I am combining long-range PCR with Illumina MiSeq technology to sequence the complete mitochondrial (mt) genomes for mitogenome phylogenetics. In a recent pilot study I sequence the mt genomes, or large fragments thereof, of Cribrilina annulata, Escharoides coccinea, Pentapora foliacea, Cryptosula pallasiana, Schizoporella dunkeri, Microporella lineata, Sertella sp., Reteporella ligulata, Chaperiopsis sp. and Chiastosella sp.
Underwater picture of cheilostome bryozoans. © Joanne Porter
Data from complete mt genomes place the phylum Bryozoa as a monophyletic clade within the Lophotrochozoa, with Phoronida forming their sister group.
Following the cyclostome phylogeny presented in Waeschenbach et al. 2009, we continue to expand the phylogeny as more specimens become available (e.g. Tennysonia stellata Taylor et al. 2011), with the latest additions being the family Diastoporidae and Crisulipora occidentalis (see below), where the phylogenetic position of the latter demonstrates the repeated origin of branch articulation in cyclostome bryozoans.
Crisulipora occidentalis © Paul Taylor
In collaboration with Leandro Vieira and Karin Fehlauer-Ale (CEBI-Mar University of São Paulo, Brazil) and Javier Souto-Derungs and Oscar Reverter-Gil (University of Santiago de Compostelo, Spain) we have generated a phylogeny of the ctenostome family Vesiculariidae, demonstrating a lack of reciprocal monophyly of the genera Amathia and Bowerbankia.
This NERC-funded project NE/E015298/1) was in collaboration with Tim Littlewood, Paul Taylor (NHM) and Joanne Porter (Heriot-Watt University, Edinburgh). We used mtDNA and ribosomal RNA genes to reconstruct:
Frontal view of the cyclostome bryozoan Hornera foliacea, showing zooids and pseudopores. © Andrea Waeschenbach
This project was led by Karin Fehlauer-Ale (CEBI-Mar University of São Paulo, Brazil) and was in collaboration with Joshua Mackie (San Jose State University, USA), Grace Lim-Fong (Randoph Macon College, Virginia, USA) and Ezequiel Ale (University of São Paulo, Brazil). Intensive anthropogenic transport of haplotypes tolerant to a wide range of sea water temperatures are proposed to be the cause for the global distribution of one of the cryptic lineages in the B. neritina species complex (Fehlauer-Ale et al. in review).
The bryozoan C. hyalina (see below) has been shown to be composed of multiple, often cryptic, lineages. I sequenced two complete mt genomes, one from Wales and one from Norway and found high nucleotide diversity, a large genome size difference and a change in gene order between them, suggesting that these mt genomes are sufficiently divergent to have originated from two distinct species. Molecular markers were developed for two regions to study species- and population-level diversity within this complex (Waeschenbach et al. 2012).
My helminth research with Tim Littlewood focuses on molecular phylogenetics of free-living and parasitic platyhelminths and nematodes.
This NSF-funded project combines the effort of tapeworm experts around the world to generate an inventory of existing and novel tapeworm diversity, where particular effort is being made to sample as yet unexplored vertebrate hosts and geographic regions. My contribution to the project is to assemble multi-gene phylogenies for seven tapeworm orders, many of which include species new to science.
In this BBSRC-funded project, we developed a methodology for sequencing pooled long PCR amplicons using next-generation sequencing (NGS). We generated 470 long PCR amplicons, mostly from flukes and tapeworms, but also from parasitic nematodes, amphibians, and fish. Short regions for each amplicon were characterised using Sanger sequencing and were used as bioinformatic tags. The pooled amplicons were sequenced using different NGS platforms (454 GLS FLX Titanium, Ion Torrent and Illumina HiSeq) and assembled with the help of the Sanger tags.
The anterior attachment organ of the tapeworm Rhinebothrium sp. © Claire Healy
Using nuclear ribosomal RNA genes and multi-gene fragments of mitochondrial DNA, we constructed ordinal-level phylogenies of tapeworms (Waeschenbach et al. 2007; Waeschenbach et al. 2012) which are now serving as framework for the study of within ordinal relationships, particularly of orders that were resolved as non-monophyletic.
In a collaboration led by Harry Palm (Universität Rostock), we produced a comprehensive molecular phylogeny of trypanorhynch tapeworms. This study revealed morphological characters, used for traditional taxonomy, to be highly homoplasious (Palm et al. 2009).
A study, led by Lukas Schärer (Universität Basel), on the free-living, hermaphroditic flatworm Macrostomum (Schärer et al. 2011), showed differences in sperm morphology to be linked to mating behaviour and sexual conflict. In a reciprocal mating system, sperm have a highly complex morphology, adapted to the shape and structure of the female sperm receptacle, to prevent sperm rejection. Whereas in the hypodermic impregnation system, sperm morphology is much simpler. By placing these observations into a phylogenetic framework, we found hypodermic impregnation to have evolved independently, at least twice, probably as a result of male strategy to by-pass female control.
The nematode Toxocara is commonly found in the intestine of cats and dogs and is the causative agent of toxocariasis in humans. Ocular larval migrans can, in severe cases, lead to blindness. © www.petcaregt.com/blog/
In a collaboration led by Robin Gasser and Aaron Jex (University of Melbourne), we sequenced several mt genomes of nematodes (Jex et al. 2009, 2008; Jex & Waeschenbach et al. 2008). The resultant data are used to provide phylogenetic estimates for this group and to develop novel molecular markers for diagnostics and population genetics.
In addition to the published mt genomes of tapeworms and monogeneans, we sequenced the mt genomes of three free-living turbellarians and two basal tapeworm lineages. This comprehensive dataset is expected to provide a well-supported phylogeny of Platyhelminthes.
Fehlauer-Ale KH, Mackie JA, Lim-Fong G, Ale E, Waeschenbach A (in review) Bayesian species delimitation of the bryozoan complex Bugula neritina and global phylogeography of a widespread cryptic species. PLOS ONE.
Scholz T, de Chambrier A, Kuchta R, Littlewood DTJ, Waeschenbach A (2013) Macrobothriotaenia ficta (Cestoda: Proteocephalidea), a parasite of sunbeam snake (Xenopeltis unicolor): example of convergent evolution. Zootaxa, 3640:485-499.
Hartikainen H, Waeschenbach A, Wöss E, Wood T, Okamura B (2013) Divergence and species discrimination in freshwater bryozoans (Bryozoa: Phylactolaemata). Zoological Journal of the Linnean Society, 168:61-80.
Bray RA, Foster GN, Waeschenbach A, Littlewood DTJ (2012) The discovery of progenetic Allocreadium neotenicum Peters, 1957 (Digenea: Allocreadiidae) in water beetles (Coleoptera: Dytiscidae) in Great Britain. Zootaxa, 3577:58-70.
Waeschenbach A, Porter JS, Hughes RN (2012) Molecular variability in the Celleporella hyalina (Bryozoa; Cheilostomata) species complex: Evidence for cryptic speciation from complete mitochondrial genomes. Molecular Biology Reports, 39:8601-8614.
Waeschenbach A, Webster BL, Littlewood DTJ (2012) Adding resolution to ordinal level relationships of tapeworms (Platyhelminthes: Cestoda) with large fragments of mtDNA, Molecular Phylogenetics and Evolution, 63:834-847.
Waeschenbach A, Taylor PD, Littlewood DTJ (2012) A molecular phylogeny of bryozoans, Molecular Phylogenetics and Evolution, 62:718-735.
Schärer L, Littlewood DTJ, Waeschenbach A, Yoshida W & Vizoso D (2011) Mating behaviour and the evolution of sperm design, Proceedings of the National Academy of Sciences, 108:1490-1495.
Taylor PD, Waeschenbach A, Florence W (2011) Phylogenetic position and systematics of the bryozoan Tennysonia: further evidence for convergence and plasticity in skeletal morphology among cyclostome bryozoans, Zootaxa, 3010:58-68.
Bray RA, Waeschenbach A, Cribb TH, Weedall G, Dyal P, Littlewood DTJ (2009) The phylogeny of the Lepocreadioidea (Platyhelminthes: Digenea) inferred from nuclear and mitochondrial genes: implications for their systematics and evolution, Acta Parasitologica, 54:310-329.
Waeschenbach A, Cox CC, Littlewood DTJ, Porter JS & Taylor PD (2009) The first molecular estimate of cyclostome bryozoan phylogeny confirms extensive homoplasy among skeletal characters used in traditional taxonomy, Molecular Phylogenetics and Evolution, 52:241-251.
Palm HW, Waeschenbach A, Olson PD & Littlewood DTJ (2009) Molecular phylogeny and evolution of the Trypanorhyncha Diesing, 1863 (Platyhelminthes: Cestoda), Molecular Phylogenetics and Evolution, 52:351-367.
Jex AR, Waeschenbach A, Hu M, van Wyk J, Beveridge I, Littlewood DTJ & Gasser RB (2009) The mitochondrial genomes of Ancylostoma caninum and Bunostomum phlebotomum – two hookworms of animal health and zoonotic importance, BMC Genomics, 10:79.
Jex AR, Waeschenbach A (joint 1st authorship), Littlewood DTJ, Hu M, Gasser RB (2008) The mitochondrial genome of Toxocara canis, PLoS Neglected Tropical Diseases, 2:e273.
Jex AR, Hu M, Littlewood DTJ, Waeschenbach A, Gasser RB (2008) Using 454 technology for long-PCR based sequencing of the complete mitochondrial genome from single Haemonchus contortus (Nematoda), BMC Genomics, 9:11.
Littlewood DTJ, Waeschenbach A, Nikolov PN (2008) In search of mitochondrial markers for resolving the phylogeny of cyclophyllidean tapeworms (Platyhelminthes, Cestoda) – a test study with Davaineidae, Acta Parasitologica, 53:133-144. doi:10.2478/s11686-008-0029-4
Bray RA, Cribb TH, Waeschenbach A & Littlewood DTJ (2007) A new species of Stephanostomum Looss, 1899 (Digenea, Acanthocolpidae) with a bizarre oral sucker: S. adlardi sp. nov. from the common coral trout Plectropomus leopardus (Lacepède, 1802) (Perciformes, Serranidae) from Lizard Island, Great Barrier Reef, Acta Parasitologica, 53:206-212. doi:10.2478/s11686-007-0025-0
Palm HW, Waeschenbach A, Littlewood DTJ (2007) Genetic diversity in the trypanorhynch cestode Tentacularia coryphaenae Bosc, 1797: evidence for a cosmopolitan distribution and low host specificity in the teleost intermediate host, Parasitology Research, 101:153-159. doi:10.1007/s00436-006-0435-1
Waeschenbach A, Webster BL, Bray RA, Littlewood DTJ (2007) Added resolution among ordinal level relationships of tapeworms (Platyhelminthes: Cestoda) with complete small and large subunit nuclear ribosomal RNA genes, Molecular Phylogenetics and Evolution, 45:311-325. doi:10.1016/j.ympev.2007.03.019
Waeschenbach A, Telford MJ, Porter JS & Littlewood DTJ (2006) The complete mitochondrial genome of Flustrellidra hispida and the phylogenetic position of Bryozoa among the Metazoa, Molecular Phylogenetics and Evolution, 40:195-207. doi:10.1016/j.ympev.2006.03.007