Evolutionary genetic analysis of an invasive population of sculpins in the Lower Rhine

Fish abundance surveys have shown that the Lower Rhine was invaded by sculpins (Cottus sp.) within two decades. These fish are found in habitats that are untypical for Cottus gobio. In order to find source populations and reasons for this invasion an evolutionary genetic analysis of populations from the Rhine and surrounding rivers was conducted. A combined analysis of nuclear and mitochondrial markers suggests that invasive sculpins are hybrids between lineages from the Rivers Scheldt and Rhine. The hybrids form a distinct genetic group and possess a unique ecological potential, attributed here to the process of hybridization. To explore the genetics of invasive sculpins 177 microsatellite markers were developed and a linkage map for Cottus was constructed from F1 crosses. BLAST searches with microsatellite flanking sequences yield significant hits with the Tetraodon nigroviridis genomic sequence for 45% of the Cottus loci. Comparisons of the map locations between the genomes reveal extensive conserved synteny, suggesting that the Tetraodon genomic sequence will serve as an excellent reference for Cottus. The novel markers and linkage information are applied in population genetic studies and to initiate first QTL approaches. Evidence that invasive sculpins have a unique ecological potential to colonize large rivers is derived from recently formed hybrid zones where secondary contact postdates the appearance of invasive sculpins in the early 1990's. Hybrid zones are moulded by exogenous selection in the absence of intrinsic reproductive barriers. Hybridization receives attention because of the role that it may play in generating evolutionary novelty, which is tested in recent hybrids. Body shape is analysed with a new distance based assignment method using morphometric data. Shape is highly informative in that populations are sufficiently different to assign 'unknowns' to their source. Recent hybrids are intermediate between parental groups but display additional differentiation. This suggests transgressive segregation and genetic divergence in developmental processes underlying body shape. Natural hybrid zones offer an alternative for QTL mapping because far-reaching associations between states of ancestry at physically linked loci are generated in segregating hybrids. Ancestry association is exploited by admixture mapping, which is applied for the first time in wild populations. The Cottus genome was screened for association with morphological characters as well as with habitat as a surrogate of ecological differentiation. Candidate regions often affect more than one trait. This implies linkage of traits affecting divergent morphology and fitness. Selection at hybrid zones likely affects linked morphological traits. Likewise, the differentiation of invasive sculpins despite past hybridization could be explained by linkage of morphological with adaptive traits

Haplotype block dynamics in hybrid populations

When species originate through hybridization, the genomes of the ancestral species are blended together. Over time genomic blocks that originate from either one of the ancestral species accumulate in the hybrid genome through genetic recombination. Modeling the accumulation of ancestry blocks can elucidate processes and patterns of genomic admixture. However, previous models have ignored ancestry block dynamics for chromosomes that consist of a discrete, finite number of chromosomal elements. Here we present an analytical treatment of the dynamics of the mean number of blocks over time, for continuous and discrete chromosomes, in finite and infinite populations. We describe the mean number of haplotype blocks as a universal function dependent on population size, the number of genomic elements per chromosome, the number of recombination events, and the initial relative frequency of the ancestral species

Shape based assignment tests suggest transgressive phenotypes in natural sculpin hybrids (Teleostei, Scorpaeniformes, Cottidae)

BACKGROUND: Hybridization receives attention because of the potential role that it may play in generating evolutionary novelty. An explanation for the emergence of novel phenotypes is given by transgressive segregation, which, if frequent, would imply an important evolutionary role for hybridization. This process is still rarely studied in natural populations as samples of recent hybrids and their parental populations are needed. Further, the detection of transgressive segregation requires phenotypes that can be easily quantified and analysed. We analyse variability in body shape of divergent populations of European sculpins (Cottus gobio complex) as well as natural hybrids among them. RESULTS: A distance-based method is developed to assign unknown specimens to known groups based on morphometric data. Apparently, body shape represents a highly informative set of characters that parallels the discriminatory power of microsatellite markers in our study system. Populations of sculpins are distinct and "unknown" specimens can be correctly assigned to their source population based on body shape. Recent hybrids are intermediate along the axes separating their parental groups but display additional differentiation that is unique and coupled with the hybrid genetic background. CONCLUSION: There is a specific hybrid shape component in natural sculpin hybrids that can be best explained by transgressive segregation. This inference of how hybrids differ from their ancestors provides basic information for future evolutionary studies. Furthermore, our approach may serve to assign candidate specimens to their source populations based on morphometric data and help in the interpretation of population differentiation

Divergence in gene regulation at young life history stages of whitefish (Coregonus sp.) and the emergence of genomic isolation

<p>Abstract</p> <p>Background</p> <p>The evolution of barriers to reproduction is of key interest to understand speciation. However, there may be a current bias towards studying intrinsic postzygotic isolation in old species pairs as compared to the emergence of barriers to gene flow through adaptive divergence. This study evaluates the relative importance of both processes in the evolution of genomic isolation in incipient species of whitefish (<it>Coregonus clupeaformis</it>) for which preliminary data suggest that postzygotic isolation emerges with intrinsic factors acting at embryo stages but also due to extrinsic factors during adult life.</p> <p>Results</p> <p>Gene expression data were screened using cDNA microarrays to identify regulatory changes at embryo and juvenile stages that provide evidence for genomic divergence at the underlying genetic factors. A comparison of different life history stages shows that 16-week old juvenile fish have 14 times more genes displaying significant regulatory divergence than embryos. Furthermore, regulatory changes in juvenile fish match patterns in adult fish suggesting that gene expression divergence is established early in juvenile fish and persists throughout the adult phase. Comparative analyses with results from previous studies on dwarf-normal species pairs show that at least 26 genetic factors identified in juvenile fish are candidate traits for adaptive divergence in adult fish. Eight of these show parallel directions of gene expression divergence independent of tissue type or age of the fish. The latter are associated with energy metabolism, a complex trait known to drive adaptive divergence in dwarf and normal whitefish.</p> <p>Conclusion</p> <p>Although experimental evidence suggests the existence of genetic factors that cause intrinsic postzygotic isolation acting in embryos, the analysis presented here provided few candidate genes in embryos, which also corroborate previous studies showing a lack of ecological divergence between sympatric dwarf and normal whitefish at the larval stage. In contrast, gene expression divergence in juveniles can be linked to adaptive traits and seems to be driven by positive selection. The results support the idea that adaptive differentiation may be more important in explaining the emergence of barriers to gene flow in an early phase of speciation by providing a broad genomic basis for extrinsic postzygotic isolation rather than intrinsic barriers.</p

An evaluation of LSU rDNA D1-D2 sequences for their use in species identification

BACKGROUND: Identification of species via DNA sequences is the basis for DNA taxonomy and DNA barcoding. Currently there is a strong focus on using a mitochondrial marker for this purpose, in particular a fragment from the cytochrome oxidase I gene (COI). While there is ample evidence that this marker is indeed suitable across a broad taxonomic range to delineate species, it has also become clear that a complementation by a nuclear marker system could be advantageous. Ribosomal RNA genes could be suitable for this purpose, because of their global occurrence and the possibility to design universal primers. However, it has so far been assumed that these genes are too highly conserved to allow resolution at, or even beyond the species level. On the other hand, it is known that ribosomal gene regions harbour also highly divergent parts. We explore here the information content of two adjacent divergence regions of the large subunit ribosomal gene, the D1-D2 region. RESULTS: Universal primers were designed to amplify the D1-D2 region from all metazoa. We show that amplification products in the size between 800–1300 bp can be obtained across a broad range of animal taxa, provided some optimizations of the PCR procedure are implemented. Although the ribosomal genes occur in multiple copies in the genomes, we find generally very little intra-individual polymorphism (<< 0.1% on average) indicating that concerted evolution is very effective in most cases. Studies in two fish taxa (genus Cottus and genus Aphyosemion) show that the D1-D2 LSU sequence can resolve even very closely related species with the same fidelity as COI sequences. In one case we can even show that a mitochondrial transfer must have occurred, since the nuclear sequence confirms the taxonomic assignment, while the mitochondrial sequence would have led to the wrong classification. We have further explored whether hybrids between species can be detected with the nuclear sequence and we show for a test case of natural hybrids among cyprinid fish species (Alburnus alburnus and Rutilus rutilus) that this is indeed possible. CONCLUSION: The D1-D2 LSU region is a suitable marker region for applications in DNA based species identification and should be considered to be routinely used as a marker complementing broad scale studies based on mitochondrial markers

The Role of Plasticity and Adaptation in the Incipient Speciation of a Fire Salamander Population

Phenotypic plasticity and local adaptation via genetic change are two major mechanisms of response to dynamic environmental conditions. These mechanisms are not mutually exclusive, since genetic change can establish similar phenotypes to plasticity. This connection between both mechanisms raises the question of how much of the variation observed between species or populations is plastic and how much of it is genetic. In this study, we used a structured population of fire salamanders (Salamandra salamandra), in which two subpopulations differ in terms of physiology, genetics, mate-, and habitat preferences. Our goal was to identify candidate genes for differential habitat adaptation in this system, and to explore the degree of plasticity compared to local adaptation. We therefore performed a reciprocal transfer experiment of stream- and pond-originated salamander larvae and analyzed changes in morphology and transcriptomic profile (using species-specific microarrays). We observed that stream- and pond-originated individuals diverge in morphology and gene expression. For instance, pond-originated larvae have larger gills, likely to cope with oxygen-poor ponds. When transferred to streams, pond-originated larvae showed a high degree of plasticity, resembling the morphology and gene expression of stream-originated larvae (reversion); however the same was not found for stream-originated larvae when transferred to ponds, where the expression of genes related to reduction-oxidation processes was increased, possibly to cope with environmental stress. The lack of symmetrical responses between transplanted animals highlights the fact that the adaptations are not fully plastic and that some level of local adaptation has already occurred in this population. This study illuminates the process by which phenotypic plasticity allows local adaptation to new environments and its potential role in the pathway of incipient speciation

Common Genetic Variation Near the Phospholamban Gene Is Associated with Cardiac Repolarisation:Meta-Analysis of Three Genome-Wide Association Studies

To identify loci affecting the electrocardiographic QT interval, a measure of cardiac repolarisation associated with risk of ventricular arrhythmias and sudden cardiac death, we conducted a meta-analysis of three genome-wide association studies (GWAS) including 3,558 subjects from the TwinsUK and BRIGHT cohorts in the UK and the DCCT/EDIC cohort from North America. Five loci were significantly associated with QT interval at P&#60;1×10&lt;sup&gt;−6&lt;/sup&gt;. To validate these findings we performed an in silico comparison with data from two QT consortia: QTSCD (n = 15,842) and QTGEN (n = 13,685). Analysis confirmed the association between common variants near NOS1AP (P = 1.4×10&lt;sup&gt;−83&lt;/sup&gt;) and the phospholamban (PLN) gene (P = 1.9×10&lt;sup&gt;−29&lt;/sup&gt;). The most associated SNP near NOS1AP (rs12143842) explains 0.82% variance; the SNP near PLN (rs11153730) explains 0.74% variance of QT interval duration. We found no evidence for interaction between these two SNPs (P = 0.99). PLN is a key regulator of cardiac diastolic function and is involved in regulating intracellular calcium cycling, it has only recently been identified as a susceptibility locus for QT interval. These data offer further mechanistic insights into genetic influence on the QT interval which may predispose to life threatening arrhythmias and sudden cardiac death

Genetic association study of QT interval highlights role for calcium signaling pathways in myocardial repolarization.

The QT interval, an electrocardiographic measure reflecting myocardial repolarization, is a heritable trait. QT prolongation is a risk factor for ventricular arrhythmias and sudden cardiac death (SCD) and could indicate the presence of the potentially lethal mendelian long-QT syndrome (LQTS). Using a genome-wide association and replication study in up to 100,000 individuals, we identified 35 common variant loci associated with QT interval that collectively explain ∼8-10% of QT-interval variation and highlight the importance of calcium regulation in myocardial repolarization. Rare variant analysis of 6 new QT interval-associated loci in 298 unrelated probands with LQTS identified coding variants not found in controls but of uncertain causality and therefore requiring validation. Several newly identified loci encode proteins that physically interact with other recognized repolarization proteins. Our integration of common variant association, expression and orthogonal protein-protein interaction screens provides new insights into cardiac electrophysiology and identifies new candidate genes for ventricular arrhythmias, LQTS and SCD