We report the extraction of a bed bug mitogenome from high-throughput sequencing projects originally focused on the nuclear genome of Cimex lectularius. The assembled mitogenome has a similar AT ...nucleotide composition bias found in other insects. Phylogenetic analysis of all protein-coding genes indicates that C. lectularius is clearly a member of a paraphyletic Cimicomorpha clade within the Order Hemiptera.
Large vertebrates, like the domestic goat (
Capra hircus
), have been transported all over the world and are an ecological disaster to numerous island and mainland ecosystems. Eradication measures ...for such species are generally centered on lethal methods of removing individuals, an increasingly difficult process as populations become smaller and individual animals become much more difficult to detect. In addition, methods of lethal removal are becoming less desirable in the public eye, prompting the necessity to explore alternatives. Here we investigate the use of the sterile males technique as an effective strategy in the eradication of large mammals. The results of our simulations suggest that the use of sterile males as a single strategy would only be an effective measure to eradicate relatively small (no more than 100 individuals) isolated feral vertebrate populations. However, our results indicate that the technique could be employed as a successful and potentially cost-effective end-point complement to lethal control and/or as a preventative measure against re-invasion.
Nuclear insertions of mitochondrial sequences (NuMts) have been identified in a wide variety of organisms. Trafficking of genetic material from the mitochondria to the nucleus has occurred frequently ...during mammalian evolution and can lead to the production of a large pool of sequences with varying degrees of homology to organellar mitochondrial DNA (mtDNA) sequences. This presents both opportunities and challenges for forensics, population genetics, evolutionary genetics, conservation biology and the study of DNA from ancient samples. Here we present a case in which difficulties in ascertaining the organellar mtDNA sequence from modern samples hindered their comparison to ancient DNA sequences.
We obtained mitochondrial hypervariable region (HVR) sequences from six ancient samples of tundra muskox (Ovibos moschatus) that were reproducible but distinct from modern muskox sequences reported previously. Using the same PCR primers applied to the ancient specimens and the primers used to generate the modern muskox DNA sequences in a previous study, we failed to definitively identify the organellar sequence from the two modern muskox samples tested. Instead of anticipated sequence homogeneity, we obtained multiple unique sequences from both hair and blood of one modern specimen. Sequencing individual clones of a >1 kb PCR fragment from modern samples did not alleviate the problem as there was not a consistent match across the entire length of the sequences to Ovibos when compared to sequences in GenBank.
In specific taxa, due to nuclear insertions some regions of the mitochondrial genome may not be useful for the characterization of modern or ancient DNA.
Celotno besedilo
Dostopno za:
DOBA, IZUM, KILJ, NUK, PILJ, PNG, SAZU, SIK, UILJ, UKNU, UL, UM, UPUK
Wild bird fecal samples collected and characterized by the USDA as part of a national surveillance effort were sequenced to study the genetic relatedness of avian, swine, and human H1 and N1 ...subtypes. Our results find that the 2009 H1N1 human outbreak is closely related to swine virus, but falls into different clades in the H1 and N1 trees. Further, there is evidence of multiple viral genetic exchanges between birds and swine. Ongoing research across host species contributes to an understanding of the circulation of influenza viruses.
For many familiar with metazoan relationships and body plans, the hypothesis of a sister group relationship between Diploblasta and Bilateria1 comes as a surprise. One of the consequences of this ...hypothesis - the independent evolution of a nervous system in Coelenterata and Bilateria - seems highly unlikely to many. However, to a small number of scientists working on Metazoa, the parallel evolution of the nervous system is not surprising at all and rather a confirmation of old morphological and new genetic knowledge.
2-4
The controversial hypothesis that the Diploblasta and Bilateria are sister taxa is, therefore, tantamount to reconciling the parallel evolution of the nervous system in Coelenterata and Bilateria. In this addendum to Schierwater et al.,
1
we discuss two aspects critical to the controversy. First we discuss the strength of the inference of the proposed sister relationship of Diploblasta and Bilateria and second we discuss the implications for the evolution of nerve cells and nervous systems.
Abstract
Background
Previous studies have suggested that the population structure of E. faecium is composed of two main clades; a commensal clade (designated clade B) and a hospital-associated clade ...(Clade A) that encompass most of the clinical and animal isolates. The phylogenetic analyses leading to these results have been accomplished with the notable absence of isolates from diverse geographical regions (including South America). We aimed to refine the worldwide population structure of E. faecium by including 55 representative genomes from isolates obtained from five Latin American countries recovered between 1998 and 2014.
Methods
We sequenced our 55 representative isolates and selected other 285 genomes, from public databases, obtained across different regions (36 countries), different sources (animal, commensal, and clinical strains) and a wide range of dates of isolation (1946–2017). We characterized the genomes by presence/absence of resistance, virulence and mobile elements, and of CRISPR-cas systems. We analyzed the phylogeny of the entire population, selected the genomes belonging to clade A to examine recombination patterns and performed Bayesian molecular clock analysis excluding recombinant regions.
Results
Two major clades were identified, as previously reported. However, a higher degree of variation in clade A was found. Indeed, we identified a subclade (subclade I) that diverged ~894 years ago, and clearly distinguished clinical isolates from those of animal origin (distributed among a number of smaller early-branching subclades). A further split within the clinical subclade (subclade II) that diverged around ~371 years ago was also evident. Latin American isolates were distributed within subclades I (48%) and II (42%). Isolates in “animal” branches exhibited an average recombination of 34 Kbp, where it was 5 Kbp and 21 Kbp for subclades I and II, respectively. More resistance determinants were found in subclade II (62%), followed by I (54%) and absence of cas was the norm in the clinical subclades.
Conclusion
Inclusion of E. faecium isolates from diverse geographical region supports a continuous evolution of these organisms causing human infections. Important evolutionary events seem to favor emergence of novel subclades capable to cause important morbidity and mortality.
Disclosures
J. Munita, Pfizer: Grant Investigator, Research grant. C. Arias, Merck & Co., Inc.: Grant Investigator, Research support. MeMed: Grant Investigator, Research support. Allergan: Grant Investigator, Research support.
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