Ken Kraaijeveld

• PhD
• Lecturer at University of Applied Sciences Leiden

Objectives The black rhinoceros ( Diceros bicornis ) is an endangered mammal for which a captive breeding program is part of the conservation effort. Black rhinos in zoo’s often suffer from chronic infections and heamochromatosis. Furthermore, breeding is hampered by low male fertility. To aid a research project studying these topics, we sequenced...

Objectives: The black rhinoceros (Diceros bicornis) is an endangered mammal for which a captive breeding program is part of the conservation effort. Black rhinos in zoo's often suffer from chronic infections and heamochromatosis. Furthermore, breeding is hampered by low male fertility. To aid a research project studying these topics, we sequenced a...

Automated genome annotation is essential for extracting biological information from sequence data. The identification and annotation of tRNA genes is frequently performed by the software package tRNAscan-SE, the output of which is listed for selected genomes in the Genomic tRNA database (GtRNAdb). Here, we highlight a pervasive error in prokaryotic...

Evolution has traditionally been a historical and descriptive science, and predicting future evolutionary processes has long been considered impossible. However, evolutionary predictions are increasingly being developed and used in medicine, agriculture, biotechnology and conservation biology. Evolutionary predictions may be used for different purp...

Automated genome annotation is an essential tool for extracting biological information from sequence data. The identification and annotation of tRNA genes is frequently performed by the software package tRNAscan-SE, the output of which is listed – for selected genomes – in the Genomic tRNA database (GtRNAdb). Given the central role of tRNA in molec...

Stable co‐evolutionary relationships between species may result in the loss of autonomous synthesis of essential nutrients when these can be obtained from the ecological partner. Parasitoid insects obtain most of their nutrients from their host, and many lineages do not increase their adult lipid reserves even when feeding on a surplus of sugars. S...

Evolution has traditionally been a historical field of study and predicting evolution has long been considered challenging or even impossible. However, evolutionary predictions are increasingly being made and used in many situations in medicine, agriculture, biotechnology and conservation biology. Because every field uses their own language and mak...

The transition to asexual reproduction is frequent and widespread across the tree of life and constitutes a major life history change. Without sexual reproduction, selection on sexually selected traits is expected to be weaker or absent, allowing the decay and ultimately loss of sexual traits. In this study, we applied an experimental approach to i...

Background: Gene duplication events play an important role in the evolution and adaptation of organisms. Duplicated genes can arise through different mechanisms, including whole-genome duplications (WGDs). Recently, WGD was suggested to be an important driver of evolution, also in hexapod animals. Results: Here, we analyzed 20 high-quality hexap...

Interspecific interactions in nature often revolve around the acquisition of nutrients. Depending on the organisms' metabolic requirements, competition for specific essential nutrients may occur, which selects for increased abilities to monopolize, consume and store these nutrients. Lipid scavengers are organisms that rely on exogenous lipid acquis...

Background: The evolution of complex organs is thought to occur via a stepwise process, each subsequent step increasing the organ's complexity by a tiny amount. This evolutionary process can be studied by comparing closely related species that vary in the presence or absence of their organs. This is the case for the placenta in the live-bearing fi...

Background Trait loss is a pervasive phenomenon in evolution, yet the underlying molecular causes have been identified in only a handful of cases. Most of these cases involve loss-of-function mutations in one or more trait-specific genes. However, in parasitoid insects the evolutionary loss of a metabolic trait is not associated with gene decay. Pa...

Loss of sex and recombination is generally assumed to impede the effectiveness of purifying selection and to result in the accumulation of slightly deleterious mutations. Empirical evidence for this has come from several studies investigating mutational load in a small number of individual genes. However, recent whole transcriptome based studies ha...

The evolution of sexually monomorphic ornamental traits is poorly understood and may require a shift in research focus away from strict sexual selection. To properly understand how selection affects such traits, we need to know to what extent they are constrained by their genetic architecture. Specifically, we need to understand how and in what sta...

Background Theory predicts that dependency within host-endosymbiont interactions results in endosymbiont genome size reduction. Unexpectedly, the largest Wolbachia genome was found in the obligate, parthenogenesis-associated wFol. In this study, we investigate possible processes underlying this genome expansion by comparing a re-annotated wFol geno...

Parasitoid insects are important model systems for a multitude of biological research topics and widely used as biological control agents against insect pests. While the parasitoid lifestyle has evolved numerous times in different insect groups, research has focused almost exclusively on Hymenoptera from the Parasitica clade. The genomes of several...

Background Selection acts on the phenotype, yet only the genotype is inherited. While both the phenotypic and genotypic response to short-term selection can be measured, the link between these is a major unsolved problem in evolutionary biology, in particular for complex behavioural phenotypes. Results Here we characterize the genomic and the tran...

Transformer (tra) is the central gear in many insect sex determination pathways and transduces a wide range of primary signals. Mediated by transformer‐2 (tra2) it directs sexual development into the female or male mode. Duplications of tra have been detected in numerous Hymenoptera, but a function in sex determination has been confirmed only in Ap...

Trait loss is a pervasive phenomenon in evolution, yet the underlying molecular causes have been identified in only a handful of cases. Most of these involve loss-of-function mutations in one or more trait-specific genes. Parasitoid insects are fatty acid auxotrophs: they lost the ability to convert dietary sugars into fatty acids, a trait that is...

Parasitoid insects are important model systems for a multitude of biological research topics and widely used as biological control agents against insect pests. While the parasitoid lifestyle has evolved numerous times in different insect groups, research has focused almost exclusively on Hymenoptera from the parasitica clade. The genomes of several...

The characteristic ground colour and banding patterns on shells of the land snail Cepaea nemoralis form a classic study system for genetics and adaptation as it varies widely between individuals. We use RNAseq analysis to identify candidate genes underlying this polymorphism. We sequenced cDNA from the foot and the mantle (the shell-producing tissu...

Differential Expression results Differential_Expression_EdgeR_csv contains the results for the differential expression analysis. For every transcript, the log Fold-Change (FC), log Counts-Per-Million (CPM), P-value, False Discovery Rate (FDR) and count values for each of the eight used samples.

Supplementary tables and figures

Gene Ontology results go_annotations.txt contains the transcripts with GO annotations. occurrences_per_go_term.txt contains the number of occurrences for every GO term.

RAD-tag alignments Each file contains the blast hits to the transcriptome including alignments.

Chemical warfare including insecticidal secondary metabolites is a well-known strategy for environmental microbes to monopolize a food source. Insects in turn have evolved behavioural and physiological defences to eradicate or neutralize the harmful microorganisms. We studied the defensive repertoire of insects in this interference competition by c...

Background: Folsomia candida is a model in soil biology, belonging to the family of Isotomidae, subclass Collembola. It reproduces parthenogenetically in the presence of Wolbachia, and exhibits remarkable physiological adaptations to stress. To better understand these features and adaptations to life in the soil, we studied its genome in the conte...

Background Parasitoid resistance in Drosophila varies considerably, among and within species. An immune response, lamellocyte-mediated encapsulation, evolved in a subclade of Drosophila and was subsequently lost in at least one species within this subclade. While the mechanisms of resistance are fairly well documented in D. melanogaster, much less...

The characteristic ground colour and banding patterns on shells of the land snail Cepaea nemoralis form a classic study system for genetics and adaptation. We use RNAseq analysis to identify candidate genes underlying this polymorphism. We sequenced cDNA from the body and the mantle (the shell-producing tissue) of four individuals of two phenotypes...

The characteristic ground colour and banding patterns on shells of the land snail Cepaea nemoralis form a classic study system for genetics and adaptation. We use RNAseq analysis to identify candidate genes underlying this polymorphism. We sequenced cDNA from the body and the mantle (the shell-producing tissue) of four individuals of two phenotypes...

Parasites are sometimes able to manipulate the behaviour of their hosts. However, the molecular cues underlying this phenomenon are poorly documented. We previously reported that the parasitoid wasp Leptopilina boulardi which develops from Drosophila larvae is often infected by an inherited DNA virus. In addition to being maternally transmitted, th...

Al ruim 40 jaar worden er in het Groene Glop op Schiermonnikoog zangvogels geringd. In 1969-1981 en 1993-2010 werd er gedurende de najaars-trek vrijwel elke dag gevangen, met vrijwel gelijke mistnetopstellingen. Deze reeks leent zich uitste-kend om veranderingen in trekpatronen te bestu-deren. In deze bijdrage nemen we de timing van de najaarstrek...

Trait loss is a widespread phenomenon with pervasive consequences for a species’ evolutionary potential. The genetic changes underlying trait loss have only been clarified in a small number of cases. None of these studies can identify whether the loss of the trait under study was a result of neutral mutation accumulation or negative selection. This...

Het type gist dat wordt gebruikt voor fermentatie van druiven heeft een grote invloed op de snelheid van de fermentatie en het smaakprofiel van de uiteindelijke wijn. Om efficiënte fermentatie en 'schone', voorspelbare smaken en aroma's te garanderen, maken wijnmakers meestal gebruik van pure gist-starter. Meestal is dat Saccharomyces cerevisiae. E...

Transposable elements (TEs) and other repetitive DNA can accumulate in the absence of recombination, a process contributing to the degeneration of Y-chromosomes and other non-recombining genome portions. A similar accumulation of repetitive DNA is expected for asexually reproducing species, given their entire genome is effectively non-recombining....

Collembola (springtails) represent a soil-living lineage of hexapods in between insects and crustaceans. Consequently, their genomes may hold key information on the early processes leading to evolution of Hexapoda from a crustacean ancestor. We assembled and annotated transcriptomes of the Collembola Folsomia candida and Orchesella cincta, and perf...

Implementation of next-generation DNA sequencing (NGS) technology into routine diagnostic genome care requires strategic choices. Instead of theoretical discussions on the consequences of such choices, we compared NGS-based diagnostic practices in eight clinical genetic centers in the Netherlands, based on genetic testing of nine pre-selected patie...

We describe an open-source kPAL package that facilitates an alignment-free assessment of the quality and comparability of sequencing datasets by analyzing k-mer frequencies. We show that kPAL can detect technical artefacts such as high duplication rates, library chimeras, contamination and differences in library preparation protocols. kPAL also suc...

The evolution of female ornamentation has been subject to considerable debate. Although originally thought to be by-products of selection on males, recent studies have emphasized the adaptive nature of female ornaments. Here, I review current knowledge on the genetic architecture of ornamental traits and how their expression is (or is not) restrict...

Background Aerobic methanotrophs can grow in hostile volcanic environments and use methane as their sole source of energy. The discovery of three verrucomicrobial Methylacidiphilum strains has revealed diverse metabolic pathways used by these methanotrophs, including mechanisms through which methane is oxidized. The basis of a complete understandin...

Background There is growing interest in odonates (damselflies and dragonflies) as model organisms in ecology and evolutionary biology but the development of genomic resources has been slow. So far only one draft genome (Ladona fulva) and one transcriptome assembly (Enallagma hageni) have been published. Odonates have some of the most advanced visua...

Wolbachia are endosymbiotic bacteria known to manipulate the reproduction of their hosts by, for example, inducing parthenogenesis. In most cases of Wolbachia-induced parthenogenesis, the infection is fixed and the entire host population consists of females. In the absence of males and sexual reproduction, genes involved in sexual reproduction are...