BaitFisher: A software package for multispecies target DNA enrichment probe design

Christoph Urs Mayer [et al.]Target DNA enrichment combined with high-throughput sequencing technologies is a powerful approach to probing a large number of loci in genomes of interest. However, software algorithms that explicitly consider nucleotide sequence information of target loci in multiple reference species for optimizing design of target enrichment baits to be applicable across a wide range of species have not been developed. Here we present an algorithm that infers target DNA enrichment baits from multiple nucleotide sequence alignments. By applying clustering methods and the combinatorial 1-center sequence optimization to bait design, we are able to minimize the total number of baits required to efficiently probe target loci in multiple species. Consequently, more loci can be probed across species with a given number of baits. Using transcript sequences of 24 apoid wasps (Hymenoptera: Crabronidae, Sphecidae) from the 1KITE project and the gene models of Nasonia vitripennis, we inferred 57,650, 120-bp-long baits for capturing 378 coding sequence sections of 282 genes in apoid wasps. Illumina reduced-representation library sequencing confirmed successful enrichment of the target DNA when applying these baits to DNA of various apoid wasps. The designed baits furthermore enriched a major fraction of the target DNA in distantly related Hymenoptera, such as Formicidae and Chalcidoidea, highlighting the baits' broad taxonomic applicability. The availability of baits with broad taxonomic applicability is of major interest in numerous disciplines, ranging from phylogenetics to biodiversity monitoring. We implemented our new approach in a software package, called BaitFisher, which is open source and freely available at https://github.com/cmayer/BaitFisher-package.git.C.B. is a “Ramon y Cajal” fellow supported by the Spanish Ministry of Science and Education (MEC) (RYC-2014-15615).Peer Reviewe

El significado de la disposición de las quetas en las sistemática de los Maldánidos (Annelida: Maldanidae)

Maldanids are usually divided into several subfamilies: Euclymeninae, Lumbriclymeninae, Maldaninae, Nicomachinae, Rhodininae, Clymenurinae, Notoproctinae, and Boguinae. The taxonomy of maldanids and the delimination of these taxa are mainly based on head morphology, total number of segments, chaetal structure, shape of the pygidium, and position of the anus. The maldanid ingroup relationships, as well as the monophyly of the proposed subfamilies, have so far not been investigated. Pilgrim (1977) described a shift of the notopodial chaetal rows from a transverse direction in anterior chaetigers to a more longitudinal one in posterior chaetigers in Clymene torquata (Leidy, 1855) and Euclymene oerstedii (Claparède, 1863), both belonging to the Euclymeninae. We investigated several maldanid species to assess the usefulness of this character for maldanid systematics and used 3D-reconstruction techniques to reveal the complete geometry of the chaetal sacs. Our investigation shows that a shift is apparent in Euclymene, Axiothella, Johnstonia (all Euclymeninae) and Clymenura (Clymenurinae), but absent in species like Maldane sarsi (Malmgren, 1865), Metasychis disparidentata (Moore, 1904) (both Maldaninae) and Petaloproctus borealis Ardwisson, 1906 (Nicomachinae). The shift is not typical for sedentary polychaetes and is apomorphic within maldanid polychaetes. It thus argues for a close relationship between Euclymeninae and Clymenurinae. The investigation of further maldanid species of different subfamilies may shed additional light on maldanid systematics.Los Maldánidos se clasifican usualmente en ocho subfamilias: Euclymeninae, Lumbriclymeninae, Maldaninae, Nicomachinae, Rhodininae, Clymenurinae, Notoproctinae, y Boguinae. La taxonomía de esta familia está basada en la morfología del prostómio, el número total de segmentos, la estructura de las quetas, la forma del pigidio y la posición del ano. Sin embargo, las relaciones dentro del grupo de los maldánidos , así como la monofília de las subfamilias propuestas, no han sido aún investigadas. Pilgrim (1977) describió en Clymene torquata (Leidy, 1855) y Euclymene oerstedii (Claparède, 1863), ambos pertenecientes a Euclymeninae, un cambio en la orientación de las filas de quetas notopodiales desde una poción transversal en los setígeros anteriores a una posición más longitudinal en los setígeros posteriores. En este trabajo se ha investigado el carácter anterior en diversas especies de maldánidos para ver si podría ser usado en la sistemática del grupo, usando reconstrucciones en tres dimensiones para observar la completa geometría de las bolsas de quetas, Nuestras investigaciones muestran que dichos cambios son aparentes en Euclymene, Axiothella, Johnstonia (todos Euclymeninae) y en Clymenura (Clymenurinae), pero no se presentan en especies como Maldane sarsi (Malmgren, 1865), Metasychis disparidentata (Moore, 1904) (ambas Maldaninae) y Petaloproctus borealis Ardwisson, 1906 (Nicomachinae). Este cambio no es típico de poliquetos sedentarios y es apomorfico dentro de los maldánidos. Todo ello lleva a argumentar una estrecha relación entre Euclymeninae y Clymenurinae. Futuras investigaciones en otras especies de maldánidos pertenecientes a otras subfamilias podría aportar aún mas luz a la sistemática de esta familia de poliquetos. &nbsp

Phylogeny of "Sphecidae" (Hymenoptera: Apoidea) based on molecular data

Die Grabwespen (Sphecidae sensu Bohart & Menke 1976; Sphecidae sensu lato in neueren, phylogenetischen Arbeiten), zu denen nach Day (1984) und späteren Autoren auch die Heterogynaidae zählen, umfassen derzeit 266 Gattungen mit 9559 beschriebene Arten (Pulawski 2006). Zusammen mit den Bienen (= Apiformes nach Michener 2000, bzw. Anthophila nach Engel 2005) bilden die Grabwespen ein gut begründetes Monophylum, das nach Michener (1986) den Namen Apoidea trägt und eine der drei Hauptlinien innerhalb der aculeaten Hymenoptera ist. Die Monophylie der aculeaten Hymenoptera, der Apoidea sowie die der Bienen ist jeweils gut begründet (z.B. Brothers 1975, Königsmann 1978, Lomholdt 1982, Alexander 1992, Brothers & Carpenter 1993). Anders verhält es sich mit den Grabwespen. Neben der phylogenetischen Untersuchung von Brothers & (1993), die die Monophylie der Grabwespen unterstützt, haben andere morphologische als auch molekularsystematische Analysen starken Zweifel an dieser Hypothese aufkommen lassen (z.B. Königsmann 1978, Lomholdt 1982, Alexander 1992, Prentice 1998, Melo 1999, Ohl & Bleidorn 2006).Sequences from the nuclear long-wavelength-rhodopsin and the mitochondrial cytochrom-c-oxidase (subunit I) from different representatives of the Apoidea, with special emphasis on digger wasps (Sphecidae sensu lat), were analysed using maximum parsimony, maximum likelihood and Baysian inference methods. Compared with previous phylogenetic studies based on morphology, the results of the molecular analyses are controversial but correspond in the absence of support for the Sphecidae s. l (sensu Bohart & Menke). The relationships within the Sphecidae sensu stricto correspond largely with recent morphological studies. There is circumstantial evidence that the Ampulicidae and Sphecidae s. str. together form a monophyletic group, whereas the relationships within this taxon are still uncertain. Although there is no evidence for a definitive phylogenetic position of the Heterogynaidae; it can be excluded that they are the sistertaxon to all other Apoidea. Instead, they are probably a derived group within the Crabronidae. In conflict to the majority of current morphological studies, the molecular analyses provide no support for the Crabronidae and Bembicinae. Some molecular analyses imply a close relationship between Philanthinae and bees

Mitochondrial sequence data expose the putative cosmopolitan polychaete Scoloplos armiger (Annelida, Orbiniidae) as a species complex

Background Polychaetes assigned as Scoloplos armiger (Orbiniidae) show a cosmopolitan distribution and have been encountered in all zoogeographic regions. Sibling S. armiger-like species have been revealed by recent studies using RAPDs and AFLP genetic data. We sequenced a ~12 kb fragment of the Scoloplos cf. armiger mitochondrial genome and developed primers for variable regions including the 3' end of the cox3 gene, trnQ, and most of nad6. A phylogenetic analysis of this 528-nucleotide fragment was carried out for S. armiger-like individuals from the Eastern North Atlantic as well as Pacific regions. The aim of this study is to test the cosmopolitan status, as well as to clarify the systematics of this species complex in the Eastern North Atlantic, while using a few specimens from the Pacific Ocean for comparision. Results Phylogenetic analysis of the cox3-trnQ-nad6 data set recovered five different clades of Scoloplos cf. armiger. The fragment of the mitochondrial genome of Scoloplos cf. armiger is 12,042 bp long and contains 13 protein coding genes, 15 of the 22 expected tRNAs, and the large ribosomal subunit (rrnl). Conclusion The sequenced cox3-trnQ-nad6 fragment proved to be very useful in phylogenetic analyses of Scoloplos cf. armiger. Due to its larger sampling scale this study goes beyond previous analyses which used RAPD and AFLP markers. The results of this study clearly supports that Scoloplos armiger represents a species complex and not a cosmopolitan species. We find at least two S. armiger-like species within the Pacific region and three different S. armiger-like species in the North Atlantic. Implications for the taxonomy and the impact on ecological studies are discussed

On the role of the proventricle region in reproduction and regeneration in Typosyllis antoni (Annelida: Syllidae)

Background: Syllids are a species rich annelid family possessing remarkable regenerative ability, which is not only the response after traumatic injury, but also a key step during the life cycle of several syllid taxa. In these animals the posterior part of the body becomes an epitoke and is later detached as a distinct unit named stolon. Such a sexual reproductive mode is named schizogamy or stolonization. The prostomium and the proventricle, a modified foregut structure, have been proposed to have a control function during this process, though the concrete mechanisms behind it have never been elucidated. Results: By using different experimental set-ups, histology and immunohistochemistry combined with subsequent cLSM analyzes, we investigate and document the regeneration and stolonization in specimens of Typosyllis antoni that were amputated at different levels throughout the antero-posterior body axis. The removal of the anterior end including the proventricle implies an incomplete anterior regeneration as well as severe deviations from the usual reproductive pattern, i.e. accelerated stolonization, masculinization and the occurrence of aberrant stolons. The detailed anatomy of aberrant stolons is described. A histological study of the proventricle revealed no signs of glandular or secretory structures. The ventricle and the caeca are composed of glandular tissue but they are not involved in the reproductive and regenerative processes. Conclusions: As in other investigated syllids, the proventricle region has a significant role during stolonization and reproduction processes in Typosyllis antoni. When the proventricle region is absent, anterior and posterior regeneration are considerably deviated from the general patterns. However, proventricle ultrastructure does not show any glandular component, thereby questioning a direct involvement of this organ itself in the control of reproduction and regeneration. Our findings offer a comprehensive starting point for further studies of regeneration and reproductive control in syllids as well as annelids in general

Wolbachia distribution in selected beetle taxa characterized by PCR screens and MLST data

Wolbachia (Alphaproteobacteria) is an inherited endosymbiont of arthropods and filarial nematodes and was reported to be widespread across insect taxa. While Wolbachia’s effects on host biology are not understood from most of these hosts, known Wolbachia-induced phenotypes cover a spectrum from obligate beneficial mutualism to reproductive manipulations and pathogenicity. Interestingly, data on Wolbachia within the most species-rich order of arthropods, the Coleoptera (beetles), are scarce. Therefore, we screened 128 species from seven beetle families (Buprestidae, Hydraenidae, Dytiscidae, Hydrophilidae, Gyrinidae, Haliplidae, and Noteridae) for the presence of Wolbachia. Our data show that, contrary to previous estimations, Wolbachia frequencies in beetles (31% overall) are comparable to the ones in other insects. In addition, we used Wolbachia MLST data and host phylogeny to explore the evolutionary history of Wolbachia strains from Hydraenidae, an aquatic lineage of beetles. Our data suggest that Wolbachia from Hydraenidae might be largely host genus specific and that Wolbachia strain phylogeny is not independent to that of its hosts. As this contrasts with most terrestrial Wolbachia–arthropod systems, one potential conclusion is that aquatic lifestyle of hosts may result in Wolbachia distribution patterns distinct from those of terrestrial hosts. Our data thus provide both insights into Wolbachia distribution among beetles in general and a first glimpse of Wolbachia distribution patterns among aquatic host lineages

Mitochondrial genome sequence and gene order of Sipunculus nudus give additional support for an inclusion of Sipuncula into Annelida

<p>Abstract</p> <p>Background</p> <p>Mitochondrial genomes are a valuable source of data for analysing phylogenetic relationships. Besides sequence information, mitochondrial gene order may add phylogenetically useful information, too. Sipuncula are unsegmented marine worms, traditionally placed in their own phylum. Recent molecular and morphological findings suggest a close affinity to the segmented Annelida.</p> <p>Results</p> <p>The first complete mitochondrial genome of a member of Sipuncula, <it>Sipunculus nudus</it>, is presented. All 37 genes characteristic for metazoan mtDNA were detected and are encoded on the same strand. The mitochondrial gene order (protein-coding and ribosomal RNA genes) resembles that of annelids, but shows several derivations so far found only in Sipuncula. Sequence based phylogenetic analysis of mitochondrial protein-coding genes results in significant bootstrap support for Annelida <it>sensu lato</it>, combining Annelida together with Sipuncula, Echiura, Pogonophora and Myzostomida.</p> <p>Conclusion</p> <p>The mitochondrial sequence data support a close relationship of Annelida and Sipuncula. Also the most parsimonious explanation of changes in gene order favours a derivation from the annelid gene order. These results complement findings from recent phylogenetic analyses of nuclear encoded genes as well as a report of a segmental neural patterning in Sipuncula.</p

The making of a branching annelid: an analysis of complete mitochondrial genome and ribosomal data of Ramisyllis multicaudata

Ramisyllis multicaudata is a member of Syllidae (Annelida, Errantia, Phyllodocida) with a remarkable branching body plan. Using a next-generation sequencing approach, the complete mitochondrial genomes of R. multicaudata and Trypanobia sp. are sequenced and analysed, representing the first ones from Syllidae. The gene order in these two syllids does not follow the order proposed as the putative ground pattern in Errantia. The phylogenetic relationships of R. multicaudata are discerned using a phylogenetic approach with the nuclear 18S and the mitochondrial 16S and cox1 genes. Ramisyllis multicaudata is the sister group of a clade containing Trypanobia species. Both genera, Ramisyllis and Trypanobia, together with Parahaplosyllis, Trypanosyllis, Eurysyllis, and Xenosyllis are located in a long branched clade. The long branches are explained by an accelerated mutational rate in the 18S rRNA gene. Using a phylogenetic backbone, we propose a scenario in which the postembryonic addition of segments that occurs in most syllids, their huge diversity of reproductive modes, and their ability to regenerate lost parts, in combination, have provided an evolutionary basis to develop a new branching body pattern as realised in Ramisyllis

On the phylogenetic position of Myzostomida: can 77 genes get it wrong?

<p>Abstract</p> <p>Background</p> <p>Phylogenomic analyses recently became popular to address questions about deep metazoan phylogeny. Ribosomal proteins (RP) dominate many of these analyses or are, in some cases, the only genes included. Despite initial hopes, phylogenomic analyses including tens to hundreds of genes still fail to robustly place many bilaterian taxa.</p> <p>Results</p> <p>Using the phylogenetic position of myzostomids as an example, we show that phylogenies derived from RP genes and mitochondrial genes produce incongruent results. Whereas the former support a position within a clade of platyzoan taxa, mitochondrial data recovers an annelid affinity, which is strongly supported by the gene order data and is congruent with morphology. Using hypothesis testing, our RP data significantly rejects the annelids affinity, whereas a platyzoan relationship is significantly rejected by the mitochondrial data.</p> <p>Conclusion</p> <p>We conclude (i) that reliance of a set of markers belonging to a single class of macromolecular complexes might bias the analysis, and (ii) that concatenation of all available data might introduce conflicting signal into phylogenetic analyses. We therefore strongly recommend testing for data incongruence in phylogenomic analyses. Furthermore, judging all available data, we consider the annelid affinity hypothesis more plausible than a possible platyzoan affinity for myzostomids, and suspect long branch attraction is influencing the RP data. However, this hypothesis needs further confirmation by future analyses.</p