and genotyping accuracy, effectively retaining more and better data. Despite comparable distributions of the metrics generated across the genome using SNP data (i.e. π, Tajima's D and FST ), window-based statistics using different references resulted in different outlier genes and enriched gene functions. A marker-based analysis of DNA methylation distributions had a comparably high overlap in outlier genes and functions, yet with distinct differences depending on the reference genome. Overall, our results highlight how using a local reference genome decreases reference bias to increase confidence in downstream analyses of the data. Such results have significant implications in all reference-genome-based population genomic analyses.
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Affiliation(s)
- Doko-Miles J Thorburn
- School of Biological and Chemical Sciences, Queen Mary University of London, London, UK
- Department of Life Sciences, Imperial College London, London, UK
| | - Kostas Sagonas
- School of Biological and Chemical Sciences, Queen Mary University of London, London, UK
- Department of Zoology, School of Biology, Aristotle University of Thessaloniki, Thessaloniki, Greece
| | - Mahesh Binzer-Panchal
- Science for Life Laboratory, Department of Medical Biochemistry and Microbiology, National Bioinformatics Infrastructure Sweden (NBIS), Uppsala University, Uppsala, Sweden
| | - Frederic J J Chain
- Department of Biological Sciences, University of Massachusetts Lowell, Lowell, Massachusetts, USA
| | - Philine G D Feulner
- Department of Fish Ecology and Evolution, Centre of Ecology, Evolution and Biogeochemistry, EAWAG Swiss Federal Institute of Aquatic Science and Technology, Kastanienbaum, Switzerland
- Division of Aquatic Ecology and Evolution, Institute of Ecology and Evolution, University of Bern, Bern, Switzerland
| | - Erich Bornberg-Bauer
- Evolutionary Bioinformatics, Institute for Evolution and Biodiversity, University of Münster, Münster, Germany
| | - Thorsten B H Reusch
- Marine Evolutionary Ecology, GEOMAR Helmholtz Centre for Ocean Research, Kiel, Germany
| | - Irene E Samonte-Padilla
- Department of Evolutionary Ecology, Max Planck Institute for Evolutionary Biology, Plön, Germany
| | - Manfred Milinski
- Department of Evolutionary Ecology, Max Planck Institute for Evolutionary Biology, Plön, Germany
| | - Tobias L Lenz
- Research Group for Evolutionary Immunogenomics, Max Planck Institute for Evolutionary Biology, Plön, Germany
- Research Unit for Evolutionary Immunogenomics, Department of Biology, University of Hamburg, Hamburg, Germany
| | - Christophe Eizaguirre
- School of Biological and Chemical Sciences, Queen Mary University of London, London, UK
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6
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Hudson CM, Cuenca Cambronero M, Moosmann M, Narwani A, Spaak P, Seehausen O, Matthews B. Environmentally independent selection for hybrids between divergent freshwater stickleback lineages in semi-natural ponds. J Evol Biol 2023; 36:1166-1184. [PMID: 37394735 DOI: 10.1111/jeb.14194] [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: 11/16/2022] [Revised: 05/03/2023] [Accepted: 05/31/2023] [Indexed: 07/04/2023]
Abstract
Hybridization following secondary contact of genetically divergent populations can influence the range expansion of invasive species, though specific outcomes depend on the environmental dependence of hybrid fitness. Here, using two genetically and ecologically divergent threespine stickleback lineages that differ in their history of freshwater colonization, we estimate fitness variation of parental lineages and hybrids in semi-natural freshwater ponds with contrasting histories of nutrient loading. In our experiment, we found that fish from the older freshwater lineage (Lake Geneva) and hybrids outperformed fish from the younger freshwater lineage (Lake Constance) in terms of both growth and survival, regardless of the environmental context of our ponds. Across all ponds, hybrids exhibited the highest survival. Although wild-caught adult populations differed in their functional and defence morphology, it is unclear which of these traits underlie the fitness differences observed among juveniles in our experiment. Overall, our work suggests that when hybrid fitness is insensitive to environmental conditions, as observed here, introgression may promote population expansion into unoccupied habitats and accelerate invasion success.
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Affiliation(s)
- Cameron Marshall Hudson
- Department of Fish Ecology and Evolution, Eawag, Swiss Federal Institute of Aquatic Science and Technology, Center of Ecology, Evolution and Biochemistry, Lucerne, Switzerland
- Division of Aquatic Ecology and Evolution, Institute of Ecology and Evolution, University of Bern, Bern, Switzerland
- Department of Aquatic Ecology, Eawag, Swiss Federal Institute of Aquatic Science and Technology, Zürich, Switzerland
| | - Maria Cuenca Cambronero
- Department of Fish Ecology and Evolution, Eawag, Swiss Federal Institute of Aquatic Science and Technology, Center of Ecology, Evolution and Biochemistry, Lucerne, Switzerland
- Aquatic Ecology Group, University of Vic, Central University of Catalonia, Vic, Spain
| | - Marvin Moosmann
- Department of Fish Ecology and Evolution, Eawag, Swiss Federal Institute of Aquatic Science and Technology, Center of Ecology, Evolution and Biochemistry, Lucerne, Switzerland
- Division of Aquatic Ecology and Evolution, Institute of Ecology and Evolution, University of Bern, Bern, Switzerland
| | - Anita Narwani
- Department of Aquatic Ecology, Eawag, Swiss Federal Institute of Aquatic Science and Technology, Zürich, Switzerland
| | - Piet Spaak
- Department of Aquatic Ecology, Eawag, Swiss Federal Institute of Aquatic Science and Technology, Zürich, Switzerland
| | - Ole Seehausen
- Department of Fish Ecology and Evolution, Eawag, Swiss Federal Institute of Aquatic Science and Technology, Center of Ecology, Evolution and Biochemistry, Lucerne, Switzerland
- Division of Aquatic Ecology and Evolution, Institute of Ecology and Evolution, University of Bern, Bern, Switzerland
| | - Blake Matthews
- Department of Fish Ecology and Evolution, Eawag, Swiss Federal Institute of Aquatic Science and Technology, Center of Ecology, Evolution and Biochemistry, Lucerne, Switzerland
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7
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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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8
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Turba R, Richmond JQ, Fitz-Gibbon S, Morselli M, Fisher RN, Swift CC, Ruiz-Campos G, Backlin AR, Dellith C, Jacobs DK. Genetic structure and historic demography of endangered unarmoured threespine stickleback at southern latitudes signals a potential new management approach. Mol Ecol 2022; 31:6515-6530. [PMID: 36205603 PMCID: PMC10092051 DOI: 10.1111/mec.16722] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2022] [Revised: 09/05/2022] [Accepted: 09/29/2022] [Indexed: 01/13/2023]
Abstract
Habitat loss, flood control infrastructure, and drought have left most of southern California and northern Baja California's native freshwater fish near extinction, including the endangered unarmoured threespine stickleback (Gasterosteus aculeatus williamsoni). This subspecies, an unusual morph lacking the typical lateral bony plates of the G. aculeatus complex, occurs at arid southern latitudes in the eastern Pacific Ocean and survives in only three inland locations. Managers have lacked molecular data to answer basic questions about the ancestry and genetic distinctiveness of unarmoured populations. These data could be used to prioritize conservation efforts. We sampled G. aculeatus from 36 localities and used microsatellites and whole genome data to place unarmoured populations within the broader evolutionary context of G. aculeatus across southern California/northern Baja California. We identified three genetic groups with none consisting solely of unarmoured populations. Unlike G. aculeatus at northern latitudes, where Pleistocene glaciation has produced similar historical demographic profiles across populations, we found markedly different demographics depending on sampling location, with inland unarmoured populations showing steeper population declines and lower heterozygosity compared to low armoured populations in coastal lagoons. One exception involved the only high elevation population in the region, where the demography and alleles of unarmoured fish were similar to low armoured populations near the coast, exposing one of several cases of artificial translocation. Our results suggest that the current "management-by-phenotype" approach, based on lateral plates, is incidentally protecting the most imperilled populations; however, redirecting efforts toward evolutionary units, regardless of phenotype, may more effectively preserve adaptive potential.
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Affiliation(s)
- Rachel Turba
- Department of Ecology and Evolutionary Biology, University of California, Los Angeles, California, USA
| | | | - Sorel Fitz-Gibbon
- Department of Ecology and Evolutionary Biology, University of California, Los Angeles, California, USA
| | - Marco Morselli
- Department of Molecular, Cell and Developmental Biology, University of California, Los Angeles, California, USA
| | | | - Camm C Swift
- Emeritus, Section of Fishes, Natural History Museum of Los Angeles County, Los Angeles, California, USA
| | - Gorgonio Ruiz-Campos
- Ichthyological Collection, Facultad de Ciencias, Universidad Autónoma de Baja California, Ensenada, Baja California, Mexico
| | - Adam R Backlin
- U.S. Geological Survey, Western Ecological Research Center, San Diego Field Station-Santa Ana Office, Santa Ana, California, USA
| | - Chris Dellith
- U.S. Fish and Wildlife Service, Ventura, California, USA
| | - David K Jacobs
- Department of Ecology and Evolutionary Biology, University of California, Los Angeles, California, USA
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9
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Ogorelec Ž, Brinker A, Straile D. Small but voracious: invasive generalist consumes more zooplankton in winter than native planktivore. NEOBIOTA 2022. [DOI: 10.3897/neobiota.78.86788] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
Abstract
In recent years, Lake Constance has experienced an invasion and domination of three-spined stickleback (Gasterosteus aculeatus) in the pelagic zone, which has coincided with a decline in the native whitefish (Coregonus wartmanni) population. Similar massive invasions of sticklebacks into pelagic zones have been recognized also in marine areas or small lakes worldwide. However, their diet overlaps with native species is rarely evaluated, especially in the winter season, which often presents a bottleneck for fish survival. In this study, we compared the diet of pelagic sticklebacks with the diet of the substantially larger native whitefish in different seasons, to evaluate the threat of the recent stickleback invasion on whitefish populations. By monthly sampling of zooplankton and both fish species diets, we could demonstrate that sticklebacks select similar prey throughout most of the year and consume more prey than whitefish during the winter. With relations between prey availability and prey selection, interspecific and intraspecific seasonal diet variability and indices like a prey-specific index of relative importance, we discuss the importance of zooplankton species traits and abundance for whitefish and stickleback predation. This study shows that sticklebacks, despite their small size, represent a serious potential diet competitor to native planktivorous fish. Sticklebacks quickly adapt to new environments, and thus we advocate precautions regarding their introduction into similar lakes as Lake Constance, as this could cause irreversible ecological changes.
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10
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Characterizing phenotypic diversity in marine populations of the threespine stickleback. Sci Rep 2022; 12:17923. [PMID: 36289364 PMCID: PMC9606258 DOI: 10.1038/s41598-022-22872-z] [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] [Received: 10/19/2021] [Accepted: 10/20/2022] [Indexed: 01/20/2023] Open
Abstract
The threespine stickleback (Gasterosteus aculeatus) is an important model for studying the evolution of vertebrate morphology. Sticklebacks inhabit freshwater, brackish, and marine northern hemisphere waters. Anadromous and marine populations (hereafter marine) are assumed to have remained unchanged morphologically from ancestral marine sticklebacks, despite marine environments varying on regional and local scales. Recent studies suggest that genetic and phenotypic structure exists in marine populations, yet the scale of this variation, and its ecological causes remain unclear. Our goal was to assess morphological trait variation in marine stickleback populations around Southern British Columbia (BC) and determine if oceanographic and habitat characteristics were associated with this variation. Between May-July 2019, we sampled 534 sticklebacks from 15 sites around Vancouver Island, a region characterized by a large diversity of oceanographic and habitat features. We characterized trait variation using two-dimensional (2D) geometric morphometric analysis, comparing individuals between oceanographic regions and habitats. We focused on head and body shape. We found that marine sticklebacks varied morphologically among and between regions and habitats, but the variation did not appear to be related to environmental variation. Sexual dimorphism was the largest source of variation, but oceanographic and habitat variables influenced differences between sexes. We concluded that marine sticklebacks offer abundant opportunities for expanding our knowledge of drivers of morphology.
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11
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Ishikawa A, Yamanouchi S, Iwasaki W, Kitano J. Convergent copy number increase of genes associated with freshwater colonization in fishes. Philos Trans R Soc Lond B Biol Sci 2022; 377:20200509. [PMID: 35634928 PMCID: PMC9149799 DOI: 10.1098/rstb.2020.0509] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2021] [Accepted: 03/14/2022] [Indexed: 07/20/2023] Open
Abstract
Copy number variation (CNV) can cause phenotypic changes. However, in contrast to amino acid substitutions and cis-regulatory changes, little is known about the functional categories of genes in which CNV is important for adaptation to novel environments. It is also unclear whether the same genes repeatedly change the copy numbers for adapting to similar environments. Here, we investigate CNV associated with freshwater colonization in fishes, which was observed multiple times across different lineages. Using 48 ray-finned fishes across diverse orders, we identified 23 genes whose copy number increases were associated with freshwater colonization. These genes showed enrichment for peptide receptor activity, hexosyltransferase activity and unsaturated fatty acid metabolism. We further revealed that three of the genes showed copy number increases in freshwater populations compared to marine ancestral populations of the stickleback genus Gasterosteus. These results indicate that copy number increases of genes involved in fatty acid metabolism (FADS2), immune function (PSMB8a) and thyroid hormone metabolism (UGT2) may be important for freshwater colonization at both the inter-order macroevolutionary scale and at the intra-genus microevolutionary scale. Further analysis across diverse taxa will help to understand the role of CNV in the adaptation to novel environments. This article is part of the theme issue 'Genetic basis of adaptation and speciation: from loci to causative mutations'.
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Affiliation(s)
- Asano Ishikawa
- Ecological Genetics Laboratory, National Institute of Genetics, Yata 1111, Mishima, Shizuoka 411-8540, Japan
- Department of Integrated Biosciences, Graduate School of Frontier Sciences, The University of Tokyo, 5-1-5 Kashiwanoha, Kashiwa, Chiba 277-8562, Japan
| | - Shun Yamanouchi
- Department of Biological Sciences, Graduate School of Science, The University of Tokyo, 2-11-16 Yayoi, Bunkyo-ku, Tokyo 113-0032, Japan
| | - Wataru Iwasaki
- Department of Integrated Biosciences, Graduate School of Frontier Sciences, The University of Tokyo, 5-1-5 Kashiwanoha, Kashiwa, Chiba 277-8562, Japan
- Department of Biological Sciences, Graduate School of Science, The University of Tokyo, 2-11-16 Yayoi, Bunkyo-ku, Tokyo 113-0032, Japan
| | - Jun Kitano
- Ecological Genetics Laboratory, National Institute of Genetics, Yata 1111, Mishima, Shizuoka 411-8540, Japan
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12
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Hesse T, Nachev M, Khaliq S, Jochmann MA, Franke F, Scharsack JP, Kurtz J, Sures B, Schmidt TC. Insights into amino acid fractionation and incorporation by compound-specific carbon isotope analysis of three-spined sticklebacks. Sci Rep 2022; 12:11690. [PMID: 35804029 PMCID: PMC9270445 DOI: 10.1038/s41598-022-15704-7] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2021] [Accepted: 06/28/2022] [Indexed: 11/17/2022] Open
Abstract
Interpretation of stable isotope data is of upmost importance in ecology to build sound models for the study of animal diets, migration patterns and physiology. However, our understanding of stable isotope fractionation and incorporation into consumer tissues is still limited. We therefore measured the δ13C values of individual amino acids over time from muscle and liver tissue of three-spined sticklebacks (Gasterosteus aculeatus) on a high protein diet. The δ13C values of amino acids in the liver quickly responded to small shifts of under ± 2.0‰ in dietary stable isotope compositions on 30-day intervals. We found on average no trophic fractionation in pooled essential (muscle, liver) and non-essential (muscle) amino acids. Negative Δδ13C values of − 0.7 ± 1.3‰ were observed for pooled non-essential (liver) amino acids and might indicate biosynthesis from small amounts of dietary lipids. Trophic fractionation of individual amino acids is reported and discussed, including unusual Δδ13C values of over + 4.9 ± 1.4‰ for histidine. Arginine and lysine showed the lowest trophic fractionation on individual sampling days and might be useful proxies for dietary sources on short time scales. We suggest further investigations using isotopically enriched materials to facilitate the correct interpretation of ecological field data.
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Affiliation(s)
- Tobias Hesse
- Instrumental Analytical Chemistry, University of Duisburg-Essen, Universitätsstr. 5, 45141, Essen, Germany
| | - Milen Nachev
- Aquatic Ecology, University of Duisburg-Essen, Universitätsstr. 5, 45141, Essen, Germany.,Centre for Water and Environmental Research, University of Duisburg-Essen, Universitätsstr. 5, 45141, Essen, Germany
| | - Shaista Khaliq
- Instrumental Analytical Chemistry, University of Duisburg-Essen, Universitätsstr. 5, 45141, Essen, Germany
| | - Maik A Jochmann
- Instrumental Analytical Chemistry, University of Duisburg-Essen, Universitätsstr. 5, 45141, Essen, Germany. .,Centre for Water and Environmental Research, University of Duisburg-Essen, Universitätsstr. 5, 45141, Essen, Germany.
| | - Frederik Franke
- Institute for Evolution & Biodiversity, University of Münster, Hüfferstr. 1, 48149, Münster, Germany.,Bavarian State Institute of Forestry, Hans-Carl-von-Carlowitz-Platz 1, 85354, Freising, Germany
| | - Jörn P Scharsack
- Institute for Evolution & Biodiversity, University of Münster, Hüfferstr. 1, 48149, Münster, Germany.,Thünen Institute of Fisheries Ecology, Herwigstr. 31, 27572, Bremerhaven, Germany
| | - Joachim Kurtz
- Institute for Evolution & Biodiversity, University of Münster, Hüfferstr. 1, 48149, Münster, Germany
| | - Bernd Sures
- Aquatic Ecology, University of Duisburg-Essen, Universitätsstr. 5, 45141, Essen, Germany.,Centre for Water and Environmental Research, University of Duisburg-Essen, Universitätsstr. 5, 45141, Essen, Germany
| | - Torsten C Schmidt
- Instrumental Analytical Chemistry, University of Duisburg-Essen, Universitätsstr. 5, 45141, Essen, Germany.,Centre for Water and Environmental Research, University of Duisburg-Essen, Universitätsstr. 5, 45141, Essen, Germany
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13
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Vernygora OV, Campbell EO, Grishin NV, Sperling FA, Dupuis JR. Gauging ages of tiger swallowtail butterflies using alternate SNP analyses. Mol Phylogenet Evol 2022; 171:107465. [DOI: 10.1016/j.ympev.2022.107465] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2022] [Revised: 02/26/2022] [Accepted: 03/15/2022] [Indexed: 10/18/2022]
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14
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Dahms C, Kemppainen P, Zanella LN, Zanella D, Carosi A, Merilä J, Momigliano P. Cast away in the Adriatic: Low degree of parallel genetic differentiation in three-spined sticklebacks. Mol Ecol 2021; 31:1234-1253. [PMID: 34843145 DOI: 10.1111/mec.16295] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2021] [Revised: 11/16/2021] [Accepted: 11/19/2021] [Indexed: 12/14/2022]
Abstract
The three-spined stickleback (Gasterosteus aculeatus) has repeatedly and independently adapted to freshwater habitats from standing genetic variation (SGV) following colonization from the sea. However, in the Mediterranean Sea G. aculeatus is believed to have gone extinct, and thus the spread of locally adapted alleles between different freshwater populations via the sea since then has been highly unlikely. This is expected to limit parallel evolution, that is the extent to which phylogenetically related alleles can be shared among independently colonized freshwater populations. Using whole genome and 2b-RAD sequencing data, we compared levels of genetic differentiation and genetic parallelism of 15 Adriatic stickleback populations to 19 Pacific, Atlantic and Caspian populations, where gene flow between freshwater populations across extant marine populations is still possible. Our findings support previous studies suggesting that Adriatic populations are highly differentiated (average FST ≈ 0.45), of low genetic diversity and connectivity, and likely to stem from multiple independent colonizations during the Pleistocene. Linkage disequilibrium network analyses in combination with linear mixed models nevertheless revealed several parallel marine-freshwater differentiated genomic regions, although still not to the extent observed elsewhere in the world. We hypothesize that current levels of genetic parallelism in the Adriatic lineages are a relic of freshwater adaptation from SGV prior to the extinction of marine sticklebacks in the Mediterranean that has persisted despite substantial genetic drift experienced by the Adriatic stickleback isolates.
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Affiliation(s)
- Carolin Dahms
- Ecological Genetics Research Unit, Organismal and Evolutionary Biology Research Programme, Faculty of Biological and Environmental Sciences, University of Helsinki, Helsinki, Finland
| | - Petri Kemppainen
- Ecological Genetics Research Unit, Organismal and Evolutionary Biology Research Programme, Faculty of Biological and Environmental Sciences, University of Helsinki, Helsinki, Finland
| | - Linda N Zanella
- Department of Zoology, Faculty of Science, University of Zagreb, Zagreb, Croatia
| | - Davor Zanella
- Department of Zoology, Faculty of Science, University of Zagreb, Zagreb, Croatia
| | - Antonella Carosi
- Department of Chemistry, Biology and Biotechnologies, University of Perugia, Perugia, Italy
| | - Juha Merilä
- Ecological Genetics Research Unit, Organismal and Evolutionary Biology Research Programme, Faculty of Biological and Environmental Sciences, University of Helsinki, Helsinki, Finland.,Division for Ecology and Biodiversity, School of Biological Sciences, Faculty of Science, The University of Hong Kong, Hong Kong SAR, Hong Kong
| | - Paolo Momigliano
- Ecological Genetics Research Unit, Organismal and Evolutionary Biology Research Programme, Faculty of Biological and Environmental Sciences, University of Helsinki, Helsinki, Finland
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15
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Piecyk A, Hahn MA, Roth O, Dheilly NM, Heins DC, Bell MA, Kalbe M. Cross-continental experimental infections reveal distinct defence mechanisms in populations of the three-spined stickleback Gasterosteus aculeatus. Proc Biol Sci 2021; 288:20211758. [PMID: 34547906 PMCID: PMC8456148 DOI: 10.1098/rspb.2021.1758] [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: 08/05/2021] [Accepted: 09/02/2021] [Indexed: 11/12/2022] Open
Abstract
Epidemiological traits of host-parasite associations depend on the effects of the host, the parasite and their interaction. Parasites evolve mechanisms to infect and exploit their hosts, whereas hosts evolve mechanisms to prevent infection and limit detrimental effects. The reasons why and how these traits differ across populations still remain unclear. Using experimental cross-infection of three-spined stickleback Gasterosteus aculeatus and their species-specific cestode parasites Schistocephalus solidus from Alaskan and European populations, we disentangled host, parasite and interaction effects on epidemiological traits at different geographical scales. We hypothesized that host and parasite main effects would dominate both within and across continents, although interaction effects would show geographical variation of natural selection within and across continents. We found that mechanisms preventing infection (qualitative resistance) occurred only in a combination of hosts and parasites from different continents, while mechanisms limiting parasite burden (quantitative resistance) and reducing detrimental effects of infection (tolerance) were host-population specific. We conclude that evolution favours distinct defence mechanisms on different geographical scales and that it is important to distinguish concepts of qualitative resistance, quantitative resistance and tolerance in studies of macroparasite infections.
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Affiliation(s)
- Agnes Piecyk
- Evolutionary Ecology, Max Planck Institute for Evolutionary Biology, Plön, Germany
- Evolutionary Ecology of Marine Fishes, GEOMAR Helmholtz Centre for Ocean Research Kiel, Kiel, Germany
| | - Megan A. Hahn
- School of Marine and Atmospheric Sciences, Stony Brook University, Stony Brook, NY, USA
| | - Olivia Roth
- Evolutionary Ecology of Marine Fishes, GEOMAR Helmholtz Centre for Ocean Research Kiel, Kiel, Germany
- Marine Evolutionary Biology, Kiel University, Kiel, Germany
| | - Nolwenn M. Dheilly
- School of Marine and Atmospheric Sciences, Stony Brook University, Stony Brook, NY, USA
| | - David C. Heins
- Department of Ecology and Evolutionary Biology, Tulane University, New Orleans, LA, USA
| | - Michael A. Bell
- University of California Museum of Paleontology, University of California, Berkeley, CA, USA
| | - Martin Kalbe
- Evolutionary Ecology, Max Planck Institute for Evolutionary Biology, Plön, Germany
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16
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Christiansen H, Heindler FM, Hellemans B, Jossart Q, Pasotti F, Robert H, Verheye M, Danis B, Kochzius M, Leliaert F, Moreau C, Patel T, Van de Putte AP, Vanreusel A, Volckaert FAM, Schön I. Facilitating population genomics of non-model organisms through optimized experimental design for reduced representation sequencing. BMC Genomics 2021; 22:625. [PMID: 34418978 PMCID: PMC8380342 DOI: 10.1186/s12864-021-07917-3] [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: 04/02/2021] [Accepted: 07/26/2021] [Indexed: 12/26/2022] Open
Abstract
BACKGROUND Genome-wide data are invaluable to characterize differentiation and adaptation of natural populations. Reduced representation sequencing (RRS) subsamples a genome repeatedly across many individuals. However, RRS requires careful optimization and fine-tuning to deliver high marker density while being cost-efficient. The number of genomic fragments created through restriction enzyme digestion and the sequencing library setup must match to achieve sufficient sequencing coverage per locus. Here, we present a workflow based on published information and computational and experimental procedures to investigate and streamline the applicability of RRS. RESULTS In an iterative process genome size estimates, restriction enzymes and size selection windows were tested and scaled in six classes of Antarctic animals (Ostracoda, Malacostraca, Bivalvia, Asteroidea, Actinopterygii, Aves). Achieving high marker density would be expensive in amphipods, the malacostracan target taxon, due to the large genome size. We propose alternative approaches such as mitogenome or target capture sequencing for this group. Pilot libraries were sequenced for all other target taxa. Ostracods, bivalves, sea stars, and fish showed overall good coverage and marker numbers for downstream population genomic analyses. In contrast, the bird test library produced low coverage and few polymorphic loci, likely due to degraded DNA. CONCLUSIONS Prior testing and optimization are important to identify which groups are amenable for RRS and where alternative methods may currently offer better cost-benefit ratios. The steps outlined here are easy to follow for other non-model taxa with little genomic resources, thus stimulating efficient resource use for the many pressing research questions in molecular ecology.
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Affiliation(s)
- Henrik Christiansen
- Laboratory of Biodiversity and Evolutionary Genomics, KU Leuven, Leuven, Belgium.
| | - Franz M Heindler
- Laboratory of Biodiversity and Evolutionary Genomics, KU Leuven, Leuven, Belgium
| | - Bart Hellemans
- Laboratory of Biodiversity and Evolutionary Genomics, KU Leuven, Leuven, Belgium
| | - Quentin Jossart
- Marine Biology Group, Vrije Universiteit Brussel (VUB), Brussels, Belgium
| | | | - Henri Robert
- OD Nature, Royal Belgian Institute of Natural Sciences, Brussels, Belgium
| | - Marie Verheye
- OD Nature, Royal Belgian Institute of Natural Sciences, Brussels, Belgium
| | - Bruno Danis
- Marine Biology Laboratory, Université Libre de Bruxelles (ULB), Brussels, Belgium
| | - Marc Kochzius
- Marine Biology Group, Vrije Universiteit Brussel (VUB), Brussels, Belgium
| | - Frederik Leliaert
- Marine Biology Research Group, Ghent University, Ghent, Belgium.,Meise Botanic Garden, Meise, Belgium
| | - Camille Moreau
- Marine Biology Laboratory, Université Libre de Bruxelles (ULB), Brussels, Belgium.,Université de Bourgogne Franche-Comté (UBFC) UMR CNRS 6282 Biogéosciences, Dijon, France
| | - Tasnim Patel
- OD Nature, Royal Belgian Institute of Natural Sciences, Brussels, Belgium
| | - Anton P Van de Putte
- Laboratory of Biodiversity and Evolutionary Genomics, KU Leuven, Leuven, Belgium.,OD Nature, Royal Belgian Institute of Natural Sciences, Brussels, Belgium.,Marine Biology Laboratory, Université Libre de Bruxelles (ULB), Brussels, Belgium
| | - Ann Vanreusel
- Marine Biology Research Group, Ghent University, Ghent, Belgium
| | - Filip A M Volckaert
- Laboratory of Biodiversity and Evolutionary Genomics, KU Leuven, Leuven, Belgium
| | - Isa Schön
- OD Nature, Royal Belgian Institute of Natural Sciences, Brussels, Belgium
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17
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Guinand B, Oral M, Tougard C. Brown trout phylogenetics: A persistent mirage towards (too) many species. JOURNAL OF FISH BIOLOGY 2021; 99:298-307. [PMID: 33483952 DOI: 10.1111/jfb.14686] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/20/2020] [Revised: 12/28/2020] [Accepted: 01/19/2021] [Indexed: 06/12/2023]
Affiliation(s)
- Bruno Guinand
- ISEM, Université de Montpellier, CNRS, IRD, EPHE, Montpellier, France
| | - Münevver Oral
- Faculty of Fisheries and Aquatic Science, Recep Tayyip Erdogan University, Rize, Turkey
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18
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James N, Bell A. Minimally invasive brain injections for viral-mediated transgenesis: New tools for behavioral genetics in sticklebacks. PLoS One 2021; 16:e0251653. [PMID: 33999965 PMCID: PMC8128275 DOI: 10.1371/journal.pone.0251653] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2021] [Accepted: 04/30/2021] [Indexed: 02/07/2023] Open
Abstract
Behavioral genetics in non-model organisms is currently gated by technological limitations. However, with the growing availability of genome editing and functional genomic tools, complex behavioral traits such as social behavior can now be explored in diverse organisms. Here we present a minimally invasive neurosurgical procedure for a classic behavioral, ecological and evolutionary system: threespine stickleback (Gasterosteus aculeatus). Direct brain injection enables viral-mediated transgenesis and pharmaceutical delivery which bypasses the blood-brain barrier. This method is flexible, fast, and amenable to statistically powerful within-subject experimental designs, making it well-suited for use in genetically diverse animals such as those collected from natural populations. Developing this minimally invasive neurosurgical protocol required 1) refining the anesthesia process, 2) building a custom surgical rig, and 3) determining the normal recovery pattern allowing us to clearly identify warning signs of failure to thrive. Our custom-built surgical rig (publicly available) and optimized anesthetization methods resulted in high (90%) survival rates and quick behavioral recovery. Using this method, we detected changes in aggression from the overexpression of either of two different genes, arginine vasopressin (AVP) and monoamine oxidase (MAOA), in outbred animals in less than one month. We successfully used multiple promoters to drive expression, allowing for tailored expression profiles through time. In addition, we demonstrate that widely available mammalian plasmids work with this method, lowering the barrier of entry to the technique. By using repeated measures of behavior on the same fish before and after transfection, we were able to drastically reduce the necessary sample size needed to detect significant changes in behavior, making this a viable approach for examining genetic mechanisms underlying complex social behaviors.
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Affiliation(s)
- Noelle James
- Neuroscience Program, University of Illinois at Urbana-Champaign, Urbana, Illinois, United States of America
- Department of Evolution, Ecology and Behavior, University of Illinois at Urbana, Urbana, Illinois, United States of America
| | - Alison Bell
- Neuroscience Program, University of Illinois at Urbana-Champaign, Urbana, Illinois, United States of America
- Department of Evolution, Ecology and Behavior, University of Illinois at Urbana, Urbana, Illinois, United States of America
- Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, Illinois, United States of America
- Program in Ecology, Evolution and Conservation Biology, University of Illinois at Urbana-Champaign, Urbana, Illinois, United States of America
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19
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Berner D. Re-evaluating the evidence for facilitation of stickleback speciation by admixture in the Lake Constance basin. Nat Commun 2021; 12:2806. [PMID: 33990572 PMCID: PMC8121923 DOI: 10.1038/s41467-021-23092-1] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2020] [Accepted: 04/15/2021] [Indexed: 02/05/2023] Open
Affiliation(s)
- Daniel Berner
- Department of Environmental Sciences, Zoology, University of Basel, Basel, Switzerland.
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20
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Marques DA, Lucek K, Sousa VC, Excoffier L, Seehausen O. Reply to "Re-evaluating the evidence for facilitation of stickleback speciation by admixture in the Lake Constance basin". Nat Commun 2021; 12:2807. [PMID: 33990586 PMCID: PMC8121787 DOI: 10.1038/s41467-021-23096-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2020] [Accepted: 04/15/2021] [Indexed: 11/09/2022] Open
Affiliation(s)
- David A Marques
- Aquatic Ecology and Evolution, Institute of Ecology and Evolution, University of Bern, Bern, Switzerland.,Department of Fish Ecology and Evolution, EAWAG Swiss Federal Institute of Aquatic Science and Technology, Center for Ecology, Evolution and Biogeochemistry, Kastanienbaum, Switzerland.,Computational and Molecular Population Genetics, Institute of Ecology and Evolution, University of Bern, Bern, Switzerland
| | - Kay Lucek
- Department of Environmental Sciences, University of Basel, Basel, Switzerland
| | - Vitor C Sousa
- Computational and Molecular Population Genetics, Institute of Ecology and Evolution, University of Bern, Bern, Switzerland.,Centre for Ecology, Evolution and Environmental Changes, University of Lisbon, Lisbon, Portugal
| | - Laurent Excoffier
- Computational and Molecular Population Genetics, Institute of Ecology and Evolution, University of Bern, Bern, Switzerland.,Swiss Institute of Bioinformatics, Lausanne, Switzerland
| | - Ole Seehausen
- Aquatic Ecology and Evolution, Institute of Ecology and Evolution, University of Bern, Bern, Switzerland. .,Department of Fish Ecology and Evolution, EAWAG Swiss Federal Institute of Aquatic Science and Technology, Center for Ecology, Evolution and Biogeochemistry, Kastanienbaum, Switzerland.
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21
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Kirch M, Romundset A, Gilbert MTP, Jones FC, Foote AD. Ancient and modern stickleback genomes reveal the demographic constraints on adaptation. Curr Biol 2021; 31:2027-2036.e8. [PMID: 33705715 DOI: 10.1016/j.cub.2021.02.027] [Citation(s) in RCA: 24] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2020] [Revised: 01/05/2021] [Accepted: 02/12/2021] [Indexed: 10/21/2022]
Abstract
Adaptation is typically studied by comparing modern populations with contrasting environments. Individuals persisting in the ancestral habitat are typically used to represent the ancestral founding population; however, it has been questioned whether these individuals are good proxies for the actual ancestors.1 To address this, we applied a paleogenomics approach2 to directly access the ancestral genepool: partially sequencing the genomes of two 11- to 13,000-year-old stickleback recovered from the transitionary layer between marine and freshwater sediments of two Norwegian isolation lakes3 and comparing them with 30 modern stickleback genomes from the same lakes and adjacent marine fjord, in addition to a global dataset of 20 genomes.4 The ancient stickleback shared genome-wide ancestry with the modern fjord population, whereas modern lake populations have lost substantial ancestral variation following founder effects, and subsequent drift and selection. Freshwater-adaptive alleles found in one ancient stickleback genome have not risen to high frequency in the present-day population from the same lake. Comparison to the global dataset suggested incomplete adaptation to freshwater in our modern lake populations. Our findings reveal the impact of population bottlenecks in constraining adaptation due to reduced efficacy of selection on standing variation present in founder populations.
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Affiliation(s)
- Melanie Kirch
- Friedrich Miescher Laboratory of the Max Planck Society, Max-Planck-Ring 9, 72076 Tübingen, Germany
| | | | - M Thomas P Gilbert
- Center for Evolutionary Hologenomics, The GLOBE Institute, University of Copenhagen, Øster Farimagsgade 5A, DK-1353 Copenhagen, Denmark; Department of Natural History, Norwegian University of Science and Technology (NTNU), University Museum, 7491 Trondheim, Norway
| | - Felicity C Jones
- Friedrich Miescher Laboratory of the Max Planck Society, Max-Planck-Ring 9, 72076 Tübingen, Germany
| | - Andrew D Foote
- Department of Natural History, Norwegian University of Science and Technology (NTNU), University Museum, 7491 Trondheim, Norway; Molecular Ecology and Fisheries Genetics Laboratory, School of Biological Sciences, Bangor University, Bangor, UK.
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22
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Fang B, Kemppainen P, Momigliano P, Merilä J. Population structure limits parallel evolution in sticklebacks. Mol Biol Evol 2021; 38:4205-4221. [PMID: 33956140 PMCID: PMC8476136 DOI: 10.1093/molbev/msab144] [Citation(s) in RCA: 23] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023] Open
Abstract
Population genetic theory predicts that small effective population sizes (Ne) and restricted gene flow limit the potential for local adaptation. In particular, the probability of evolving similar phenotypes based on shared genetic mechanisms (i.e., parallel evolution), is expected to be reduced. We tested these predictions in a comparative genomic study of two ecologically similar and geographically codistributed stickleback species (viz. Gasterosteus aculeatus and Pungitius pungitius). We found that P. pungitius harbors less genetic diversity and exhibits higher levels of genetic differentiation and isolation-by-distance than G. aculeatus. Conversely, G. aculeatus exhibits a stronger degree of genetic parallelism across freshwater populations than P. pungitius: 2,996 versus 379 single nucleotide polymorphisms located within 26 versus 9 genomic regions show evidence of selection in multiple freshwater populations of G. aculeatus and P. pungitius, respectively. Most regions involved in parallel evolution in G. aculeatus showed increased levels of divergence, suggestive of selection on ancient haplotypes. In contrast, haplotypes involved in freshwater adaptation in P. pungitius were younger. In accordance with theory, the results suggest that connectivity and genetic drift play crucial roles in determining the levels and geographic distribution of standing genetic variation, providing evidence that population subdivision limits local adaptation and therefore also the likelihood of parallel evolution.
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Affiliation(s)
- Bohao Fang
- Ecological Genetics Research Unit, Organismal and Evolutionary Biology Research Programme, Faculty of Biological and Environmental Sciences, FI-00014 University of Helsinki, Finland
| | - Petri Kemppainen
- Ecological Genetics Research Unit, Organismal and Evolutionary Biology Research Programme, Faculty of Biological and Environmental Sciences, FI-00014 University of Helsinki, Finland
| | - Paolo Momigliano
- Ecological Genetics Research Unit, Organismal and Evolutionary Biology Research Programme, Faculty of Biological and Environmental Sciences, FI-00014 University of Helsinki, Finland
| | - Juha Merilä
- Ecological Genetics Research Unit, Organismal and Evolutionary Biology Research Programme, Faculty of Biological and Environmental Sciences, FI-00014 University of Helsinki, Finland.,Research Division of Ecology and Biodiversity, Faculty of Science, Kadoorie Building, The University of Hong Kong, Hong Kong SAR
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23
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Magalhaes IS, Whiting JR, D'Agostino D, Hohenlohe PA, Mahmud M, Bell MA, Skúlason S, MacColl ADC. Intercontinental genomic parallelism in multiple three-spined stickleback adaptive radiations. Nat Ecol Evol 2021; 5:251-261. [PMID: 33257817 PMCID: PMC7858233 DOI: 10.1038/s41559-020-01341-8] [Citation(s) in RCA: 27] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2019] [Accepted: 10/05/2020] [Indexed: 12/22/2022]
Abstract
Parallelism, the evolution of similar traits in populations diversifying in similar conditions, provides strong evidence of adaptation by natural selection. Many studies of parallelism focus on comparisons of different ecotypes or contrasting environments, defined a priori, which could upwardly bias the apparent prevalence of parallelism. Here, we estimated genomic parallelism associated with components of environmental and phenotypic variation at an intercontinental scale across four freshwater adaptive radiations (Alaska, British Columbia, Iceland and Scotland) of the three-spined stickleback (Gasterosteus aculeatus). We combined large-scale biological sampling and phenotyping with restriction site associated DNA sequencing (RAD-Seq) data from 73 freshwater lake populations and four marine ones (1,380 fish) to associate genome-wide allele frequencies with continuous distributions of environmental and phenotypic variation. Our three main findings demonstrate that (1) quantitative variation in phenotypes and environments can predict genomic parallelism; (2) genomic parallelism at the early stages of adaptive radiations, even at large geographic scales, is founded on standing variation; and (3) similar environments are a better predictor of genome-wide parallelism than similar phenotypes. Overall, this study validates the importance and predictive power of major phenotypic and environmental factors likely to influence the emergence of common patterns of genomic divergence, providing a clearer picture than analyses of dichotomous phenotypes and environments.
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Affiliation(s)
- Isabel S Magalhaes
- School of Life Sciences, University of Nottingham, University Park, Nottingham, UK.
- Department of Life Sciences, Whitelands College, University of Roehampton, London, UK.
| | - James R Whiting
- School of Life Sciences, University of Nottingham, University Park, Nottingham, UK.
- Biosciences, College of Life and Environmental Sciences, Geoffrey Pope, University of Exeter, London, UK.
| | - Daniele D'Agostino
- School of Life Sciences, University of Nottingham, University Park, Nottingham, UK
| | - Paul A Hohenlohe
- Institute for Bioinformatics and Evolutionary Studies, Department of Biological Sciences, University of Idaho, Moscow, ID, USA
| | - Muayad Mahmud
- School of Life Sciences, University of Nottingham, University Park, Nottingham, UK
- Erbil Polytechnic University, Kurdistan Region, Iraq
| | - Michael A Bell
- Museum of Paleontology, University of California, Berkeley, CA, USA
| | - Skúli Skúlason
- Department of Aquaculture and Fish Biology, Hólar University, Sauðárkrókur, Iceland
- Icelandic Museum of Natural History, Suðurlandsbraut, Reykjavík, Iceland
| | - Andrew D C MacColl
- School of Life Sciences, University of Nottingham, University Park, Nottingham, UK
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24
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Hudson CM, Lucek K, Marques DA, Alexander TJ, Moosmann M, Spaak P, Seehausen O, Matthews B. Threespine Stickleback in Lake Constance: The Ecology and Genomic Substrate of a Recent Invasion. Front Ecol Evol 2021. [DOI: 10.3389/fevo.2020.611672] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022] Open
Abstract
Invasive species can be powerful models for studying contemporary evolution in natural environments. As invading organisms often encounter new habitats during colonization, they will experience novel selection pressures. Threespine stickleback (Gasterosteus aculeatus complex) have recently colonized large parts of Switzerland and are invasive in Lake Constance. Introduced to several watersheds roughly 150 years ago, they spread across the Swiss Plateau (400–800 m a.s.l.), bringing three divergent hitherto allopatric lineages into secondary contact. As stickleback have colonized a variety of different habitat types during this recent range expansion, the Swiss system is a useful model for studying contemporary evolution with and without secondary contact. For example, in the Lake Constance region there has been rapid phenotypic and genetic divergence between a lake population and some stream populations. There is considerable phenotypic variation within the lake population, with individuals foraging in and occupying littoral, offshore pelagic, and profundal waters, the latter of which is a very unusual habitat for stickleback. Furthermore, adults from the lake population can reach up to three times the size of adults from the surrounding stream populations, and are large by comparison to populations globally. Here, we review the historical origins of the threespine stickleback in Switzerland, and the ecomorphological variation and genomic basis of its invasion in Lake Constance. We also outline the potential ecological impacts of this invasion, and highlight the interest for contemporary evolution studies.
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Gahr CL, Boehm T, Milinski M. Male validation factor for three-spined stickleback ( Gasterosteus aculeatus) mate choice likely evolutionarily conserved since 50 thousand years. ETHOL ECOL EVOL 2021. [DOI: 10.1080/03949370.2020.1789748] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
Affiliation(s)
- Christoph L. Gahr
- Department of Evolutionary Ecology, Max Planck Institute for Evolutionary Biology, Plön, Germany
| | - Thomas Boehm
- Department of Developmental Immunology, Max-Planck-Institute for Immunobiology and Epigenetics, Freiburg, Germany
| | - Manfred Milinski
- Department of Evolutionary Ecology, Max Planck Institute for Evolutionary Biology, Plön, Germany
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26
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Mobley RB, Boughman JW. Variation in the Sensory Space of Three-spined Stickleback Populations. Integr Comp Biol 2020; 61:50-61. [PMID: 33382869 DOI: 10.1093/icb/icaa145] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023] Open
Abstract
The peripheral sensory systems, whose morphological attributes help determine the acquisition of distinct types of information, provide a means to quantitatively compare multiple modalities of a species' sensory ecology. We used morphological metrics to characterize multiple sensory modalities-the visual, olfactory, and mechanosensory lateral line sensory systems-for Gasterosteus aculeatus, the three-spined stickleback, to compare how sensory systems vary in animals that evolve in different ecological conditions. We hypothesized that the dimensions of sensory organs and correlations among sensory systems vary in populations adapted to marine and freshwater environments, and have diverged further among freshwater lake-dwelling populations. Our results showed that among environments, fish differed in which senses are relatively elaborated or reduced. When controlling for body length, littoral fish had larger eyes, more neuromasts, and smaller olfactory tissue area than pelagic or marine populations. We also found differences in the direction and magnitude of correlations among sensory systems for populations even within the same habitat type. Our data suggest that populations take different trajectories in how visual, olfactory, and lateral line systems respond to their environment. For the populations we studied, sensory modalities do not conform in a predictable way to the ecological categories we assigned.
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Affiliation(s)
- Robert B Mobley
- Department of Integrative Biology, Ecology, Evolutionary Biology and Behavior, BEACON, Michigan State University, East Lansing, MI, USA
| | - Janette W Boughman
- Department of Integrative Biology, Ecology, Evolutionary Biology and Behavior, BEACON, Michigan State University, East Lansing, MI, USA
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Kakioka R, Mori S, Kokita T, Hosoki TK, Nagano AJ, Ishikawa A, Kume M, Toyoda A, Kitano J. Multiple waves of freshwater colonization of the three-spined stickleback in the Japanese Archipelago. BMC Evol Biol 2020; 20:143. [PMID: 33143638 PMCID: PMC7641863 DOI: 10.1186/s12862-020-01713-5] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2020] [Accepted: 10/27/2020] [Indexed: 12/03/2022] Open
Abstract
Background The three-spined stickleback (Gasterosteus aculeatus) is a remarkable system to study the genetic mechanisms underlying parallel evolution during the transition from marine to freshwater habitats. Although the majority of previous studies on the parallel evolution of sticklebacks have mainly focused on postglacial freshwater populations in the Pacific Northwest of North America and northern Europe, we recently use Japanese stickleback populations for investigating shared and unique features of adaptation and speciation between geographically distant populations. However, we currently lack a comprehensive phylogeny of the Japanese three-spined sticklebacks, despite the fact that a good phylogeny is essential for any evolutionary and ecological studies. Here, we conducted a phylogenomic analysis of the three-spined stickleback in the Japanese Archipelago. Results We found that freshwater colonization occurred in multiple waves, each of which may reflect different interglacial isolations. Some of the oldest freshwater populations from the central regions of the mainland of Japan (hariyo populations) were estimated to colonize freshwater approximately 170,000 years ago. The next wave of colonization likely occurred approximately 100,000 years ago. The inferred origins of several human-introduced populations showed that introduction occurred mainly from nearby habitats. We also found a new habitat of the three-spined stickleback sympatric with the Japan Sea stickleback (Gasterosteus nipponicus). Conclusions These Japanese stickleback systems differ from those in the Pacific Northwest of North America and northern Europe in terms of divergence time and history. Stickleback populations in the Japanese Archipelago offer valuable opportunities to study diverse evolutionary processes in historical and contemporary timescales.
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Affiliation(s)
- Ryo Kakioka
- Ecological Genetics Laboratory, National Institute of Genetics, Mishima, Shizuoka, 411-8540, Japan.,Tropical Biosphere Research Center, University of the Ryukyus, Nishihara, Nakagami-gun, Okinawa, 903-0213, Japan
| | - Seiichi Mori
- Biological Laboratory, Gifu Kyoritsu University, Ogaki, Gifu, 503-8550, Japan
| | - Tomoyuki Kokita
- Department of Marine Bioscience, Fukui Prefectural University, Obama, Fukui, 917-0003, Japan
| | - Takuya K Hosoki
- Ecological Genetics Laboratory, National Institute of Genetics, Mishima, Shizuoka, 411-8540, Japan.,Department of Genetics, The Graduate University for Advanced Studies, Mishima, Shizuoka, 411-8540, Japan
| | - Atsushi J Nagano
- Faculty of Agriculture, Ryukoku University, Otsu, Shiga, 520-2194, Japan
| | - Asano Ishikawa
- Ecological Genetics Laboratory, National Institute of Genetics, Mishima, Shizuoka, 411-8540, Japan.,Department of Genetics, The Graduate University for Advanced Studies, Mishima, Shizuoka, 411-8540, Japan
| | - Manabu Kume
- Field Science Education and Research Center, Kyoto University, Kyoto, 606-8502, Japan
| | - Atsushi Toyoda
- Comparative Genomics Laboratory, National Institute of Genetics, Mishima, Shizuoka, 411-8540, Japan
| | - Jun Kitano
- Ecological Genetics Laboratory, National Institute of Genetics, Mishima, Shizuoka, 411-8540, Japan. .,Department of Genetics, The Graduate University for Advanced Studies, Mishima, Shizuoka, 411-8540, Japan.
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Laakkonen HM, Hardman M, Strelkov P, Väinölä R. Cycles of trans-Arctic dispersal and vicariance, and diversification of the amphi-boreal marine fauna. J Evol Biol 2020; 34:73-96. [PMID: 32671913 DOI: 10.1111/jeb.13674] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2019] [Revised: 06/05/2020] [Accepted: 06/29/2020] [Indexed: 02/06/2023]
Abstract
The amphi-boreal faunal element comprises closely related species and conspecific populations with vicarious distributions in the North Atlantic and North Pacific basins. It originated from an initial trans-Arctic dispersal in the Pliocene after the first opening of the Bering Strait, and subsequent inter-oceanic vicariance through the Pleistocene when the passage through the Arctic was severed by glaciations and low sea levels. Opportunities for further trans-Arctic dispersal have risen at times, however, and molecular data now expose more complex patterns of inter-oceanic affinities and dispersal histories. For a general view on the trans-Arctic dynamics and of the roles of potential dispersal-vicariance cycles in generating systematic diversity, we produced new phylogeographic data sets for amphi-boreal taxa in 21 genera of invertebrates and vertebrates, and combined them with similar published data sets of mitochondrial coding gene variation, adding up to 89 inter-oceanic comparisons involving molluscs, crustaceans, echinoderms, polychaetes, fishes and mammals. Only 39% of the cases correspond to a simple history of Pliocene divergence; in most taxonomical groups, the range of divergence estimates implies connections through the entire Pliocene-Pleistocene-Holocene time frame. Repeated inter-oceanic exchange was inferred for 23 taxa, and the latest connection was usually post-glacial. Such repeated invasions have usually led to secondary contacts and occasionally to widespread hybridization between the different invasion waves. Late- or post-glacial exchange was inferred in 46% of the taxa, stressing the importance of the relatively recent invasions to the current diversity in the North Atlantic. Individual taxa also showed complex idiosyncratic patterns and histories, and several instances of cryptic speciation were recognized. In contrast to a simple inter-oceanic vicariance scenario underlying amphi-boreal speciation, the data expose complex patterns of reinvasion and reticulation that complicate the interpretation of taxon boundaries in the region.
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Affiliation(s)
- Hanna M Laakkonen
- Finnish Museum of Natural History, University of Helsinki, Helsinki, Finland
| | - Michael Hardman
- Finnish Museum of Natural History, University of Helsinki, Helsinki, Finland
| | - Petr Strelkov
- Department of Ichthyology and Hydrobiology, Saint Petersburg State University, St. Petersburg, Russia
| | - Risto Väinölä
- Finnish Museum of Natural History, University of Helsinki, Helsinki, Finland
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Arai T, Ueno D, Kitamura T, Goto A. Habitat preference and diverse migration in threespine sticklebacks, Gasterosteus aculeatus and G. nipponicus. Sci Rep 2020; 10:14311. [PMID: 32868826 PMCID: PMC7459310 DOI: 10.1038/s41598-020-71400-4] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2020] [Accepted: 08/17/2020] [Indexed: 11/20/2022] Open
Abstract
Threespine sticklebacks of the genus Gasterosteus, are small teleost fish that are widely distributed across the northern hemisphere. The fish is believed to have two major types of life history, freshwater resident and anadromous; however little is known about their migration ecology. Comprehensive research on the migratory history, habitat use and relative composition of migratory types was conducted by analysing the otolith strontium and calcium concentrations collected in various environments of northern Japan. The present study first demonstrated that approximately 90% of morphologically anadromous sticklebacks had estuarine resident migration pattern, consistently living in brackish water and/or marine environments through their life cycle without any time spent in freshwater. The dominant occurrence of the estuarine resident was temporally and spatially consistent with their general migration ecology. The estuarine resident is thought to be the ancestral migrations of G. aculeatus and G. nipponicus, which thereafter gradually immigrated into freshwater habitats and settled in the anadromous form in both species and finally became the freshwater resident G. aculeatus. Thus, this study provides novel insights into the evolutionary migration of these fish, as well as a new discovery regarding the dominant migratory history and habitat use in threespine sticklebacks.
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Affiliation(s)
- Takaomi Arai
- Faculty of Science, Universiti Brunei Darussalam, Jalan Tungku Link, Gadong, 1410, Brunei Darussalam. .,Faculty of Fisheries and Marine, Universitas Airlangga, Surabaya, 60113, Indonesia.
| | - Daisuke Ueno
- Graduate School of Fisheries Sciences, Kitasato University, 160-4 Sanriku, Ofunato, Iwate, 022-0101, Japan
| | - Takefumi Kitamura
- Graduate School of Fisheries Sciences, Hokkaido University, Hakodate, 041-8611, Japan
| | - Akira Goto
- Graduate School of Fisheries Sciences, Hokkaido University, Hakodate, 041-8611, Japan
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30
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On the causes of geographically heterogeneous parallel evolution in sticklebacks. Nat Ecol Evol 2020; 4:1105-1115. [DOI: 10.1038/s41559-020-1222-6] [Citation(s) in RCA: 53] [Impact Index Per Article: 13.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2019] [Accepted: 05/14/2020] [Indexed: 12/22/2022]
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31
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Maltseva AL, Varfolomeeva MA, Lobov AA, Tikanova P, Panova M, Mikhailova NA, Granovitch AI. Proteomic similarity of the Littorinid snails in the evolutionary context. PeerJ 2020; 8:e8546. [PMID: 32095363 PMCID: PMC7024583 DOI: 10.7717/peerj.8546] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2019] [Accepted: 01/10/2020] [Indexed: 01/24/2023] Open
Abstract
BACKGROUND The introduction of DNA-based molecular markers made a revolution in biological systematics. However, in cases of very recent divergence events, the neutral divergence may be too slow, and the analysis of adaptive part of the genome is more informative to reconstruct the recent evolutionary history of young species. The advantage of proteomics is its ability to reflect the biochemical machinery of life. It may help both to identify rapidly evolving genes and to interpret their functions. METHODS Here we applied a comparative gel-based proteomic analysis to several species from the gastropod family Littorinidae. Proteomes were clustered to assess differences related to species, geographic location, sex and body part, using data on presence/absence of proteins in samples and data on protein occurrence frequency in samples of different species. Cluster support was assessed using multiscale bootstrap resampling and the stability of clustering-using cluster-wise index of cluster stability. Taxon-specific protein markers were derived using IndVal method. Proteomic trees were compared to consensus phylogenetic tree (based on neutral genetic markers) using estimates of the Robinson-Foulds distance, the Fowlkes-Mallows index and cophenetic correlation. RESULTS Overall, the DNA-based phylogenetic tree and the proteomic similarity tree had consistent topologies. Further, we observed some interesting deviations of the proteomic littorinid tree from the neutral expectations. (1) There were signs of molecular parallelism in two Littoraria species that phylogenetically are quite distant, but live in similar habitats. (2) Proteome divergence was unexpectedly high between very closely related Littorina fabalis and L. obtusata, possibly reflecting their ecology-driven divergence. (3) Conservative house-keeping proteins were usually identified as markers for cryptic species groups ("saxatilis" and "obtusata" groups in the Littorina genus) and for genera (Littoraria and Echinolittorina species pairs), while metabolic enzymes and stress-related proteins (both potentially adaptively important) were often identified as markers supporting species branches. (4) In all five Littorina species British populations were separated from the European mainland populations, possibly reflecting their recent phylogeographic history. Altogether our study shows that proteomic data, when interpreted in the context of DNA-based phylogeny, can bring additional information on the evolutionary history of species.
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Affiliation(s)
- Arina L. Maltseva
- Department of Invertebrate Zoology, St. Petersburg State University, St. Petersburg, Russia
| | - Marina A. Varfolomeeva
- Department of Invertebrate Zoology, St. Petersburg State University, St. Petersburg, Russia
| | - Arseniy A. Lobov
- Department of Invertebrate Zoology, St. Petersburg State University, St. Petersburg, Russia
- Laboratory of Regenerative Biomedicine, Institute of Cytology Russian Academy of Sciences, St. Petersburg, Russia
| | - Polina Tikanova
- Department of Invertebrate Zoology, St. Petersburg State University, St. Petersburg, Russia
| | - Marina Panova
- Department of Invertebrate Zoology, St. Petersburg State University, St. Petersburg, Russia
- Department of Marine Sciences, Tjärnö, University of Gothenburg, Sweden
| | - Natalia A. Mikhailova
- Department of Invertebrate Zoology, St. Petersburg State University, St. Petersburg, Russia
- Centre of Cell Technologies, Institute of Cytology Russian Academy of Sciences, St. Petersburg, Russia
| | - Andrei I. Granovitch
- Department of Invertebrate Zoology, St. Petersburg State University, St. Petersburg, Russia
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32
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Ishikawa A, Kitano J. Diversity in reproductive seasonality in the three-spined stickleback, Gasterosteus aculeatus. ACTA ACUST UNITED AC 2020; 223:223/Suppl_1/jeb208975. [PMID: 32034046 DOI: 10.1242/jeb.208975] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
The annual timing of reproduction is a key life history trait with a large effect on fitness. Populations often vary in the timing and duration of reproduction to adapt to different seasonality of ecological and environmental variables between habitats. However, little is known about the molecular genetic mechanisms underlying interpopulation variation in reproductive seasonality. Here, we demonstrate that the three-spined stickleback (Gasterosteus aculeatus) is a good model for molecular genetic analysis of variations in reproductive seasonality. We first compiled data on reproductive seasons of diverse ecotypes, covering marine-anadromous, lake and stream ecotypes, of three-spined stickleback inhabiting a wide range of latitudes. Our analysis showed that both ecotype and latitude significantly contribute to variation in reproductive seasons. Stream ecotypes tend to start breeding earlier and end later than other ecotypes. Populations from lower latitudes tend to start breeding earlier than those from higher latitudes in all three ecotypes. Additionally, stream ecotypes tend to have extended breeding seasons at lower latitudes than at higher latitudes, leading to nearly year-round reproduction in the most southern stream populations. A review of recent progress in our understanding of the physiological mechanisms underlying seasonal reproduction in the three-spined stickleback indicates that photoperiod is an important external cue that stimulates and/or suppresses reproduction in this species. Taking advantage of genomic tools available for this species, the three-spined stickleback will be a good model to investigate what kinds of genes and mutations underlie variations in the physiological signalling pathways that regulate reproduction in response to photoperiod.
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Affiliation(s)
- Asano Ishikawa
- Ecological Genetics Laboratory, National Institute of Genetics, Yata 1111, Mishima, Shizuoka 411-8540, Japan .,Department of Genetics, Graduate University for Advanced Studies (SOKENDAI), Yata 1111, Mishima, Shizuoka 411-8540, Japan
| | - Jun Kitano
- Ecological Genetics Laboratory, National Institute of Genetics, Yata 1111, Mishima, Shizuoka 411-8540, Japan.,Department of Genetics, Graduate University for Advanced Studies (SOKENDAI), Yata 1111, Mishima, Shizuoka 411-8540, Japan
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Hughes LC, Cardoso YP, Sommer JA, Cifuentes R, Cuello M, Somoza GM, González‐Castro M, Malabarba LR, Cussac V, Habit EM, Betancur‐R. R, Ortí G. Biogeography, habitat transitions and hybridization in a radiation of South American silverside fishes revealed by mitochondrial and genomic RAD data. Mol Ecol 2020; 29:738-751. [DOI: 10.1111/mec.15350] [Citation(s) in RCA: 23] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2019] [Revised: 12/23/2019] [Accepted: 01/03/2020] [Indexed: 01/23/2023]
Affiliation(s)
- Lily C. Hughes
- Department of Biological Sciences George Washington University Washington DC USA
- Department of Vertebrate Zoology National Museum of Natural History Smithsonian Institution Washington DC USA
| | - Yamila P. Cardoso
- Laboratorio de Sistemática y Biología Evolutiva‐CONICET Facultad de Ciencias Naturales y Museo Universidad Nacional de La Plata La Plata Argentina
| | - Julie A. Sommer
- Vice Chancellor for Research Office University of Nebraska Medical Center Omaha NE USA
| | - Roberto Cifuentes
- Departmento de Sistemas Acuáticos Facultad de Ciencias Ambientales y Centro EULA Universidad de Concepción y Centro de Investigaciones en Ecosistemas Patagónicos Concepción Chile
| | - Mariela Cuello
- Facultad de Ciencias Naturales y Museo Universidad Nacional de La Plata‐CONICET Buenos Aires Argentina
| | - Gustavo M. Somoza
- Instituto Tecnológico de Chascomus (CONICET‐UNSAM) Chascomús, Buenos Aires Argentina
| | - Mariano González‐Castro
- Grupo de Biotaxonomía Morfológica y molecular de peces IIMyC‐CONICET Universidad Nacional de Mar del Plata Mar del Plata Argentina
| | - Luiz R. Malabarba
- Departamento de Zoologia Instituto de Biociências Universidade Federal do Rio Grande do Sul Porto Alegre Brazil
| | - Victor Cussac
- Centro Científico Tecnológico CONICET Patagonia Norte – Universidad Nacional del Comahue Bariloche, Rio Negro Argentina
| | - Evelyn M. Habit
- Departmento de Sistemas Acuáticos Facultad de Ciencias Ambientales y Centro EULA Universidad de Concepción y Centro de Investigaciones en Ecosistemas Patagónicos Concepción Chile
| | - Ricardo Betancur‐R.
- Department of Vertebrate Zoology National Museum of Natural History Smithsonian Institution Washington DC USA
- Department of Biology University of Oklahoma Norman OK USA
| | - Guillermo Ortí
- Department of Biological Sciences George Washington University Washington DC USA
- Department of Vertebrate Zoology National Museum of Natural History Smithsonian Institution Washington DC USA
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Fang B, Merilä J, Matschiner M, Momigliano P. Estimating uncertainty in divergence times among three-spined stickleback clades using the multispecies coalescent. Mol Phylogenet Evol 2020; 142:106646. [DOI: 10.1016/j.ympev.2019.106646] [Citation(s) in RCA: 26] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2019] [Revised: 08/20/2019] [Accepted: 10/09/2019] [Indexed: 01/19/2023]
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Varadharajan S, Rastas P, Löytynoja A, Matschiner M, Calboli FCF, Guo B, Nederbragt AJ, Jakobsen KS, Merilä J. A High-Quality Assembly of the Nine-Spined Stickleback (Pungitius pungitius) Genome. Genome Biol Evol 2019; 11:3291-3308. [PMID: 31687752 PMCID: PMC7145574 DOI: 10.1093/gbe/evz240] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 10/30/2019] [Indexed: 12/22/2022] Open
Abstract
The Gasterosteidae fish family hosts several species that are important models for eco-evolutionary, genetic, and genomic research. In particular, a wealth of genetic and genomic data has been generated for the three-spined stickleback (Gasterosteus aculeatus), the "ecology's supermodel," whereas the genomic resources for the nine-spined stickleback (Pungitius pungitius) have remained relatively scarce. Here, we report a high-quality chromosome-level genome assembly of P. pungitius consisting of 5,303 contigs (N50 = 1.2 Mbp) with a total size of 521 Mbp. These contigs were mapped to 21 linkage groups using a high-density linkage map, yielding a final assembly with 98.5% BUSCO completeness. A total of 25,062 protein-coding genes were annotated, and about 23% of the assembly was found to consist of repetitive elements. A comprehensive analysis of repetitive elements uncovered centromere-specific tandem repeats and provided insights into the evolution of retrotransposons. A multigene phylogenetic analysis inferred a divergence time of about 26 million years ago (Ma) between nine- and three-spined sticklebacks, which is far older than the commonly assumed estimate of 13 Ma. Compared with the three-spined stickleback, we identified an additional duplication of several genes in the hemoglobin cluster. Sequencing data from populations adapted to different environments indicated potential copy number variations in hemoglobin genes. Furthermore, genome-wide synteny comparisons between three- and nine-spined sticklebacks identified chromosomal rearrangements underlying the karyotypic differences between the two species. The high-quality chromosome-scale assembly of the nine-spined stickleback genome obtained with long-read sequencing technology provides a crucial resource for comparative and population genomic investigations of stickleback fishes and teleosts.
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Affiliation(s)
- Srinidhi Varadharajan
- Department of Biology, Centre for Ecological and Evolutionary Synthesis, University of Oslo, Norway
| | - Pasi Rastas
- Ecological Genetics Research Unit, Research Programme in Organismal and Evolutionary Biology, Faculty of Biological and Environmental Sciences, University of Helsinki, Finland
| | - Ari Löytynoja
- Institute of Biotechnology, University of Helsinki, Finland
| | - Michael Matschiner
- Department of Biology, Centre for Ecological and Evolutionary Synthesis, University of Oslo, Norway
- Department of Paleontology and Museum, University of Zurich, Switzerland
| | - Federico C F Calboli
- Ecological Genetics Research Unit, Research Programme in Organismal and Evolutionary Biology, Faculty of Biological and Environmental Sciences, University of Helsinki, Finland
- Laboratory of Biodiversity and Evolutionary Genomics, KU Leuven, Leuven, Belgium
| | - Baocheng Guo
- Ecological Genetics Research Unit, Research Programme in Organismal and Evolutionary Biology, Faculty of Biological and Environmental Sciences, University of Helsinki, Finland
- Key Laboratory of Zoological Systematics and Evolution, Institute of Zoology Chinese Academy of Sciences, Beijing, China
| | - Alexander J Nederbragt
- Department of Biology, Centre for Ecological and Evolutionary Synthesis, University of Oslo, Norway
- Biomedical Informatics Research Group, Department of Informatics, University of Oslo, Norway
| | - Kjetill S Jakobsen
- Department of Biology, Centre for Ecological and Evolutionary Synthesis, University of Oslo, Norway
| | - Juha Merilä
- Ecological Genetics Research Unit, Research Programme in Organismal and Evolutionary Biology, Faculty of Biological and Environmental Sciences, University of Helsinki, Finland
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Marques DA, Lucek K, Sousa VC, Excoffier L, Seehausen O. Admixture between old lineages facilitated contemporary ecological speciation in Lake Constance stickleback. Nat Commun 2019; 10:4240. [PMID: 31534121 PMCID: PMC6751218 DOI: 10.1038/s41467-019-12182-w] [Citation(s) in RCA: 32] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2017] [Accepted: 08/27/2019] [Indexed: 01/25/2023] Open
Abstract
Ecological speciation can sometimes rapidly generate reproductively isolated populations coexisting in sympatry, but the origin of genetic variation permitting this is rarely known. We previously explored the genomics of very recent ecological speciation into lake and stream ecotypes in stickleback from Lake Constance. Here, we reconstruct the origin of alleles underlying ecological speciation by combining demographic modelling on genome-wide single nucleotide polymorphisms, phenotypic data and mitochondrial sequence data in the wider European biogeographical context. We find that parallel differentiation between lake and stream ecotypes across replicate lake-stream ecotones resulted from recent secondary contact and admixture between old East and West European lineages. Unexpectedly, West European alleles that introgressed across the hybrid zone at the western end of the lake, were recruited to genomic islands of differentiation between ecotypes at the eastern end of the lake. Our results highlight an overlooked outcome of secondary contact: ecological speciation facilitated by admixture variation. Ecological speciation can proceed rapidly, but the origin of genetic variation facilitating it has remained elusive. Here, the authors show that secondary contact and introgression between deeply diverged lineages of stickleback fish facilitated rapid ecological speciation into lake and stream ecotypes in Lake Constance.
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Affiliation(s)
- David A Marques
- Aquatic Ecology and Evolution, Institute of Ecology and Evolution, University of Bern, Baltzerstrasse 6, CH-3012, Bern, Switzerland.,Department of Fish Ecology and Evolution, EAWAG Swiss Federal Institute of Aquatic Science and Technology, Center for Ecology, Evolution and Biogeochemistry, Seestrasse 79, CH-6047, Kastanienbaum, Switzerland.,Computational and Molecular Population Genetics, Institute of Ecology and Evolution, University of Bern, Baltzerstrasse 6, CH-3012, Bern, Switzerland
| | - Kay Lucek
- Department of Environmental Sciences, University of Basel, Schönbeinstrasse 6, CH-4056, Basel, Switzerland
| | - Vitor C Sousa
- Computational and Molecular Population Genetics, Institute of Ecology and Evolution, University of Bern, Baltzerstrasse 6, CH-3012, Bern, Switzerland.,Centre for Ecology, Evolution and Environmental Changes, University of Lisbon, Campo Grande 016, 1749-016, Lisbon, Portugal
| | - Laurent Excoffier
- Computational and Molecular Population Genetics, Institute of Ecology and Evolution, University of Bern, Baltzerstrasse 6, CH-3012, Bern, Switzerland.,Swiss Institute of Bioinformatics, 1015, Lausanne, Switzerland
| | - Ole Seehausen
- Aquatic Ecology and Evolution, Institute of Ecology and Evolution, University of Bern, Baltzerstrasse 6, CH-3012, Bern, Switzerland. .,Department of Fish Ecology and Evolution, EAWAG Swiss Federal Institute of Aquatic Science and Technology, Center for Ecology, Evolution and Biogeochemistry, Seestrasse 79, CH-6047, Kastanienbaum, Switzerland.
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37
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Dean LL, Magalhaes IS, Foote A, D'Agostino D, McGowan S, MacColl ADC. Admixture between ancient lineages, selection, and the formation of sympatric stickleback species-pairs. Mol Biol Evol 2019; 36:2481-2497. [PMID: 31297536 PMCID: PMC6805233 DOI: 10.1093/molbev/msz161] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2019] [Revised: 07/02/2019] [Accepted: 07/07/2019] [Indexed: 12/14/2022] Open
Abstract
Ecological speciation has become a popular model for the development and maintenance of reproductive isolation in closely related sympatric pairs of species or ecotypes. An implicit assumption has been that such pairs originate (possibly with gene flow) from a recent, genetically homogeneous ancestor. However, recent genomic data has revealed that currently sympatric taxa are often a result of secondary contact between ancestrally allopatric lineages. This has sparked an interest in the importance of initial hybridization upon secondary contact, with genomic re-analysis of classic examples of ecological speciation often implicating admixture in speciation. We describe a novel occurrence of unusually well-developed reproductive isolation in a model system for ecological speciation: the three-spined stickleback (Gasterosteus aculeatus), breeding sympatrically in multiple lagoons on the Scottish island of North Uist. Using morphological data, targeted genotyping and genome-wide single nucleotide polymorphism (SNP) data we show that lagoon resident and anadromous ecotypes are strongly reproductively isolated with an estimated hybridization rate of only ∼1%. We use palaeoecological and genetic data to test three hypotheses to explain the existence of these species-pairs. Our results suggest that recent, purely ecological speciation from a genetically homogeneous ancestor is probably not solely responsible for the evolution of species-pairs. Instead we reveal a complex colonisation history with multiple ancestral lineages contributing to the genetic composition of species-pairs, alongside strong disruptive selection. Our results imply a role for admixture upon secondary contact and are consistent with the recent suggestion that the genomic underpinning of ecological speciation often has an older, allopatric origin.
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Affiliation(s)
- Laura L Dean
- School of Life Sciences, The University of Nottingham, University Park, Nottingham, UK
| | - Isabel S Magalhaes
- School of Life Sciences, The University of Nottingham, University Park, Nottingham, UK.,Department of Life Sciences, Whitelands College, University of Roehampton, London, UK
| | - Andrew Foote
- Molecular Ecology and Fisheries Genetics Laboratory, Bangor University, Bangor, Gwynedd, UK
| | - Daniele D'Agostino
- School of Life Sciences, The University of Nottingham, University Park, Nottingham, UK
| | - Suzanne McGowan
- School of Geography, The University of Nottingham, University Park, Nottingham, UK
| | - Andrew D C MacColl
- School of Life Sciences, The University of Nottingham, University Park, Nottingham, UK
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38
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Anaya-Rojas JM, Best RJ, Brunner FS, Eizaguirre C, Leal MC, Melián CJ, Seehausen O, Matthews B. An experimental test of how parasites of predators can influence trophic cascades and ecosystem functioning. Ecology 2019; 100:e02744. [PMID: 31135996 DOI: 10.1002/ecy.2744] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/04/2018] [Revised: 03/21/2019] [Accepted: 03/29/2019] [Indexed: 11/07/2022]
Abstract
Parasites can shape the structure and function of ecosystems by influencing both the density and traits of their hosts. Such changes in ecosystems are particularly likely when the host is a predator that mediates the dynamics of trophic cascades. Here, we experimentally tested how parasite load of a small predatory fish, the threespine stickleback, can affect the occurrence and strength of trophic cascades and ecosystem functioning. In a factorial mesocosm experiment, we manipulated the density of stickleback (low vs. high), and the level of parasite load (natural vs. reduced). In addition, we used two stickleback populations from different lineages: an eastern European lineage with a more pelagic phenotype (Lake Constance) and a western European lineage with a more benthic phenotype (Lake Geneva). We found that stickleback caused trophic cascades in the pelagic but not the benthic food chain. Evidence for pelagic trophic cascades was stronger in treatments where parasite load of stickleback was reduced with an antihelmintic medication, and where fish originated from Lake Constance (i.e., the more pelagic lineage). A structural equation model revealed that differences in stickleback lineage and parasite load were most likely to impact trophic cascades via changes in the composition, rather than overall biomass, of zooplankton communities. Overall, our results provide experimental evidence that parasites of predators can influence the cascading effects of fish on lower trophic levels with consequences on ecosystem functioning.
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Affiliation(s)
- Jaime M Anaya-Rojas
- Department of Biological Science, Florida State University, Tallahassee, Florida, 32306, USA.,Center for Evolution & Biogeochemistry, Eawag, Swiss Federal Institute for Aquatic Science and Technology, Aquatic Ecology Seestrasse 79, Kastanienbaum, 6047, Switzerland
| | - Rebecca J Best
- Center for Evolution & Biogeochemistry, Eawag, Swiss Federal Institute for Aquatic Science and Technology, Aquatic Ecology Seestrasse 79, Kastanienbaum, 6047, Switzerland.,School of Earth and Sustainability, Northern Arizona University, 525 South Beaver Street, Flagstaff, Arizona, 86011, USA
| | - Franziska S Brunner
- Institute of Integrative Biology, University of Liverpool, Liverpool, L69 3BX, UK.,School of Biological and Chemical Sciences, Queen Mary University of London, Mile End Road, London, E1 4NS, UK
| | - Christophe Eizaguirre
- School of Biological and Chemical Sciences, Queen Mary University of London, Mile End Road, London, E1 4NS, UK
| | - Miguel Costa Leal
- MARE - Marine and Environmental Sciences Centre, Faculdade de Ciências da Universidade de Lisboa, Campo Grande, Lisboa, 1749-016, Portugal.,Fish Ecology and Evolution Department, Center for Evolution & Biogeochemistry, Eawag, Swiss Federal Institute for Aquatic Science and Technology, Seestrasse 79, Kastanienbaum, 6047, Switzerland
| | - Carlos J Melián
- Fish Ecology and Evolution Department, Center for Evolution & Biogeochemistry, Eawag, Swiss Federal Institute for Aquatic Science and Technology, Seestrasse 79, Kastanienbaum, 6047, Switzerland
| | - Ole Seehausen
- Fish Ecology and Evolution Department, Center for Evolution & Biogeochemistry, Eawag, Swiss Federal Institute for Aquatic Science and Technology, Seestrasse 79, Kastanienbaum, 6047, Switzerland.,Institute of Ecology & Evolution, Aquatic Ecology & Evolution, University of Bern, Baltzerstrasse 6, Bern, 3012, Switzerland
| | - Blake Matthews
- Center for Evolution & Biogeochemistry, Eawag, Swiss Federal Institute for Aquatic Science and Technology, Aquatic Ecology Seestrasse 79, Kastanienbaum, 6047, Switzerland
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