David L.J. Vendrami

David L.J. Vendrami
Bielefeld University · Molecular ecology group - Joe Hoffman's Lab

About

40
Publications
3,751
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194
Citations

Publications

Publications (40)
Article
Nuclear copies of mitochondrial genes (numts) are commonplace in vertebrate genomes and have been characterized in many species. However, relatively little attention has been paid to understanding their evolutionary origins and to disentangling alternative sources of insertions. Numts containing genes with intact mitochondrial reading frames repres...
Article
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Much debate surrounds the importance of top-down and bottom-up effects in the Southern Ocean, where the harvesting of over two million whales in the mid twentieth century is thought to have produced a massive surplus of Antarctic krill. This excess of krill may have allowed populations of other predators, such as seals and penguins, to increase, a...
Article
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Individuals are unique in how they interact with and respond to their environment. Correspondingly, unpredictable challenges or environmental stressors often produce an individualized response of the hypothalamic‐pituitary‐adrenal (HPA) axis and its downstream effector cortisol. We used a fully crossed, repeated measures design to investigate the f...
Preprint
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Individuals are unique in how they interact with and respond to their environment. Correspondingly, unpredictable challenges or stressors often produce an individualized response of the hypothalamic-pituitary-adrenal axis and its downstream effector cortisol. We used a fully crossed, repeated measures design to investigate the factors shaping indiv...
Article
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A long-standing paradox of marine populations is chaotic genetic patchiness (CGP), temporally unstable patterns of genetic differentiation that occur below the geographic scale of effective dispersal. Several mechanisms are hypothesized to explain CGP including natural selection, spatiotemporal fluctuations in larval source populations, self-recrui...
Article
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Mussels belonging to the Mytilus species complex (M. edulis, ME; M. galloprovincialis, MG; and M. trossulus, MT) often occur in sympatry, facilitating introgressive hybridisation. This may be further promoted by mussel aquaculture practices, with MT introgression often resulting in commercially unfavourable traits such as low meat yield and weak sh...
Article
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The three mussel species comprising the Mytilus complex are widespread across Europe and readily hybridize when they occur in sympatry, resulting in a mosaic of populations with varying genomic backgrounds. Two of these species, M. edulis and M. galloprovincialis, are extensively cultivated across Europe, with annual production exceeding 230,000 to...
Article
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Most molluscs possess shells, constructed from a vast array of microstructures and architectures. The fully formed shell is composed of calcite or aragonite. These CaCO3 crystals form complex biocomposites with proteins, which although typically less than 5% of total shell mass, play significant roles in determining shell microstructure. Despite mu...
Article
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The soft-shell clam Mya arenaria is one of the most ancient invaders of European coasts and is present in many coastal ecosystems, yet little is known about its genetic structure in Europe. We collected 266 samples spanning a latitudinal cline from the Mediterranean to the North Sea and genotyped them at 12 microsatellite loci. In parallel, geometr...
Article
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Recent developments in genomics are advancing our understanding of the processes shaping population structure in wild organisms. In particular, reduced representation sequencing has facilitated the generation of dense genetic marker datasets that provide greater power for resolving population structure, investigating the role of selection and recon...
Article
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Background Restriction site-associated DNA sequencing (RADseq) has revolutionized the study of wild organisms by allowing cost-effective genotyping of thousands of loci. However, for species lacking reference genomes, it can be challenging to select the restriction enzyme that offers the best balance between the number of obtained RAD loci and dept...
Article
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Cultivated bivalves are hugely important not only because of their economic value, but also due to their impacts on natural ecosystems. The Pacific oyster (Crassostrea gigas) is the world's most heavily cultivated shellfish species and has been introduced to all continents except Antarctica for aquaculture. We therefore used a medium density single...
Article
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Comparative studies can provide powerful insights into processes that affect population divergence and thereby help to elucidate the mechanisms by which contemporary populations may respond to environmental change. Furthermore, approaches such as genotyping by sequencing (GBS) provide unprecedented power for resolving genetic differences among spec...
Article
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The field of molecular ecology is transitioning from the use of small panels of classical genetic markers such as microsatellites to much larger panels of single nucleotide polymorphisms (SNPs) generated by approaches like RAD sequencing. However, few empirical studies have directly compared the ability of these methods to resolve population struct...
Data
Supplementary table 5: Summary of the results obtained from different de novo assemblies of the ddRAD data generated using different values for three main parameters −m, −M and −n within the denovo_map.pl Script in Stacks. −m and −M define the minimum number of raw reads and the maximum number of mismatches between loci when creating a stack within...
Data
Supplementary figure 2: Mean +/− SE Ln P(D) values of five replicate Structure runs for each value of K, the hypothesised number of clusters in the data, ranging from one to nine, based on (a) 180 individuals genotyped at 13 microsatellites; and (b) 10,539 SNPs genotyped in 45 individuals
Data
Supplementary figure 3: Heat map depicting pairwise Fst values calculated using a restricted dataset of 45 individuals genotyped at 13 microsatellites.
Data
Supplementary figure 1: Illustration of the process of generating scallop shell outline coordinates for the geometric morphometrics analysis. From left to right: scaled digital photograph, isolated shell outline, and 1000 pseudo-landmarks placed along the shell perimeter
Data
Supplementary figure 5: Results of shell outline analysis. (a) Contribution of the first three shape variables to the outline description. The shape variability was represented for increasing values along each PC (−3s.d., mean, +3s.d.). (b) Deformation grid depicting the bindings required to pass the average shape for population one to the average...
Data
Supplementary figure 6: Heat maps depicting pairwise Fst values calculated using SNP datasets derived from different runs of the denovo_map.pl script in Stacks in which different values were used for the three main parameters −m, −M and −n
Data
Supplementary information 1: Design of the P7 adapters used during the preparation of the ddRAD library
Data
Supplementary information 3: Computer code and accompanying documentation for morphometrics and colourimetric analyses
Data
Supplementary table 3: Pairwise Fst values (below diagonal) and corresponding p-values (above diagonal) calculated using13 microsatellites genotyped in 45 individuals
Data
Supplementary figure 4: Results of the Structure analysis of a restricted dataset of 45 individuals genotyped at 13 microsatellites. Panel (a) shows the mean +/− SE Ln P(D) values of five replicate Structure runs for each value of K, the hypothesised number of clusters in the data, ranging from one to nine. Panel (b) shows the resulting cluster mem...
Data
Supplementary figure 7: Results of the Structure analysis after having excluded samples collected from Mulroy Bay. Results are shown for 13 microsatellites (panels a and b) and 10,539 SNPs (panels c and d). Panels (a) and (c) show mean +/− SE Ln P(D) values of five replicate Structure runs for each value of K, the hypothesised number of clusters in...
Data
Supplementary table 1: Details of the 15 microsatellite loci used in this study together with their polymorphism characteristics in 180 great scallops sampled from nine different populations
Data
Supplementary table 2: Pairwise Fst values (below diagonal) and corresponding p-values (above diagonal) calculated using (a) 13 microsatellites genotyped in 180 individuals and (b) 10,539 SNPs genotyped in 45 individuals
Data
Supplementary table 4: Summary of the results of the General Linear Mixed Models (GLMMs) with response variables shell shape PC1 and CI, population included as a random effect, and PC1 and PC2 from the PCA of the SNP dataset fitted as a predictor variables

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Project
Our world is changing: our oceans are becoming warmer and more acidic. Understanding the consequences of this is one of the big science challenges of the 21st Century. The oceans of the planet are closely linked with human health and wellbeing, through their impact on climate and their socio-economic importance. This network studied how shells are produced and controlled in four of Europe’s most important commercial marine shellfish species, oysters, mussels, clams and scallops. http://www.cache-itn.eu/about-cache/