101
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Ravinet M, Westram A, Johannesson K, Butlin R, André C, Panova M. Shared and nonshared genomic divergence in parallel ecotypes of Littorina saxatilis at a local scale. Mol Ecol 2015. [PMID: 26222268 DOI: 10.1111/mec.13332] [Citation(s) in RCA: 111] [Impact Index Per Article: 12.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Parallel speciation occurs when selection drives repeated, independent adaptive divergence that reduces gene flow between ecotypes. Classical examples show parallel speciation originating from shared genomic variation, but this does not seem to be the case in the rough periwinkle (Littorina saxatilis) that has evolved considerable phenotypic diversity across Europe, including several distinct ecotypes. Small 'wave' ecotype snails inhabit exposed rocks and experience strong wave action, while thick-shelled, 'crab' ecotype snails are larger and experience crab predation on less exposed shores. Crab and wave ecotypes appear to have arisen in parallel, and recent evidence suggests only marginal sharing of molecular variation linked to evolution of similar ecotypes in different parts of Europe. However, the extent of genomic sharing is expected to increase with gene flow and more recent common ancestry. To test this, we used de novo RAD-sequencing to quantify the extent of shared genomic divergence associated with phenotypic similarities amongst ecotype pairs on three close islands (<10 km distance) connected by weak gene flow (Nm ~ 0.03) and with recent common ancestry (<10 000 years). After accounting for technical issues, including a large proportion of null alleles due to a large effective population size, we found ~8-28% of positive outliers were shared between two islands and ~2-9% were shared amongst all three islands. This low level of sharing suggests that parallel phenotypic divergence in this system is not matched by shared genomic divergence despite a high probability of gene flow and standing genetic variation.
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Affiliation(s)
- Mark Ravinet
- Department of Marine Sciences-Tjärnö, University of Gothenburg, Hättesbäckvägen 8, 452 96, Strömstad, Sweden.,Ecological Genetics Laboratory, National Institute of Genetics, Yata 1111, Mishima, 411-8540, Japan
| | - Anja Westram
- Department of Animal and Plant Sciences, University of Sheffield, Western Bank, Sheffield, S10 2TN, UK
| | - Kerstin Johannesson
- Department of Marine Sciences-Tjärnö, University of Gothenburg, Hättesbäckvägen 8, 452 96, Strömstad, Sweden
| | - Roger Butlin
- Department of Marine Sciences-Tjärnö, University of Gothenburg, Hättesbäckvägen 8, 452 96, Strömstad, Sweden.,Department of Animal and Plant Sciences, University of Sheffield, Western Bank, Sheffield, S10 2TN, UK
| | - Carl André
- Department of Marine Sciences-Tjärnö, University of Gothenburg, Hättesbäckvägen 8, 452 96, Strömstad, Sweden
| | - Marina Panova
- Department of Marine Sciences-Tjärnö, University of Gothenburg, Hättesbäckvägen 8, 452 96, Strömstad, Sweden
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102
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Berner D, Salzburger W. The genomics of organismal diversification illuminated by adaptive radiations. Trends Genet 2015; 31:491-9. [DOI: 10.1016/j.tig.2015.07.002] [Citation(s) in RCA: 72] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2015] [Revised: 06/09/2015] [Accepted: 07/15/2015] [Indexed: 02/07/2023]
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103
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Bragg JG, Supple MA, Andrew RL, Borevitz JO. Genomic variation across landscapes: insights and applications. THE NEW PHYTOLOGIST 2015; 207:953-67. [PMID: 25904408 DOI: 10.1111/nph.13410] [Citation(s) in RCA: 66] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/11/2014] [Accepted: 03/09/2015] [Indexed: 05/22/2023]
Abstract
The distribution of genomic variation across landscapes can provide insights into the complex interactions between the environment and the genome that influence the distribution of species, and mediate phenotypic adaptation to local conditions. High throughput sequencing technologies now offer unprecedented power to explore these interactions, allowing powerful inferences about historical processes of colonization, gene flow and divergence, as well as the identification of loci that mediate local adaptation. These 'landscape genomic' approaches have been validated in model species and are now being applied to nonmodel organisms, including foundation species that have substantial effects on ecosystem processes. Here we review the growing field of landscape genomics from a very broad perspective. In particular, we describe the inferential power that is gained by taking a genome-wide view of genetic variation, strategies for study design to best capture adaptive variation, and how to apply this information to practical challenges, such as restoration.
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Affiliation(s)
- Jason G Bragg
- Research School of Biology and Centre for Biodiversity Analysis, Australian National University, Canberra, ACT, 0200, Australia
| | - Megan A Supple
- Research School of Biology and Centre for Biodiversity Analysis, Australian National University, Canberra, ACT, 0200, Australia
| | - Rose L Andrew
- Research School of Biology and Centre for Biodiversity Analysis, Australian National University, Canberra, ACT, 0200, Australia
- School of Environmental and Rural Science, University of New England, Armidale, NSW, 2350, Australia
| | - Justin O Borevitz
- Research School of Biology and Centre for Biodiversity Analysis, Australian National University, Canberra, ACT, 0200, Australia
- ARC Centre of Excellence in Plant Energy Biology, Australian National University, Canberra, ACT, 0200, Australia
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104
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Rolshausen G, Muttalib S, Kaeuffer R, Oke KB, Hanson D, Hendry AP. When maladaptive gene flow does not increase selection. Evolution 2015. [DOI: 10.1111/evo.12739] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Affiliation(s)
- Gregor Rolshausen
- Redpath Museum and Department of Biology; McGill University; 859 Sherbrooke St. W. Montreal Quebec H3A0C4 Canada
| | - Shahin Muttalib
- Redpath Museum and Department of Biology; McGill University; 859 Sherbrooke St. W. Montreal Quebec H3A0C4 Canada
| | - Renaud Kaeuffer
- Redpath Museum and Department of Biology; McGill University; 859 Sherbrooke St. W. Montreal Quebec H3A0C4 Canada
| | - Krista B. Oke
- Redpath Museum and Department of Biology; McGill University; 859 Sherbrooke St. W. Montreal Quebec H3A0C4 Canada
| | - Dieta Hanson
- Redpath Museum and Department of Biology; McGill University; 859 Sherbrooke St. W. Montreal Quebec H3A0C4 Canada
| | - Andrew P. Hendry
- Redpath Museum and Department of Biology; McGill University; 859 Sherbrooke St. W. Montreal Quebec H3A0C4 Canada
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105
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Behrman EL, Watson SS, O'Brien KR, Heschel MS, Schmidt PS. Seasonal variation in life history traits in two Drosophila species. J Evol Biol 2015; 28:1691-704. [PMID: 26174167 DOI: 10.1111/jeb.12690] [Citation(s) in RCA: 61] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2015] [Revised: 06/30/2015] [Accepted: 07/01/2015] [Indexed: 01/16/2023]
Abstract
Seasonal environmental heterogeneity is cyclic, persistent and geographically widespread. In species that reproduce multiple times annually, environmental changes across seasonal time may create different selection regimes that may shape the population ecology and life history adaptation in these species. Here, we investigate how two closely related species of Drosophila in a temperate orchard respond to environmental changes across seasonal time. Natural populations of Drosophila melanogaster and Drosophila simulans were sampled at four timepoints from June through November to assess seasonal change in fundamental aspects of population dynamics as well as life history traits. D. melanogaster exhibit pronounced change across seasonal time: early in the season, the population is inferred to be uniformly young and potentially represents the early generation following overwintering survivorship. D. melanogaster isofemale lines derived from the early population and reared in a common garden are characterized by high tolerance to a variety of stressors as well as a fast rate of development in the laboratory environment that declines across seasonal time. In contrast, wild D. simulans populations were inferred to be consistently heterogeneous in age distribution across seasonal collections; only starvation tolerance changed predictably over seasonal time in a parallel manner as in D. melanogaster. These results suggest fundamental differences in population and evolutionary dynamics between these two taxa associated with seasonal heterogeneity in environmental parameters and associated selection pressures.
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Affiliation(s)
- E L Behrman
- Department of Biology, University of Pennsylvania, Philadelphia, PA, USA
| | - S S Watson
- Department of Mathematics, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - K R O'Brien
- Department of Biology, University of Pennsylvania, Philadelphia, PA, USA.,School of Biological Sciences, University of Nebraska, Lincoln, NE, USA
| | - M S Heschel
- Department of Organismal Biology & Ecology, Colorado College, Colorado Springs, CO, USA
| | - P S Schmidt
- Department of Biology, University of Pennsylvania, Philadelphia, PA, USA
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106
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Seear PJ, Rosato E, Goodall-Copestake WP, Barber I. The molecular evolution of spiggin nesting glue in sticklebacks. Mol Ecol 2015; 24:4474-88. [PMID: 26173374 PMCID: PMC4989455 DOI: 10.1111/mec.13317] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2014] [Revised: 07/06/2015] [Accepted: 07/09/2015] [Indexed: 11/26/2022]
Abstract
Gene duplication and subsequent divergence can lead to the evolution of new functions and lineage-specific traits. In sticklebacks, the successive duplication of a mucin gene (MUC19) into a tandemly arrayed, multigene family has enabled the production of copious amounts of 'spiggin', a secreted adhesive protein essential for nest construction. Here, we examine divergence between spiggin genes among three-spined sticklebacks (Gasterosteus aculeatus) from ancestral marine and derived freshwater populations, and propose underpinning gene duplication mechanisms. Sanger sequencing revealed substantial diversity among spiggin transcripts, including alternatively spliced variants and interchromosomal spiggin chimeric genes. Comparative analysis of the sequenced transcripts and all other spiggin genes in the public domain support the presence of three main spiggin lineages (spiggin A, spiggin B and spiggin C) with further subdivisions within spiggin B (B1, B2) and spiggin C (C1, C2). Spiggin A had diverged least from the ancestral MUC19, while the spiggin C duplicates had diversified most substantially. In silico translations of the spiggin gene open reading frames predicted that spiggins A and B are secreted as long mucin-like polymers, while spiggins C1 and C2 are secreted as short monomers, with putative antimicrobial properties. We propose that diversification of duplicated spiggin genes has facilitated local adaptation of spiggin to a range of aquatic habitats.
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Affiliation(s)
- P J Seear
- Department of Neuroscience, Psychology and Behaviour, College of Medicine, Biological Sciences and Psychology, University of Leicester, Leicester, LE1 7RH, UK
| | - E Rosato
- Department of Genetics, College of Medicine, Biological Sciences and Psychology, University of Leicester, Leicester, LE1 7RH, UK
| | | | - I Barber
- Department of Neuroscience, Psychology and Behaviour, College of Medicine, Biological Sciences and Psychology, University of Leicester, Leicester, LE1 7RH, UK
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107
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Fraïsse C, Belkhir K, Welch JJ, Bierne N. Local interspecies introgression is the main cause of extreme levels of intraspecific differentiation in mussels. Mol Ecol 2015; 25:269-86. [DOI: 10.1111/mec.13299] [Citation(s) in RCA: 78] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2015] [Revised: 06/19/2015] [Accepted: 06/19/2015] [Indexed: 12/15/2022]
Affiliation(s)
- Christelle Fraïsse
- Institut des Sciences de l'Evolution (UMR 5554); CNRS - Université Montpellier; Place Eugène Bataillon 34095 Montpellier France
- Station Marine; Université Montpellier; 2 rue des Chantiers 34200 Sète France
- Department of Genetics; University of Cambridge; Downing Street CB2 3EH Cambridge UK
| | - Khalid Belkhir
- Institut des Sciences de l'Evolution (UMR 5554); CNRS - Université Montpellier; Place Eugène Bataillon 34095 Montpellier France
| | - John J. Welch
- Department of Genetics; University of Cambridge; Downing Street CB2 3EH Cambridge UK
| | - Nicolas Bierne
- Institut des Sciences de l'Evolution (UMR 5554); CNRS - Université Montpellier; Place Eugène Bataillon 34095 Montpellier France
- Station Marine; Université Montpellier; 2 rue des Chantiers 34200 Sète France
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108
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Gagnaire PA, Broquet T, Aurelle D, Viard F, Souissi A, Bonhomme F, Arnaud-Haond S, Bierne N. Using neutral, selected, and hitchhiker loci to assess connectivity of marine populations in the genomic era. Evol Appl 2015; 8:769-86. [PMID: 26366195 PMCID: PMC4561567 DOI: 10.1111/eva.12288] [Citation(s) in RCA: 140] [Impact Index Per Article: 15.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2015] [Accepted: 06/05/2015] [Indexed: 12/14/2022] Open
Abstract
Estimating the rate of exchange of individuals among populations is a central concern to evolutionary ecology and its applications to conservation and management. For instance, the efficiency of protected areas in sustaining locally endangered populations and ecosystems depends on reserve network connectivity. The population genetics theory offers a powerful framework for estimating dispersal distances and migration rates from molecular data. In the marine realm, however, decades of molecular studies have met limited success in inferring genetic connectivity, due to the frequent lack of spatial genetic structure in species exhibiting high fecundity and dispersal capabilities. This is especially true within biogeographic regions bounded by well-known hotspots of genetic differentiation. Here, we provide an overview of the current methods for estimating genetic connectivity using molecular markers and propose several directions for improving existing approaches using large population genomic datasets. We highlight several issues that limit the effectiveness of methods based on neutral markers when there is virtually no genetic differentiation among samples. We then focus on alternative methods based on markers influenced by selection. Although some of these methodologies are still underexplored, our aim was to stimulate new research to test how broadly they are applicable to nonmodel marine species. We argue that the increased ability to apply the concepts of cline analyses will improve dispersal inferences across physical and ecological barriers that reduce connectivity locally. We finally present how neutral markers hitchhiking with selected loci can also provide information about connectivity patterns within apparently well-mixed biogeographic regions. We contend that one of the most promising applications of population genomics is the use of outlier loci to delineate relevant conservation units and related eco-geographic features across which connectivity can be measured.
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Affiliation(s)
- Pierre-Alexandre Gagnaire
- Université de Montpellier Montpellier, France ; CNRS - Institut des Sciences de l'Evolution, UMR 5554 UM-CNRS-IRD-EPHE, Station Méditerranéenne de l'Environnement Littoral Sète, France
| | - Thomas Broquet
- CNRS team Diversity and connectivity of coastal marine landscapes, Station Biologique de Roscoff Roscoff, France ; Sorbonne Universités, UPMC Université Paris 06, UMR 7144, Station Biologique de Roscoff Roscoff, France
| | - Didier Aurelle
- Aix Marseille Université, CNRS-IRD-Avignon Université, IMBE UMR 7263 Marseille, France
| | - Frédérique Viard
- CNRS team Diversity and connectivity of coastal marine landscapes, Station Biologique de Roscoff Roscoff, France ; Sorbonne Universités, UPMC Université Paris 06, UMR 7144, Station Biologique de Roscoff Roscoff, France
| | | | - François Bonhomme
- Université de Montpellier Montpellier, France ; CNRS - Institut des Sciences de l'Evolution, UMR 5554 UM-CNRS-IRD-EPHE, Station Méditerranéenne de l'Environnement Littoral Sète, France
| | - Sophie Arnaud-Haond
- Université de Montpellier Montpellier, France ; Ifremer, UMR "Ecosystèmes Marins Exploités" Sète, France
| | - Nicolas Bierne
- Université de Montpellier Montpellier, France ; CNRS - Institut des Sciences de l'Evolution, UMR 5554 UM-CNRS-IRD-EPHE, Station Méditerranéenne de l'Environnement Littoral Sète, France
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109
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Nested Levels of Adaptive Divergence: The Genetic Basis of Craniofacial Divergence and Ecological Sexual Dimorphism. G3-GENES GENOMES GENETICS 2015; 5:1613-24. [PMID: 26038365 PMCID: PMC4528318 DOI: 10.1534/g3.115.018226] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
Exemplary systems for adaptive divergence are often characterized by their large degrees of phenotypic variation. This variation represents the outcome of generations of diversifying selection. However, adaptive radiations can also contain a hierarchy of differentiation nested within them where species display only subtle phenotypic differences that still have substantial effects on ecology, function, and ultimately fitness. Sexual dimorphisms are also common in species displaying adaptive divergence and can be the result of differential selection between sexes that produce ecological differences between sexes. Understanding the genetic basis of subtle variation (between certain species or sexes) is therefore important for understanding the process of adaptive divergence. Using cichlids from the dramatic adaptive radiation of Lake Malawi, we focus on understanding the genetic basis of two aspects of relatively subtle phenotypic variation. This included a morphometric comparison of the patterns of craniofacial divergence between two ecologically similar species in relation to the larger adaptive radiation of Malawi, and male-female morphological divergence between their F2 hybrids. We then genetically map craniofacial traits within the context of sex and locate several regions of the genome that contribute to variation in craniofacial shape that is relevant to sexual dimorphism within species and subtle divergence between closely related species, and possibly to craniofacial divergence in the Malawi radiation as a whole. To enhance our search for candidate genes we take advantage of population genomic data and a genetic map that is anchored to the cichlid genome to determine which genes within our QTL regions are associated with SNPs that are alternatively fixed between species. This study provides a holistic understanding of the genetic underpinnings of adaptive divergence in craniofacial shape.
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110
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Souche EL, Hellemans B, Babbucci M, MacAoidh E, Guinand B, Bargelloni L, Chistiakov DA, Patarnello T, Bonhomme F, Martinsohn JT, Volckaert FAM. Range-wide population structure of European sea bassDicentrarchus labrax. Biol J Linn Soc Lond 2015. [DOI: 10.1111/bij.12572] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2023]
Affiliation(s)
- Erika L. Souche
- Laboratory of Biodiversity and Evolutionary Genomics; University of Leuven; Ch. Deberiotstraat 32 - PO Box 2439 B-3000 Leuven Belgium
- Center of Human Genetics; University of Leuven; O&N I Herestraat 49 - PO Box 602 B-3000 Leuven Belgium
| | - Bart Hellemans
- Laboratory of Biodiversity and Evolutionary Genomics; University of Leuven; Ch. Deberiotstraat 32 - PO Box 2439 B-3000 Leuven Belgium
| | - Massimiliano Babbucci
- Dipartimento di Biomedicina Comparata e Alimentazione; Università di Padova; I-35124 Padova Italy
| | - Eoin MacAoidh
- Joint Research Centre; Institute for the Protection and Security of the Citizen; European Commission; Maritime Affairs Unit (G.03) - TP051 (Bldg. 51), Via Enrico Fermi nr. 2749 I-21027 Ispra Italy
| | - Bruno Guinand
- Institut des Sciences de l'Evolution de Montpellier; Université de Montpellier; UMR CNRS 5554, Place Eugène Bataillon - cc63 F-34095 Montpellier Cedex 5 France
| | - Luca Bargelloni
- Dipartimento di Biomedicina Comparata e Alimentazione; Università di Padova; I-35124 Padova Italy
| | - Dimitry A. Chistiakov
- Laboratory of Biodiversity and Evolutionary Genomics; University of Leuven; Ch. Deberiotstraat 32 - PO Box 2439 B-3000 Leuven Belgium
- Department of Medical Nanobiotechnology; Pirogov Russian State Medical University Research Center; Ulitsa Ostrovityanova 1 117997 Moscow Russia
| | - Tomaso Patarnello
- Dipartimento di Biomedicina Comparata e Alimentazione; Università di Padova; I-35124 Padova Italy
| | - François Bonhomme
- Institut des Sciences de l'Evolution de Montpellier; Université de Montpellier; UMR CNRS 5554, Place Eugène Bataillon - cc63 F-34095 Montpellier Cedex 5 France
| | - Jann T. Martinsohn
- Joint Research Centre; Institute for the Protection and Security of the Citizen; European Commission; Maritime Affairs Unit (G.03) - TP051 (Bldg. 51), Via Enrico Fermi nr. 2749 I-21027 Ispra Italy
| | - Filip A. M. Volckaert
- Laboratory of Biodiversity and Evolutionary Genomics; University of Leuven; Ch. Deberiotstraat 32 - PO Box 2439 B-3000 Leuven Belgium
- Department of Biological and Environmental Sciences; CeMEB; University of Gothenburg; Box 463 SE-405 30 Gothenburg Sweden
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111
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Berg PR, Jentoft S, Star B, Ring KH, Knutsen H, Lien S, Jakobsen KS, André C. Adaptation to Low Salinity Promotes Genomic Divergence in Atlantic Cod (Gadus morhua L.). Genome Biol Evol 2015; 7:1644-63. [PMID: 25994933 PMCID: PMC4494048 DOI: 10.1093/gbe/evv093] [Citation(s) in RCA: 106] [Impact Index Per Article: 11.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
How genomic selection enables species to adapt to divergent environments is a fundamental question in ecology and evolution. We investigated the genomic signatures of local adaptation in Atlantic cod (Gadus morhua L.) along a natural salinity gradient, ranging from 35‰ in the North Sea to 7‰ within the Baltic Sea. By utilizing a 12 K SNPchip, we simultaneously assessed neutral and adaptive genetic divergence across the Atlantic cod genome. Combining outlier analyses with a landscape genomic approach, we identified a set of directionally selected loci that are strongly correlated with habitat differences in salinity, oxygen, and temperature. Our results show that discrete regions within the Atlantic cod genome are subject to directional selection and associated with adaptation to the local environmental conditions in the Baltic- and the North Sea, indicating divergence hitchhiking and the presence of genomic islands of divergence. We report a suite of outlier single nucleotide polymorphisms within or closely located to genes associated with osmoregulation, as well as genes known to play important roles in the hydration and development of oocytes. These genes are likely to have key functions within a general osmoregulatory framework and are important for the survival of eggs and larvae, contributing to the buildup of reproductive isolation between the low-salinity adapted Baltic cod and the adjacent cod populations. Hence, our data suggest that adaptive responses to the environmental conditions in the Baltic Sea may contribute to a strong and effective reproductive barrier, and that Baltic cod can be viewed as an example of ongoing speciation.
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Affiliation(s)
- Paul R Berg
- Centre for Ecological and Evolutionary Synthesis (CEES), Department of Biosciences, University of Oslo, Norway
| | - Sissel Jentoft
- Centre for Ecological and Evolutionary Synthesis (CEES), Department of Biosciences, University of Oslo, Norway
| | - Bastiaan Star
- Centre for Ecological and Evolutionary Synthesis (CEES), Department of Biosciences, University of Oslo, Norway
| | - Kristoffer H Ring
- Centre for Development and the Environment (SUM), University of Oslo, Norway
| | - Halvor Knutsen
- Centre for Ecological and Evolutionary Synthesis (CEES), Department of Biosciences, University of Oslo, Norway Institute of Marine Research (IMR), Flødevigen, His, Norway University of Agder, Kristiansand, Norway
| | - Sigbjørn Lien
- Centre for Integrative Genetics (CIGENE), Department of Animal and Aquacultural Sciences, Norwegian University of Life Sciences, Aas, Norway
| | - Kjetill S Jakobsen
- Centre for Ecological and Evolutionary Synthesis (CEES), Department of Biosciences, University of Oslo, Norway
| | - Carl André
- Department of Biology and Environmental Sciences-Tjärnö, University of Gothenburg, Strömstad, Sweden
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112
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Twyford AD, Streisfeld MA, Lowry DB, Friedman J. Genomic studies on the nature of species: adaptation and speciation inMimulus. Mol Ecol 2015; 24:2601-9. [DOI: 10.1111/mec.13190] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2015] [Revised: 03/25/2015] [Accepted: 03/27/2015] [Indexed: 12/27/2022]
Affiliation(s)
- Alex D. Twyford
- Ashworth Laboratories; Institute of Evolutionary Biology; The University of Edinburgh; Charlotte Auerbach Road Edinburgh EH9 3FL UK
- Department of Biology; Syracuse University; 107 College Place Syracuse NY 13244 USA
| | | | - David B. Lowry
- Plant Biology Laboratories; Department of Plant Biology; Michigan State University; 612 Wilson Road Room 166 East Lansing MI 48824 USA
| | - Jannice Friedman
- Department of Biology; Syracuse University; 107 College Place Syracuse NY 13244 USA
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113
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Ravinet M, Hynes R, Poole R, Cross TF, McGinnity P, Harrod C, Prodöhl PA. Where the lake meets the sea: strong reproductive isolation is associated with adaptive divergence between lake resident and anadromous three-spined sticklebacks. PLoS One 2015; 10:e0122825. [PMID: 25874617 PMCID: PMC4397041 DOI: 10.1371/journal.pone.0122825] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2014] [Accepted: 02/14/2015] [Indexed: 11/28/2022] Open
Abstract
Contact zones between divergent forms of the same species are often characterised by high levels of phenotypic diversity over small geographic distances. What processes are involved in generating such high phenotypic diversity? One possibility is that introgression and recombination between divergent forms in contact zones results in greater phenotypic and genetic polymorphism. Alternatively, strong reproductive isolation between forms may maintain distinct phenotypes, preventing homogenisation by gene flow. Contact zones between divergent freshwater-resident and anadromous stickleback (Gasterosteus aculeatus L.) forms are numerous and common throughout the species distribution, offering an opportunity to examine these contrasting hypotheses in greater detail. This study reports on an interesting new contact zone located in a tidally influenced lake catchment in western Ireland, characterised by high polymorphism for lateral plate phenotypes. Using neutral and QTL-linked microsatellite markers, we tested whether the high diversity observed in this contact zone arose as a result of introgression or reproductive isolation between divergent forms: we found strong support for the latter hypothesis. Three phenotypic and genetic clusters were identified, consistent with two divergent resident forms and a distinct anadromous completely plated population that migrates in and out of the system. Given the strong neutral differentiation detected between all three morphotypes (mean FST = 0.12), we hypothesised that divergent selection between forms maintains reproductive isolation. We found a correlation between neutral genetic and adaptive genetic differentiation that support this. While strong associations between QTL linked markers and phenotypes were also observed in this wild population, our results support the suggestion that such associations may be more complex in some Atlantic populations compared to those in the Pacific. These findings provide an important foundation for future work investigating the dynamics of gene flow and adaptive divergence in this newly discovered stickleback contact zone.
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Affiliation(s)
- Mark Ravinet
- School of Biological Sciences, Queen’s University Belfast, Belfast, United Kingdom
| | - Rosaleen Hynes
- School of Biological Sciences, Queen’s University Belfast, Belfast, United Kingdom
- Institute for Global Food Security, School of Biological Sciences, Queen’s University Belfast, Belfast, United Kingdom
| | - Russell Poole
- Marine Institute, Furnace, Newport, County Mayo, Ireland
| | - Tom F. Cross
- Aquaculture, Fisheries and Development Centre, School of Biological, Earth & Environmental Sciences, University College Cork, Cork, Ireland
| | - Phil McGinnity
- Aquaculture, Fisheries and Development Centre, School of Biological, Earth & Environmental Sciences, University College Cork, Cork, Ireland
| | - Chris Harrod
- School of Biological Sciences, Queen’s University Belfast, Belfast, United Kingdom
| | - Paulo A. Prodöhl
- School of Biological Sciences, Queen’s University Belfast, Belfast, United Kingdom
- Institute for Global Food Security, School of Biological Sciences, Queen’s University Belfast, Belfast, United Kingdom
- * E-mail:
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114
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Guo B, DeFaveri J, Sotelo G, Nair A, Merilä J. Population genomic evidence for adaptive differentiation in Baltic Sea three-spined sticklebacks. BMC Biol 2015; 13:19. [PMID: 25857931 PMCID: PMC4410466 DOI: 10.1186/s12915-015-0130-8] [Citation(s) in RCA: 84] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2014] [Accepted: 03/12/2015] [Indexed: 11/30/2022] Open
Abstract
Background The degree of genetic differentiation among populations experiencing high levels of gene flow is expected to be low for neutral genomic sites, but substantial divergence can occur in sites subject to directional selection. Studies of highly mobile marine fish populations provide an opportunity to investigate this kind of heterogeneous genomic differentiation, but most studies to this effect have focused on a relatively low number of genetic markers and/or few populations. Hence, the patterns and extent of genomic divergence in high-gene-flow marine fish populations remain poorly understood. Results We here investigated genome-wide patterns of genetic variability and differentiation in ten marine populations of three-spined stickleback (Gasterosteus aculeatus) distributed across a steep salinity and temperature gradient in the Baltic Sea, by utilizing >30,000 single nucleotide polymorphisms obtained with a pooled RAD-seq approach. We found that genetic diversity and differentiation varied widely across the genome, and identified numerous fairly narrow genomic regions exhibiting signatures of both divergent and balancing selection. Evidence was uncovered for substantial genetic differentiation associated with both salinity and temperature gradients, and many candidate genes associated with local adaptation in the Baltic Sea were identified. Conclusions The patterns of genetic diversity and differentiation, as well as candidate genes associated with adaptation, in Baltic Sea sticklebacks were similar to those observed in earlier comparisons between marine and freshwater populations, suggesting that similar processes may be driving adaptation to brackish and freshwater environments. Taken together, our results provide strong evidence for heterogenic genomic divergence driven by local adaptation in the face of gene flow along an environmental gradient in the post-glacially formed Baltic Sea. Electronic supplementary material The online version of this article (doi:10.1186/s12915-015-0130-8) contains supplementary material, which is available to authorized users.
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Rieseberg L, Vines T, Gow J, Geraldes A. Editorial 2015. Mol Ecol 2015; 24:1-17. [DOI: 10.1111/mec.12997] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2014] [Accepted: 11/10/2014] [Indexed: 11/30/2022]
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Terekhanova NV, Logacheva MD, Penin AA, Neretina TV, Barmintseva AE, Bazykin GA, Kondrashov AS, Mugue NS. Fast evolution from precast bricks: genomics of young freshwater populations of threespine stickleback Gasterosteus aculeatus. PLoS Genet 2014; 10:e1004696. [PMID: 25299485 PMCID: PMC4191950 DOI: 10.1371/journal.pgen.1004696] [Citation(s) in RCA: 82] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2013] [Accepted: 08/22/2014] [Indexed: 12/03/2022] Open
Abstract
Adaptation is driven by natural selection; however, many adaptations are caused by weak selection acting over large timescales, complicating its study. Therefore, it is rarely possible to study selection comprehensively in natural environments. The threespine stickleback (Gasterosteus aculeatus) is a well-studied model organism with a short generation time, small genome size, and many genetic and genomic tools available. Within this originally marine species, populations have recurrently adapted to freshwater all over its range. This evolution involved extensive parallelism: pre-existing alleles that adapt sticklebacks to freshwater habitats, but are also present at low frequencies in marine populations, have been recruited repeatedly. While a number of genomic regions responsible for this adaptation have been identified, the details of selection remain poorly understood. Using whole-genome resequencing, we compare pooled genomic samples from marine and freshwater populations of the White Sea basin, and identify 19 short genomic regions that are highly divergent between them, including three known inversions. 17 of these regions overlap protein-coding genes, including a number of genes with predicted functions that are relevant for adaptation to the freshwater environment. We then analyze four additional independently derived young freshwater populations of known ages, two natural and two artificially established, and use the observed shifts of allelic frequencies to estimate the strength of positive selection. Adaptation turns out to be quite rapid, indicating strong selection acting simultaneously at multiple regions of the genome, with selection coefficients of up to 0.27. High divergence between marine and freshwater genotypes, lack of reduction in polymorphism in regions responsible for adaptation, and high frequencies of freshwater alleles observed even in young freshwater populations are all consistent with rapid assembly of G. aculeatus freshwater genotypes from pre-existing genomic regions of adaptive variation, with strong selection that favors this assembly acting simultaneously at multiple loci. Adaptation to novel environments is a keystone of evolution. There is only a handful of natural and experimental systems in which the process of adaptation has been studied in detail, and each studied system brings its own surprises with regard to the number of loci involved, dynamics of adaptation, extent of interactions between loci and of parallelism between different adapting populations. The threespine stickleback is an excellent model organism for evolutionary studies. Marine-derived freshwater populations of this species have consistently acquired a specific set of morphological, physiological and behavioral traits allowing them to reside in freshwater for their whole lifespan. Previous studies identified several genomic regions responsible for this adaptation. Here, using whole-genome sequencing, we compare the allele frequencies at such regions in four derived freshwater populations of known ages: two natural, and two artificially established in 1978. Knowledge of population ages allows us to infer the strength of selection that acted at these loci. Adaptation of threespine stickleback to freshwater is typically fast, and is driven by strong selection favoring pre-existing alleles that are likely present in the ancestral marine population at low frequencies; however, some of the adaptation may also be due to young population-specific alleles.
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Affiliation(s)
- Nadezhda V. Terekhanova
- Department of Bioinformatics and Bioengineering, M. V. Lomonosov Moscow State University, Moscow, Russia
- * E-mail: (NVT); (NSM)
| | - Maria D. Logacheva
- Department of Bioinformatics and Bioengineering, M. V. Lomonosov Moscow State University, Moscow, Russia
- A. N. Belozersky Institute of Physico-Chemical Biology, M. V. Lomonosov Moscow State University, Moscow, Russia
| | - Aleksey A. Penin
- Department of Bioinformatics and Bioengineering, M. V. Lomonosov Moscow State University, Moscow, Russia
- Department of Genetics, Biological faculty, M. V. Lomonosov Moscow State University, Moscow, Russia
| | - Tatiana V. Neretina
- Department of Bioinformatics and Bioengineering, M. V. Lomonosov Moscow State University, Moscow, Russia
- White Sea Biological Station, Biological faculty, M. V. Lomonosov Moscow State University, Moscow, Russia
| | - Anna E. Barmintseva
- Laboratory of Molecular genetics, Russian Institute of Fisheries and Oceanology, Russian Federal Research Institute of Fisheries and Oceanography, Moscow, Russia
| | - Georgii A. Bazykin
- Department of Bioinformatics and Bioengineering, M. V. Lomonosov Moscow State University, Moscow, Russia
- Sector for Molecular Evolution, Institute for Information Transmission Problems of the RAS (Kharkevich Institute), Moscow, Russia
| | - Alexey S. Kondrashov
- Department of Bioinformatics and Bioengineering, M. V. Lomonosov Moscow State University, Moscow, Russia
- Department of Ecology and Evolutionary Biology and Life Sciences Institute, University of Michigan, Ann Arbor, Michigan, United States of America
| | - Nikolai S. Mugue
- Laboratory of Molecular genetics, Russian Institute of Fisheries and Oceanology, Russian Federal Research Institute of Fisheries and Oceanography, Moscow, Russia
- N. K. Koltsov Institute of Developmental Biology RAS, Moscow, Russia
- * E-mail: (NVT); (NSM)
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Berner D, Moser D, Roesti M, Buescher H, Salzburger W. GENETIC ARCHITECTURE OF SKELETAL EVOLUTION IN EUROPEAN LAKE AND STREAM STICKLEBACK. Evolution 2014; 68:1792-805. [DOI: 10.1111/evo.12390] [Citation(s) in RCA: 38] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2013] [Accepted: 02/11/2014] [Indexed: 01/17/2023]
Affiliation(s)
- Daniel Berner
- Zoological Institute; University of Basel; Vesalgasse 1, CH-4051 Basel Switzerland
| | - Dario Moser
- Zoological Institute; University of Basel; Vesalgasse 1, CH-4051 Basel Switzerland
| | - Marius Roesti
- Zoological Institute; University of Basel; Vesalgasse 1, CH-4051 Basel Switzerland
| | - Heinz Buescher
- Zoological Institute; University of Basel; Vesalgasse 1, CH-4051 Basel Switzerland
| | - Walter Salzburger
- Zoological Institute; University of Basel; Vesalgasse 1, CH-4051 Basel Switzerland
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