Molecular Phylogenetics of Physa acuta (Pulmonata: Basommatophora): an Invasive species in Central Punjab Pakistan

Physids belong to Class Gastropoda; belong to Phylum Mollusca and being bioindicators, intermediate hosts of parasites and pests hold a key position in the ecosystem. There are three species of Genus Physa i.e. P. fontinalis, Physa acuta and P. gyrina water bodies of Central Punjab and were characterized on the basis of molecular markers High level of genetic diversity was revealed by polymorphic RAPD, however SSR markers were not amplified. The multivariate analysis revealed polymorphism ranging from 9.09 percent to 50 percent among the three Physid species. Total number of 79 loci were observed for the three species under study and 24 loci were observed to be polymorphic. These RAPD fragment(s) can be developed into co dominant markers (SCAR) by cloning and can be further sequenced for the development of the Physa species specific markers to identify the introduced and native species in Pakistan.

Perspectives in Earthworm Molecular Phylogeny: Recent Advances in Lumbricoidea and Standing Questions

Earthworm systematics have been limited by the small number of taxonomically informative morphological characters and high levels of homoplasy in this group. However, molecular phylogenetic techniques have yielded significant improvements in earthworm taxonomy in the last 15 years. Several different approaches based on the use of different molecular markers, sequencing techniques, and compromises between specimen/taxon coverage and phylogenetic information have recently emerged (DNA barcoding, multigene phylogenetics, mitochondrial genome analysis, transcriptome analysis, targeted enrichment methods, and reduced representation techniques), providing solutions to different evolutionary questions regarding European earthworms. Molecular phylogenetics have led to significant advances being made in Lumbricidae systematics, such as the redefinition or discovery of new genera (Galiciandrilus, Compostelandrilus, Vindoboscolex, Castellodrilus), delimitation and revision of previously existing genera (Kritodrilus, Eophila, Zophoscolex, Bimastos), and changes to the status of subspecific taxa (such as the Allolobophorachaetophora complex). These approaches have enabled the identification of problems that can be resolved by molecular phylogenetics, including the revision of Aporrectodea, Allolobophora, Helodrilus, and Dendrobaena, as well as the examination of small taxa such as Perelia, Eumenescolex, and Iberoscolex. Similar advances have been made with the family Hormogastridae, in which integrative systematics have contributed to the description of several new species, including the delimitation of (formerly) cryptic species. At the family level, integrative systematics have provided a new genus system that better reflects the diversity and biogeography of these earthworms, and phylogenetic comparative methods provide insight into earthworm macroevolution. Despite these achievements, further research should be performed on the Tyrrhenian cryptic complexes, which are of special eco-evolutionary interest. These examples highlight the potential value of applying molecular phylogenetic techniques to other earthworm families, which are very diverse and occupy different terrestrial habitats across the world. The systematic implementation of such approaches should be encouraged among the different expert groups worldwide, with emphasis on collaboration and cooperation.

A somatic UBA2 variant preceded ETV6-RUNX1 in the concordant BCP-ALL of monozygotic twins

Genetic analysis of leukemic clones in monozygotic twins with concordant ALL has proved a unique opportunity to gain insight into the molecular phylogenetics of leukemogenesis. Using whole genome sequencing, we characterized constitutional and somatic SNVs/indels and structural variants in a monozygotic twin pair with concordant ETV6-RUNX1 positive B-cell precursor acute lymphoblastic leukemia (BCP-ALL). In addition, digital PCR (dPCR) was applied to evaluate the presence of and quantify selected somatic variants at birth, diagnosis and remission. A shared somatic complex rearrangement involving chromosomes 11, 12 and 21 with identical fusion sequences in leukemias of both twins offered direct proof of a common clonal origin. The ETV6-RUNX1 fusion detected at diagnosis was found to originate from this complex rearrangement. A shared somatic frameshift deletion in UBA2 was also identified in diagnostic samples. In addition, each leukemia independently acquired analogous deletions of three genes recurrently targeted in BCP-ALLs (ETV6, ATF7IP and RAG1/RAG2) providing evidence of a convergent clonal evolution, only explained by a strong concurrent selective pressure. Quantification of the UBA2 deletion by dPCR surprisingly indicated it persisted in remission. This, for the first time to our knowledge, provided evidence of a UBA2 variant preceding the well-established initiating event ETV6-RUNX1. Further, we suggest the UBA2 deletion exerted a leukemia predisposing effect and that its essential role in SUMOylation, regulating nearly all physiological and pathological cellular processes such as DNA-repair by non-homologous end joining, may hold a mechanistic explanation for the predisposition.

Molecular Phylogenetics and Mitochondrial Evolution

The myth of a “typical” mitochondrial genome (mtDNA) is a rock-hard belief in the field of genetics, at least for the animal kingdom [...]

The cnidarian parasite Ceratonova shasta utilizes inherited and recruited venom-like compounds during infection

Background Cnidarians are the most ancient venomous organisms. They store a cocktail of venom proteins inside unique stinging organelles called nematocysts. When a cnidarian encounters chemical and physical cues from a potential threat or prey animal, the nematocyst is triggered and fires a harpoon-like tubule to penetrate and inject venom into the prey. Nematocysts are present in all Cnidaria, including the morphologically simple Myxozoa, which are a speciose group of microscopic, spore-forming, obligate parasites of fish and invertebrates. Rather than predation or defense, myxozoans use nematocysts for adhesion to hosts, but the involvement of venom in this process is poorly understood. Recent work shows some myxozoans have a reduced repertoire of venom-like compounds (VLCs) relative to free-living cnidarians, however the function of these proteins is not known. Methods We searched for VLCs in the nematocyst proteome and a time-series infection transcriptome of Ceratonova shasta, a myxozoan parasite of salmonid fish. We used four parallel approaches to detect VLCs: BLAST and HMMER searches to preexisting cnidarian venom datasets, the machine learning tool ToxClassifier, and structural modeling of nematocyst proteomes. Sequences that scored positive by at least three methods were considered VLCs. We then mapped their time-series expressions in the fish host and analyzed their phylogenetic relatedness to sequences from other venomous animals. Results We identified eight VLCs, all of which have closely related sequences in other myxozoan datasets, suggesting a conserved venom profile across Myxozoa, and an overall reduction in venom diversity relative to free-living cnidarians. Expression of the VLCs over the 3-week fish infection varied considerably: three sequences were most expressed at one day post-exposure in the fish’s gills; whereas expression of the other five VLCs peaked at 21 days post-exposure in the intestines, coinciding with the formation of mature parasite spores with nematocysts. Expression of VLC genes early in infection, prior to the development of nematocysts, suggests venoms in C. shasta have been repurposed to facilitate parasite invasion and proliferation within the host. Molecular phylogenetics suggested some VLCs were inherited from a cnidarian ancestor, whereas others were more closely related to sequences from venomous non-Cnidarian organisms and thus may have gained qualities of venom components via convergent evolution. The presence of VLCs and their differential expression during parasite infection enrich the concept of what functions a “venom” can have and represent targets for designing therapeutics against myxozoan infections.

Hydra collecting for citizen scientists v2

The freshwater cnidarian Hydra has been a model system for regeneration and developmental biology for over 250 years, but much remains unknown about their biodiversity and global distribution. As a citizen scientist, you can contribute to our understanding of Hydra in the wild by becoming a "Hydra Hunter". All it takes is a few simple materials and a little patience. Collecting Hydra in the wild can be challenging. You will certainly not find them everywhere you look. Keep in mind that NOT finding Hydra is still useful information because this will help us understand the environmental factors that effect their distribution. Metadata submission form: https://forms.gle/cAZCiiRCyE922G5t5 Please contact [email protected] for more information or to receive a Hydra collecting kit. Hydra collecting kits were purchased with a grant to Kimberly Sladek from the University of San Diego Associated Students Government. Thank you to Rob Steele for helpful feedback on this protocol. References: Campbell, R. D. (1983). Hydra Collecting. In H. M. Lenhoff (Ed.). Hydra: Research Methods. New York: Springer Science + Business Media. Martínez, D. E., et al. (2010). Phylogeny and biogeography of Hydra (Cnidaria: Hydridae) using mitochondrial and nuclear DNA sequence. Molecular Phylogenetics and Evolution, 57, 403-410. doi:10.1016/j.ympev.2010.06.016

Twenty Years after De Ley and Blaxter—How Far Did We Progress in Understanding the Phylogeny of the Phylum Nematoda?

Molecular phylogenetics brought radical changes to our understanding of nematode evolution, resulting in substantial modifications to nematode classification implemented by De Ley and Blaxter and widely accepted now. Numerous phylogenetic studies were subsequently published that both improved and challenged this classification. Here we present a summary of these changes. We created cladograms that summarise phylogenetic relationships within Nematoda using phylum-wide to superfamily-wide molecular phylogenies published in since 2005, and supplemented with the phylogenetic analyses for Enoplia and Chromadoria with the aim of clarifying the position of several taxa. The results show which parts of the Nematode tree are well resolved and understood, and which parts require more research, either by adding taxa that have not been included yet (increasing taxon coverage), or by changing the phylogenetic approach (improving data quality, using different types of data or different methods of analysis). The currently used classification of the phylum Nematoda in many cases does not reflect the phylogeny and in itself requires numerous improvements and rearrangements.

Hydra collecting for citizen scientists v2

The freshwater cnidarian Hydra has been a model system for regeneration and developmental biology for over 250 years, but much remains unknown about their biodiversity and global distribution. As a citizen scientist, you can contribute to our understanding of Hydra in the wild by becoming a "Hydra Hunter". All it takes is a few simple materials and a little patience. Collecting Hydra in the wild can be challenging. You will certainly not find them everywhere you look. Keep in mind that NOT finding Hydra is still useful information because this will help us understand the environmental factors that effect their distribution. Metadata submission form: https://forms.gle/cAZCiiRCyE922G5t5 Please contact [email protected] for more information or to receive a Hydra collecting kit. Hydra collecting kits were purchased with a grant to Kimberly Sladek from the University of San Diego Associated Students Government. Thank you to Rob Steele for helpful feedback on this protocol. References: Campbell, R. D. (1983). Hydra Collecting. In H. M. Lenhoff (Ed.). Hydra: Research Methods. New York: Springer Science + Business Media. Martínez, D. E., et al. (2010). Phylogeny and biogeography of Hydra (Cnidaria: Hydridae) using mitochondrial and nuclear DNA sequence. Molecular Phylogenetics and Evolution, 57, 403-410. doi:10.1016/j.ympev.2010.06.016