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  • 1
    Publication Date: 2019-04-30
    Description: First, the generated raw reads (11,569 reads) were processed with Roche's demultiplexing and converting tools (sffinfo, sfffile) and sequences of primer annealing sites were removed. For quality filtering we applied a filter for too short reads (≤ 150 bp), we only allowed 1% of ambiguous bases (N) and filtered out low quality sequences (Mean ≥ 15). These sequences were imported into Geneious (6.1.6 Biomatters Ltd, www.geneious.com) and de novo assembled (with custom sensitivity: minimum overlap identity of 95 % and maximum ambiguity 4 using all reads from one species. This resulted in contigs of single individuals with highly identical reads (pairwise identity: median 99.50 %) and contigs of several individuals sharing these reads (pairwise identity: median 99.40 %). The coverage ranged from 2 to 131 for single individual contigs and 2 to 337 reads for contigs originating from multiple individuals. We also kept low coverage contigs as we use our data for measuring genetic diversity among tribes and not for investigating functionality or selection processes (indicated with suffix “low” in the alignment). However, if more than 3 bp of a read were different than the rest of the contig, the read was excluded and also singletons, which differed dramatically (≥ 10 mutations) to other contigs, were removed from the data set (reads N=517). Consensus sequences were generated within Geneious using 50 % strict rule from each contig and for each individual. Most homopolymer regions were correctly called with these settings and ambiguous positions were coded according to IUPAC rules. The obtained variants were aligned using MAFFT (--auto; 200PAM/k=2, 1.53 open penalty/0.123 offset) (Katoh & Standley, 2013) and insertions of ambiguous positions, homopolymers and misalignments were manually checked. This resulted in an alignment of 751 base pairs containing both intronic and exonic regions. A blast search of the alleles led to the exclusion of further sequences (removed contigs N=266). In a next step we shortened the alleles to exon 2 only, in order to (i) reduce our data set to coding nucleotides and (ii) to reduce the amount of missing data and ambiguities. This resulted in a total number of 844 MHC exon 2 variants of 160 bp lengths. Despite our methodological limitations, short reads and relatively low sequence coverage for some contigs, our results are valid as a valuable measurement of immunogenetic diversity that is comparable across all tribes of Lake Tanganyika cichlids as these biases are expected to be similarly distributed across the different tribes. The available alignment was generated as described above and saved as a fasta file. It includes 844 MHC exon 2 variants (160 base pairs). The header of each entry includes information about the scientific species name (e.g. Tropheus moorii) with a specific variant name (e.g. 04_01). This can be followed by the indication "low", which was added if the variant was called with very low coverage (〈=2x).
    Type: Dataset
    Format: application/zip, 9343 Bytes
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  • 2
    Publication Date: 2018-11-03
    Description: For the parasitological survey, 23 cichlid species were screened for metazoan ecto- and endoparasites (Supplementary Table 1). Sampling was conducted at Toby's place on the Zambian shoreline of Lake Tanganyika. While most fish species were obtained in August 2012, S. diagramma and H. microlepis were captured in August 2011 and July 2013, respectively. One species, A. burtoni, was obtained in July 2013 at Kapata, which is about 20 km southward. About 7 to 18 individuals per species (usually ten) were caught by chasing fish into standing nets (Supplementary Table 1). After capture the fish were kept in tanks of 0.8 m x 0.8 m x 1.2 m depth or 0.8 m x 0.8 m x 2 m depth. Before usage, tanks were cleaned, dried and filled with lake water. All fish were dissected in the field within four days post-capture. The day of dissection (0, 1, 2 or 3 days after capture) was recorded in order to keep track of changes in parasitological parameters while the fish were kept in the tanks. Individual fish were killed with an overdose of MS222. The parasitological survey consisted of three parts. First, the outer surface and the mouth cavity of the fish were inspected for ectoparasitic monogeneans and crustaceans (copepods, branchiurans, isopods), bivalves, and any kind of helminthic cysts. Second, the four gill-branches on the left were dissected and stored on 100% analytical ethanol (EtOH), and later in the lab screened for ectoparasitic monogeneans, crustaceans (copepods and branchiurans), bivalves, and any kind of helminthic cysts. Third, fish were screened for intestinal monogeneans, digeneans, acanthocephalans, nematodes, and any kind of helminthic cysts. To do so, stomach, intestines, gall and urinary bladder were dissected and inspected in a petridish with lake water. Finally, the sex of the fish was determined by visual inspection of the genital papilla and gonad development. The parasitological survey was performed with a stereomicroscope and by multiple observers. Observers were recorded in order to keep track of observer bias. A single observer screened the outer surface and the mouth cavity of the fish. The number of observers varied between years for gills and intestines (gills: two observers in each year; intestines: three, four and one observer(s) in 2011, 2012 and 2013, respectively). All parasites were counted and identified to genus or class level and preserved as follows. Monogeneans were isolated using dissection needles and were either mounted on slides in ammonium picrate glycerine for further morphological characterization, or stored on 100 % EtOH. Acanthocephalans and nematodes were stored on 80 % EtOH, while intestinal monogeneans, branchiurans, copepods, any kind of helminthic cysts, bivalves and unknown groups were stored on 100 % EtOH.
    Type: Dataset
    Format: text/tab-separated-values, 5491 data points
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  • 3
    Publication Date: 2018-11-09
    Description: The origin of novel phenotypic characters is a key component in organismal diversification; yet, the mechanisms underlying the emergence of such evolutionary novelties are largely unknown. Here we examine the origin of egg-spots, an evolutionary innovation of the most species-rich group of cichlids, the haplochromines, where these conspicuous male fin colour markings are involved in mating. Applying a combination of RNAseq, comparative genomics and functional experiments, we identify two novel pigmentation genes, fhl2a and fhl2b, and show that especially the more rapidly evolving b-paralog is associated with egg-spot formation. We further find that egg-spot bearing haplochromines, but not other cichlids, feature a transposable element in the cis-regulatory region of fhl2b. Using transgenic zebrafish, we finally demonstrate that this region shows specific enhancer activities in iridophores, a type of pigment cells found in egg-spots, suggesting that a cis-regulatory change is causally linked to the gain of expression in egg-spot bearing haplochromines
    Type: Article , PeerReviewed
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  • 4
    Publication Date: 2018-11-09
    Description: Highlights: • We provide a new phylogeny for Lake Tanganyika cichlids using 42 nuclear makers. • Data concatenation and a Bayesian concordance analysis lead to congruent results. • Gene tree discordance hints to past hybridization or incomplete lineage sorting. • The Lamprologini are the sister-group to the ‘H-lineage’. • The Eretmodini are nested within the ‘H-lineage’. Abstract: The species-flocks of cichlid fishes in the East African Great Lakes Victoria, Malawi and Tanganyika constitute the most diverse extant adaptive radiations in vertebrates. Lake Tanganyika, the oldest of the lakes, harbors the morphologically and genetically most diverse assemblage of cichlids and contains the highest number of endemic cichlid genera of all African lakes. Based on morphological grounds, the Tanganyikan cichlid species have been grouped into 12–16 distinct lineages, so-called tribes. While the monophyly of most of the tribes is well established, the phylogenetic relationships among the tribes remain largely elusive. Here, we present a new tribal level phylogenetic hypothesis for the cichlid fishes of Lake Tanganyika that is based on the so far largest set of nuclear markers and a total alignment length of close to 18 kb. Using next-generation amplicon sequencing with the 454 pyrosequencing technology, we compiled a dataset consisting of 42 nuclear loci in 45 East African cichlid species, which we subjected to maximum likelihood and Bayesian inference phylogenetic analyses. We analyzed the entire concatenated dataset and each marker individually, and performed a Bayesian concordance analysis and gene tree discordance tests. Overall, we find strong support for a position of the Oreochromini, Boulengerochromini, Bathybatini and Trematocarini outside of a clade combining the substrate spawning Lamprologini and the mouthbrooding tribes of the ‘H-lineage’, which are both strongly supported to be monophyletic. The Eretmodini are firmly placed within the ‘H-lineage’, as sister-group to the most species-rich tribe of cichlids, the Haplochromini. The phylogenetic relationships at the base of the ‘H-lineage’ received less support, which is likely due to high speciation rates in the early phase of the radiation. Discordance among gene trees and marker sets further suggests the occurrence of past hybridization and/or incomplete lineage sorting in the cichlid fishes of Lake Tanganyika.
    Type: Article , PeerReviewed
    Format: text
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  • 5
    Publication Date: 2019-01-23
    Description: The species flocks of cichlid fishes in the East African Great Lakes are the largest vertebrate adaptive radiations in the world and illustrious textbook examples of convergent evolution between independent species assemblages. Although recent studies suggest some degrees of genetic exchange between riverine taxa and the lake faunas, not a single cichlid species is known from Lakes Tanganyika, Malawi and Victoria that is derived from the radiation associated with another of these lakes. Here, we report the discovery of a haplochromine cichlid species in Lake Tanganyika, which belongs genetically to the species flock of haplochromines of the Lake Victoria region. The new species colonized Lake Tanganyika only recently, suggesting that faunal exchange across watersheds and, hence, between isolated ichthyofaunas, is more common than previously thought.
    Type: Article , PeerReviewed
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  • 6
    Publication Date: 2019-04-30
    Type: Dataset
    Format: text/tab-separated-values, 6240 data points
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  • 7
    Publication Date: 2019-04-30
    Type: Dataset
    Format: text/tab-separated-values, 21816 data points
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  • 8
    Publication Date: 2019-04-30
    Type: Dataset
    Format: text/tab-separated-values, 33856 data points
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  • 9
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    PANGAEA
    In:  Supplement to: Heckwolf, Melanie; Meyer, Britta S; Döring, Talisa; Eizaguirre, Christophe; Reusch, Thorsten B H (2018): Transgenerational plasticity and selection shape the adaptive potential of sticklebacks to salinity change. Evolutionary Applications, 11(10), 1873-1885, https://doi.org/10.1111/eva.12688
    Publication Date: 2019-04-30
    Description: To assess the phenotypic effects of transgenerational salinity change in sticklebacks, offspring were sampled as eggs, freshly hatched larvae, as well as 12, 30 and 90 days post hatch (dph). We measured egg size, yolk-sac size to length ratio of fish larvae from pictures taken under a stereomicroscope. At 12, 30 and 90 days post hatch we measured length and weight of the larvae. Additionally, dissections were performed at 30 and 90 dph to assess the hepatosomatic index (HSI) of juveniles. Mortality was monitored throughout the experiment to account for possible non-random mortality.
    Type: Dataset
    Format: application/zip, 4 datasets
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  • 10
    Publication Date: 2019-04-30
    Type: Dataset
    Format: text/tab-separated-values, 44780 data points
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