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Book ChapterDOI

Genetic diversity and evolution

TL;DR: A current methodological shift from single-gene approaches to genome-wide studies will help in distinguishing genes and patterns of variation that are affected by selection from those that merely reflect population structure, and in identifying characters that account for the adaptations to the unique Baltic Sea environment.
Abstract: 1. Genetic variability among individuals, populations and species represents the basic level of biodiversity, and is a prerequisite of adaptive evolution. 2. Adaptive evolution is driven by natural selection that acts at the level of individual phenotypes. 3. Genetic variation can also be used as a tool to study the history of species and populations, and to explore their current structure and reproductive strategies. 4. Genetic markers that are presumably neutral to selection are used in measuring connectivity among Baltic populations and their uniqueness compared to those in the neighbouring marine or freshwater habitats. Genetic markers have often revealed the presence of previously unknown cryptic species that are much older than the Baltic Sea. 5. In most taxa studied, some genetic differentiation has arisen post-glacially between the Baltic Sea and North Sea populations, e.g. in the Atlantic herring Clupea harengus and the Atlantic cod Gadus morhua . 6. Despite such differentiation, few of the Baltic organisms are considered as locally evolved endemic taxa. An exception is the partly asexually reproducing brown algal species Fucus radicans, which has evolved locally and now coexists with its ancestor Fucus vesiculosus in the northern Baltic Sea. 7. The unique blue mussel and Baltic clam populations in the Baltic Sea are closely related to Pacific lineages ( Mytilus trossulus and Macoma balthica balthica ) but are distinct from the neighbouring North Sea populations ( Mytilus edulis and Macoma balthica rubra ). They have been modified by interbreeding in the transition zone between the Baltic Sea and the North Sea, and now constitute hybrid swarms. 8. A current methodological shift from single-gene approaches to genome-wide studies will help in distinguishing genes and patterns of variation that are affected by selection from those that merely reflect population structure, and in identifying characters that account for the adaptations to the unique Baltic Sea environment.
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Journal ArticleDOI
TL;DR: It is argued that the Baltic Sea can serve as a time machine to study consequences and mitigation of future coastal perturbations, due to its unique combination of an early history of multistressor disturbance and ecosystem deterioration and early implementation of cross-border environmental management to address these problems.
Abstract: Coastal global oceans are expected to undergo drastic changes driven by climate change and increasing anthropogenic pressures in coming decades. Predicting specific future conditions and assessing the best management strategies to maintain ecosystem integrity and sustainable resource use are difficult, because of multiple interacting pressures, uncertain projections, and a lack of test cases for management. We argue that the Baltic Sea can serve as a time machine to study consequences and mitigation of future coastal perturbations, due to its unique combination of an early history of multistressor disturbance and ecosystem deterioration and early implementation of cross-border environmental management to address these problems. The Baltic Sea also stands out in providing a strong scientific foundation and accessibility to long-term data series that provide a unique opportunity to assess the efficacy of management actions to address the breakdown of ecosystem functions. Trend reversals such as the return of top predators, recovering fish stocks, and reduced input of nutrient and harmful substances could be achieved only by implementing an international, cooperative governance structure transcending its complex multistate policy setting, with integrated management of watershed and sea. The Baltic Sea also demonstrates how rapidly progressing global pressures, particularly warming of Baltic waters and the surrounding catchment area, can offset the efficacy of current management approaches. This situation calls for management that is (i) conservative to provide a buffer against regionally unmanageable global perturbations, (ii) adaptive to react to new management challenges, and, ultimately, (iii) multisectorial and integrative to address conflicts associated with economic trade-offs.

274 citations

Journal ArticleDOI
TL;DR: In a review of 23 marine species' genetic divergence over a postglacial salinity gradient, many showed steep genetic clines supported by divergent selection and/or temporal or spatial segregation.
Abstract: Barriers to gene flow between divergent populations result in contact (hybrid) zones. Locations where multiple contact zones overlap can be used in comparative studies asking: what mechanisms maintain barriers; what is the origin of the genetic variation involved; and do differences in life history affect the nature of barriers? In a review of 23 marine species' genetic divergence over a postglacial salinity gradient, many showed steep genetic clines supported by divergent selection and/or temporal or spatial segregation. Contacts were primary or secondary and shaped by ancestral variation sometimes involving inversions. The dispersal potential of species seemed less important in shaping clines. Studies of multispecies contact zones will increase our understanding of speciation, but we need to address the taxonomic bias and focus more on postzygotic isolation.

56 citations

Journal ArticleDOI
TL;DR: In this paper, a combination of models was applied to predict the fate of one of the dominant foundation species in the Baltic Sea, the bladder wrack Fucus vesiculosus.
Abstract: Aim The Baltic Sea forms a unique regional sea with its salinity gradient ranging from marine to nearly freshwater conditions. It is one of the most environmentally impacted brackish seas worldwide, and the low biodiversity makes it particularly sensitive to anthropogenic pressures including climate change. We applied a novel combination of models to predict the fate of one of the dominant foundation species in the Baltic Sea, the bladder wrack Fucus vesiculosus. Location The Baltic Sea. Methods We used a species distribution model to predict climate change-induced displacement of F. vesiculosus and combined these projections with a biophysical model of dispersal and connectivity to explore whether the dispersal rate of locally adapted genotypes may match estimated climate velocities to recolonize the receding salinity gradient. In addition, we used a population dynamic model to assess possible effects of habitat fragmentation. Results The species distribution model showed that the habitat of F. vesiculosus is expected to dramatically shrink, mainly caused by the predicted reduction of salinity. In addition, the dispersal rate of locally adapted genotypes may not keep pace with estimated climate velocities rendering the recolonization of the receding salinity gradient more difficult. A simplistic model of population dynamics also indicated that the risk of local extinction may increase due to future habitat fragmentation. Main conclusions Results point to a significant risk of locally adapted genotypes being unable to shift their ranges sufficiently fast considering the restricted dispersal and long generation time. The worst scenario is that F. vesiculosus may disappear from large parts of the Baltic Sea before the end of this century with large effects on the biodiversity and ecosystem functioning. We finally discuss how to reduce this risk through conservation actions, including assisted colonization and assisted evolution.

37 citations


Cites background from "Genetic diversity and evolution"

  • ...…to the Baltic environment (Berg et al., 2015; Johansson, Pereyra, Rafajlovic, & Johannesson, 2017; Momigliano et al., 2017; Pereyra, Bergström, Kautsky, & Johannesson, 2009; Serrão, Kautsky, & Brawley, 1996; Sjöqvist, Godhe, Jonsson, Sundqvist, & Kremp, 2015; Väinölä & Johannesson, 2017)....

    [...]

  • ...This may apply to F. vesiculosus where poor dispersal ability with zygotes or clonal adventitious branches is generally expected (Johansson et al., 2017; Pereyra et al., 2013; Väinölä & Johannesson, 2017)....

    [...]

Patent
17 Oct 2016
TL;DR: A new species of circovirus was identified from sows with clinical symptoms normally associated with porcine circoviruses type 2 (PCV2) infection and in aborted fetuses as discussed by the authors.
Abstract: A new species of circovirus, porcine circovirus type 3 (PCV3), was identified from sows with clinical symptoms normally associated with porcine circovirus type 2 (PCV2) infection and in aborted fetuses. Molecular and serological analyses suggest PCV3 commonly circulates in U.S. swine. The present disclosure provides immunological compositions and methods related to the production and administration of such compositions.

31 citations

References
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Book
03 Jan 2000
TL;DR: This chapter discusses the history and Purview of Phylogeography, Genealogical Concordance, and Speciation Processes and Extended Genealogy Works and its applications to Speciation and Beyond.
Abstract: Preface I. History and Conceptual Background 1. The History and Purview of Phylogeography 2. Demography-Phylogeny Connections II. Empirical Intraspecific Phylogeography 3. Lessons from Human Analyses 4. Intraspecific Patterns in other Animals III. Genealogical Concordance: Toward Speciation and Beyond 5. Genealogical Concordance 6. Speciation Processes and Extended Genealogy Works Cited Index

4,753 citations

Journal ArticleDOI
TL;DR: Despite the short geological history of the Baltic Sea, populations inhabiting the Baltic have evolved substantially different from Atlantic populations, probably as a consequence of isolation and bottlenecks, as well as selection on adaptive traits.
Abstract: Marginal populations are often isolated and under extreme selection pressures resulting in anomalous genetics. Consequently, ecosystems that are geographically and ecologically marginal might have a large share of genetically atypical populations, in need of particular concern in management of these ecosystems. To test this prediction, we analysed genetic data from 29 species inhabiting the low saline Baltic Sea, a geographically and ecologically marginal ecosystem. On average Baltic populations had lost genetic diversity compared to Atlantic populations: a pattern unrelated to dispersal capacity, generation time of species and taxonomic group of organism, but strongly related to type of genetic marker (mitochondrial DNA loci had lost c. 50% diversity, and nuclear loci 10%). Analyses of genetic isolation by geographic distance revealed clinal patterns of differentiation between Baltic and Atlantic regions. For a majority of species, clines were sigmoid with a sharp slope around the Baltic Sea entrance, indicating impeded gene flows between Baltic and Atlantic populations. Some species showed signs of allele frequencies being perturbed at the edge of their distribution inside the Baltic Sea. Despite the short geological history of the Baltic Sea (8000 years), populations inhabiting the Baltic have evolved substantially different from Atlantic populations, probably as a consequence of isolation and bottlenecks, as well as selection on adaptive traits. In addition, the Baltic Sea also acts a refuge for unique evolutionary lineages. This marginal ecosystem is thus vulnerable but also exceedingly valuable, housing unique genes, genotypes and populations that constitute an important genetic resource for management and conservation.

441 citations

Journal ArticleDOI
TL;DR: The study of hybrid zones is central to the understanding of the genetic basis of reproductive isolation and speciation, and using a model‐based clustering method for individual admixture analysis, the existence of intermediate genotypes in all samples from the transition area is demonstrated.
Abstract: The study of hybrid zones is central to our understanding of the genetic basis of reproductive isolation and speciation, yet very little is known about the extent and significance of hybrid zones in marine fishes. We examined the population structure of cod in the transition area between the North Sea and the Baltic Sea employing nine microsatellite loci. Genetic differentiation between the North Sea sample and the rest increased along a transect to the Baltic proper, with a large increase in level of differentiation occurring in the Western Baltic area. Our objective was to determine whether this pattern was caused purely by varying degrees of mechanical mixing of North Sea and Baltic Sea cod or by interbreeding and formation of a hybrid swarm. Simulation studies revealed that traditional Hardy-Weinberg analysis did not have sufficient power for detection of a Wahlund effect. However, using a model-based clustering method for individual admixture analysis, we were able to demonstrate the existence of intermediate genotypes in all samples from the transition area. Accordingly, our data were explained best by a model of a hybrid swarm flanked by pure nonadmixed populations in the North Sea and the Baltic Sea proper. Significant correlation of gene identities across loci (gametic phase disequilibrium) was found only in a sample from the Western Baltic, suggesting this area as the centre of the apparent hybrid zone. A hybrid zone for cod in the ecotone between the high-saline North Sea and the low-saline Baltic Sea is discussed in relation to its possible origin and maintenance, and in relation to a classical study of haemoglobin variation in cod from the Baltic Sea/Danish Belt Sea, suggesting mixing of two divergent populations without interbreeding.

265 citations

Journal ArticleDOI
TL;DR: This study provides insights concerning the population structure of an important marine fish and establishes the Atlantic herring as a model for population genetic studies of adaptation and natural selection.
Abstract: The Atlantic herring (Clupea harengus), one of the most abundant marine fishes in the world, has historically been a critical food source in Northern Europe. It is one of the few marine species that can reproduce throughout the brackish salinity gradient of the Baltic Sea. Previous studies based on few genetic markers have revealed a conspicuous lack of genetic differentiation between geographic regions, consistent with huge population sizes and minute genetic drift. Here, we present a cost-effective genome-wide study in a species that lacks a genome sequence. We first assembled a muscle transcriptome and then aligned genomic reads to the transcripts, creating an “exome assembly,” capturing both exons and flanking sequences. We then resequenced pools of fish from a wide geographic range, including the Northeast Atlantic, as well as different regions in the Baltic Sea, aligned the reads to the exome assembly, and identified 440,817 SNPs. The great majority of SNPs showed no appreciable differences in allele frequency among populations; however, several thousand SNPs showed striking differences, some approaching fixation for different alleles. The contrast between low genetic differentiation at most loci and striking differences at others implies that the latter category primarily reflects natural selection. A simulation study confirmed that the distribution of the fixation index FST deviated significantly from expectation for selectively neutral loci. This study provides insights concerning the population structure of an important marine fish and establishes the Atlantic herring as a model for population genetic studies of adaptation and natural selection.

242 citations

Journal ArticleDOI
TL;DR: The development of a medium‐density Atlantic salmon single nucleotide polymorphism (SNP) array based on expressed sequence tags (ESTs) and genomic sequencing is described and the potential for the array to disentangle neutral and putative adaptive divergence of SNP allele frequencies across populations and among regional groups is assessed.
Abstract: Atlantic salmon (Salmo salar) is one of the most extensively studied fish species in the world due to its significance in aquaculture, fisheries and ongoing conservation efforts to protect declining populations Yet, limited genomic resources have hampered our understanding of genetic architecture in the species and the genetic basis of adaptation to the wide range of natural and artificial environments it occupies In this study, we describe the development of a medium-density Atlantic salmon single nucleotide polymorphism (SNP) array based on expressed sequence tags (ESTs) and genomic sequencing The array was used in the most extensive assessment of population genetic structure performed to date in this species A total of 6176 informative SNPs were successfully genotyped in 38 anadromous and freshwater wild populations distributed across the species natural range Principal component analysis clearly differentiated European and North American populations, and within Europe, three major regional genetic groups were identified for the first time in a single analysis We assessed the potential for the array to disentangle neutral and putative adaptive divergence of SNP allele frequencies across populations and among regional groups In Europe, secondary contact zones were identified between major clusters where endogenous and exogenous barriers could be associated, rendering the interpretation of environmental influence on potentially adaptive divergence equivocal A small number of markers highly divergent in allele frequencies (outliers) were observed between (multiple) freshwater and anadromous populations, between northern and southern latitudes, and when comparing Baltic populations to all others We also discuss the potential future applications of the SNP array for conservation, management and aquaculture

231 citations

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How has the definition of molecular genetic diversity and evolution changed over the last 10 years?

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