Maria Victoria Schneider

Speciation through sensory drive in cichlid fish

Theoretically, divergent selection on sensory systems can cause speciation through sensory drive. However, empirical evidence is rare and incomplete. Here we demonstrate sensory drive speciation within island populations of cichlid fish. We identify the ecological and molecular basis of divergent evolution in the cichlid visual system, demonstrate associated divergence in male colouration and female preferences, and show subsequent differentiation at neutral loci, indicating reproductive isolation. Evidence is replicated in several pairs of sympatric populations and species. Variation in the slope of the environmental gradients explains variation in the progress towards speciation: speciation occurs on all but the steepest gradients. This is the most complete demonstration so far of speciation through sensory drive without geographical isolation. Our results also provide a mechanistic explanation for the collapse of cichlid fish species diversity during the anthropogenic eutrophication of Lake Victoria.

The Male Sex Pheromone of the Butterfly Bicyclus anynana: Towards an Evolutionary Analysis

Background Female sex pheromones attracting mating partners over long distances are a major determinant of reproductive isolation and speciation in Lepidoptera. Males can also produce sex pheromones but their study, particularly in butterflies, has received little attention. A detailed comparison of sex pheromones in male butterflies with those of female moths would reveal patterns of conservation versus novelty in the associated behaviours, biosynthetic pathways, compounds, scent-releasing structures and receiving systems. Here we assess whether the African butterfly Bicyclus anynana, for which genetic, genomic, phylogenetic, ecological and ethological tools are available, represents a relevant model to contribute to such comparative studies. Methodology/Principal Findings Using a multidisciplinary approach, we determined the chemical composition of the male sex pheromone (MSP) in the African butterfly B. anynana, and demonstrated its behavioural activity. First, we identified three compounds forming the presumptive MSP, namely (Z)-9-tetradecenol (Z9-14:OH), hexadecanal (16:Ald ) and 6,10,14-trimethylpentadecan-2-ol (6,10,14-trime-15-2-ol), and produced by the male secondary sexual structures, the androconia. Second, we described the male courtship sequence and found that males with artificially reduced amounts of MSP have a reduced mating success in semi-field conditions. Finally, we could restore the mating success of these males by perfuming them with the synthetic MSP. Conclusions/Significance This study provides one of the first integrative analyses of a MSP in butterflies. The toolkit it has developed will enable the investigation of the type of information about male quality that is conveyed by the MSP in intraspecific communication. Interestingly, the chemical structure of B. anynana MSP is similar to some sex pheromones of female moths making a direct comparison of pheromone biosynthesis between male butterflies and female moths relevant to future research. Such a comparison will in turn contribute to understanding the evolution of sex pheromone production and reception in butterflies.

Nuclear markers reveal unexpected genetic variation and a Congolese-Nilotic origin of the Lake Victoria cichlid species flock

Phylogenetic analyses based on mitochondrial (mt) DNA have indicated that the cichlid species flock of the Lake Victoria region is derived from a single ancestral species found in East African rivers, closely related to the ancestor of the Lake Malawi cichlid species flock. The Lake Victoria flock contains ten times less mtDNA variation than the Lake Malawi radiation, consistent with current estimates of the ages of the lakes. We present results of a phylogenetic investigation using nuclear (amplified fragment length polymorphism) markers and a wider coverage of riverine haplochromines. We demonstrate that the Lake Victoria–Edward flock is derived from the morphologically and ecologically diverse cichlid genus Thoracochromis from the Congo and Nile, rather than from the phenotypically conservative East African Astatotilapia. This implies that the ability to express much of the morphological diversity found in the species flock may by far pre–date the origin of the flock. Our data indicate that the nuclear diversity of the Lake Victoria–Edward species flock is similar to that of the Lake Malawi flock, indicating that the genetic diversity is considerably older than the 15 000 years that have passed since the lake began to refill. Most of this variation is manifested in trans–species polymorphisms, indicating very recent cladogenesis from a genetically very diverse founder stock. Our data do not confirm strict monophyly of either of the species flocks, but raise the possibility that these flocks have arisen from hybrid swarms.

Geographical distribution and genetic relatedness of sympatrical thelytokous and arrhenotokous populations of the parasitoid Venturia canescens (Hymenoptera)

Theory predicts that asexual reproduction has a competitive advantage over sexual reproduction because of the twofold cost of producing males. Few systems are suitable for directly testing this prediction. In the solitary parasitoid wasp Venturia canescens both arrhenotokously (sexual) and thelytokously (asexual) reproducing individuals occur sympatrically. We sampled 922 wasps from 22 localities along the coast of south‐eastern France. Thelytokous wasps were less abundant (23%) than arrhenotokous wasps and were almost always found in sympatry with arrhenotokous ones. An analysis of genetic relatedness using amplified fragment length polymorphism (AFLP) markers showed the existence of a widespread thelytokous clone. In addition, a few thelytokous individuals were found to be closely related to arrhenotokous ones and vice versa. These data suggest the occurrence of occasional gene flow between both reproductive modes and/or recurrent origin of thelytokous clones from coexisting arrhenotokous populations in the area. The results are discussed in the context of the paradox of sex.

Omics Technologies, Data and Bioinformatics Principles

We provide an overview on the state of the art for the Omics technologies, the types of omics data and the bioinformatics resources relevant and related to Omics. We also illustrate the bioinformatics challenges of dealing with high-throughput data. This overview touches several fundamental aspects of Omics and bioinformatics: data standardisation, data sharing, storing Omics data appropriately and exploring Omics data in bioinformatics. Though the principles and concepts presented are true for the various different technological fields, we concentrate in three main Omics fields namely: genomics, transcriptomics and proteomics. Finally we address the integration of Omics data, and provide several useful links for bioinformatics and Omics.

Bioinformatics Curriculum Guidelines: Toward a Definition of Core Competencies

Rapid advances in the life sciences and in related information technologies necessitate the ongoing refinement of bioinformatics educational programs in order to maintain their relevance. As the discipline of bioinformatics and computational biology expands and matures, it is important to characterize the elements that contribute to the success of professionals in this field. These individuals work in a wide variety of settings, including bioinformatics core facilities, biological and medical research laboratories, software development organizations, pharmaceutical and instrument development companies, and institutions that provide education, service, and training. In response to this need, the Curriculum Task Force of the International Society for Computational Biology (ISCB) Education Committee seeks to define curricular guidelines for those who train and educate bioinformaticians. The previous report of the task force summarized a survey that was conducted to gather input regarding the skill set needed by bioinformaticians [1]. The current article details a subsequent effort, wherein the task force broadened its perspectives by examining bioinformatics career opportunities, surveying directors of bioinformatics core facilities, and reviewing bioinformatics education programs. The bioinformatics literature provides valuable perspectives on bioinformatics education by defining skill sets needed by bioinformaticians, presenting approaches for providing informatics training to biologists, and discussing the roles of bioinformatics core facilities in training and education. The skill sets required for success in the field of bioinformatics are considered by several authors: Altman [2] defines five broad areas of competency and lists key technologies; Ranganathan [3] presents highlights from the Workshops on Education in Bioinformatics, discussing challenges and possible solutions; Yales interdepartmental PhD program in computational biology and bioinformatics is described in [4], which lists the general areas of knowledge of bioinformatics; in a related article, a graduate of Yales PhD program reflects on the skills needed by a bioinformatician [5]; Altman and Klein [6] describe the Stanford Biomedical Informatics (BMI) Training Program, presenting observed trends among BMI students; the American Medical Informatics Association defines competencies in the related field of biomedical informatics in [7]; and the approaches used in several German universities to implement bioinformatics education are described in [8]. Several approaches to providing bioinformatics training for biologists are described in the literature. Tan et al. [9] report on workshops conducted to identify a minimum skill set for biologists to be able to address the informatics challenges of the “-omics” era. They define a requisite skill set by analyzing responses to questions about the knowledge, skills, and abilities that biologists should possess. The authors in [10] present examples of strategies and methods for incorporating bioinformatics content into undergraduate life sciences curricula. Pevzner and Shamir [11] propose that undergraduate biology curricula should contain an additional course, “Algorithmic, Mathematical, and Statistical Concepts in Biology.” Wingren and Botstein [12] present a graduate course in quantitative biology that is based on original, pathbreaking papers in diverse areas of biology. Johnson and Friedman [13] evaluate the effectiveness of incorporating biological informatics into a clinical informatics program. The results reported are based on interviews of four students and informal assessments of bioinformatics faculty. The challenges and opportunities relevant to training and education in the context of bioinformatics core facilities are discussed by Lewitter et al. [14]. Relatedly, Lewitter and Rebhan [15] provide guidance regarding the role of a bioinformatics core facility in hiring biologists and in furthering their education in bioinformatics. Richter and Sexton [16] describe a need for highly trained bioinformaticians in core facilities and provide a list of requisite skills. Similarly, Kallioniemi et al. [17] highlight the roles of bioinformatics core units in education and training. This manuscript expands the body of knowledge pertaining to bioinformatics curriculum guidelines by presenting the results from a broad set of surveys (of core facility directors, of career opportunities, and of existing curricula). Although there is some overlap in the findings of the surveys, they are reported separately, in order to avoid masking the unique aspects of each of the perspectives and to demonstrate that the same themes arise, even when different perspectives are considered. The authors derive from their surveys an initial set of core competencies and relate the competencies to three different categories of professions that have a need for bioinformatics training.

Color Polymorphism and Predation in a Lake Victoria Cichlid Fish

Abstract Haplochromine cichlid fish have radiated into hundreds of species in East-African lakes, possibly driven by divergent sexual selection on body coloration. We studied the color polymorphic Lake Victoria cichlid Neochromis omnicaeruleus, in which a presumably ancestral phenotype with blue males and brown females co-occurs with two distinct classes of blotched phenotypes in both sexes. Similar blotch polymorphisms occur in other haplochromine species, and in all studied cases blotched females are much more common than blotched males. In N. omnicaeruleus, the near absence of blotched males seems to be partly due to genetic linkage to a dominant female determiner that turns blotched males into females. However, laboratory breeding suggests that blotched males should be much more common than observed. Here we studied whether differential predation on blotched males contributes to their scarcity. First, in a predation experiment with wild birds, blotched fish indeed incurred more predator attacks. Second, underwater observations revealed behavioral differences between the sexes, consistent with an additional predation risk for males. These data suggest that differential predation with regard to color pattern and sex may be an important selective force in the evolution and maintenance of this color polymorphism. However, we also carried out a population census which revealed that blotched males were rare already as juveniles. To explain the scarcity of blotched males in nature, we therefore have to invoke either selection against blotched males early in life, or a more complex genetic model. These results emphasize the need for further research on the ecology and genetics of this widespread color polymorphism in cichlid fish.

Divergent selection and phenotypic plasticity during incipient speciation in Lake Victoria cichlid fish

Divergent selection acting on several different traits that cause multidimensional shifts are supposed to promote speciation, but the outcome of this process is highly dependent on the balance between the strength of selection vs. gene flow. Here, we studied a pair of sister species of Lake Victoria cichlids at a location where they hybridize and tested the hypothesis that divergent selection acting on several traits can maintain phenotypic differentiation despite gene flow. To explore the possible role of selection we tested for correlations between phenotypes and environment and compared phenotypic divergence (PST) with that based on neutral markers (FST). We found indications for disruptive selection acting on male breeding colour and divergent selection acting on several morphological traits. By performing common garden experiments we also separated the environmental and heritable components of divergence and found evidence for phenotypic plasticity in some morphological traits contributing to species differences.

Bioinformatics training: a review of challenges, actions and support requirements

As bioinformatics becomes increasingly central to research in the molecular life sciences, the need to train non-bioinformaticians to make the most of bioinformatics resources is growing. Here, we review the key challenges and pitfalls to providing effective training for users of bioinformatics services, and discuss successful training strategies shared by a diverse set of bioinformatics trainers. We also identify steps that trainers in bioinformatics could take together to advance the state of the art in current training practices. The ideas presented in this article derive from the first Trainer Networking Session held under the auspices of the EU-funded SLING Integrating Activity, which took place in November 2009.

Gene flow between arrhenotokous and thelytokous populations of Venturia canescens (Hymenoptera).

In the solitary parasitoid wasp Venturia canescens both arrhenotokously (sexual) and thelytokously (parthenogenetical) reproducing individuals occur sympatrically. We found in the laboratory that thelytokous wasps are able to mate, receive and use sperm of arrhenotokous males. Using nuclear (amplified fragment length polymorphism, virus-like protein) and mitochondrial (restriction fragment length polymorphism) markers, we show the occurrence of gene flow from the arrhenotokous to the thelytokous mode in the field. Our results reinforce the paradox of sex in this species.