A multi criterion approach for the selection of optimal outgroups in phylogeny: recovering some support for Mandibulata over Myriochelata using mitogenomics

The choice of an appropriate outgroup is a fundamental prerequisite when the difference between two conflicting phylogenetic hypotheses depends on the position of the root. This is the case for the myriapods that may group either with Pancrustacea forming a clade called Mandibulata, in accordance with morphological characters, or with chelicerates to form Myriochelata (also called Paradoxopoda) as has recently been proposed by mitochondrial and ribosomal RNA gene phylogenies. In order to understand the impact that outgroup choice may have on phylogenetic reconstruction, we have investigated compositional heterogeneity and genetic distance in mtDNA sequences of several different outgroups to the arthropods, selected from deuterostomes, lophotrochozoans and ecdysozoans, and have used them to root a phylogenetically balanced and compositionarily homogeneous arthropod dataset. Results indicate that some outgroups, in particular from lophotrochozoans, nematodes and an onychophoran have G+C content and strand specific biases which are very different from those of arthropods, suggesting that the use of such outgroups may interfere with the stationarity of the model to create a random outgroup effect. We suggest a multi criterion approach for the selection of optimal outgroup species on the basis of (1) low substitution rate, (2) ingroup-like G+C composition, (3) a new strand bias estimator called the skew index, (4) the ability of the outgroup to avoid a "random branching effect" and (5) phylogenetic proximity to arthropods. Inference of phylogeny using various outgroups shows that use of phylogenetically distant and compositionally distinct lophotrochozoans as outgroups strongly supports Myriochelata and use of more closely related, but fast evolving nematodes supports Mandibulata. A dataset comprising multiple ecdysozoan outgroups also supports Mandibulata, unless the compositionally distant Onychophora are included. A group of the best outgroups selected according to our multi criteria selection, and including the most closely related, least genetically distant and most compositionally similar outgroup, a priapulid worm, supports Mandibulata. We conclude that support for the Myriochelata hypothesis from mitochondrial sequences may depend on the nature of the outgroup sequences rather than a true phylogenetic signal. Finally, we advocate a careful analysis and an objective choice of outgroup when dealing with derived sequences, such as mitochondrial genomes.     

Temporal and palaeoclimatic context of the evolution of insular woodiness in the Canary Islands

Insular woodiness (IW), referring to the evolutionary transition from herbaceousness toward woodiness on islands, has arisen more than 30 times on the Canary Islands (Atlantic Ocean). One of the IW hypotheses suggests that drought has been a major driver of wood formation, but we do not know in which palaeoclimatic conditions the insular woody lineages originated. Therefore, we provided an updated review on the presence of IW on the Canaries, reviewed the palaeoclimate, and estimated the timing of origin of woodiness of 24 insular woody lineages that represent a large majority of the insular woody species diversity on the Canaries. Our single, broad‐scale dating analysis shows that woodiness in 60%–65% of the insular woody lineages studied originated within the last 3.2 Myr, during which Mediterranean seasonality (yearly summer droughts) became established on the Canaries. Consequently, our results are consistent with palaeoclimatic aridification as a potential driver of woodiness in a considerable proportion of the insular woody Canary Island lineages. However, the observed pattern between insular woodiness and palaeodrought during the last couple of million years could potentially have emerged as a result of the typically young age of the native insular flora, characterized by a high turnover.     

New insights of membrane environment effects on MscL channel mechanics from theoretical approaches

The prokaryotic mechanosensitive channel of large conductance (MscL) is a remarkable integral membrane protein. During hypo-osmotic shock, it responses to membrane tension through large conformational changes, that lead to an open state of the pore. The structure of the channel from Mycobacterium tuberculosis has been resolved in the closed state. Numerous experiments have attempted to trap the channel in its open state but they did not succeed in obtaining a structure. A gating mechanism has been proposed based on different experimental data but there is no experimental technique available to follow this process in atomic details. In addition, it has been shown that a decrease of the lipid bilayer thickness lowered MscL activation energy and stabilized a structurally distinct closed channel intermediate. Here, we use atomistic molecular dynamics simulations to investigate the effect of the lipid bilayer thinning on our model of the structure of the Escherichia coli. We thoroughly analyze simulations of the channel embedded in two pre-equilibrated membranes differing by their hydrophobic tail length (DMPE and POPE). The MscL structure remains stable in POPE, whereas a distinct structural state is obtained in DMPE in response to hydrophobic mismatch. This latter is obtained by tilts and kinks of the transmembrane helices, leading to a widening and a diminution of the channel height. Part of these motions is guided by a competition between solvent and lipids for the interaction with the periplasmic loops. We finally conduct a principal component analysis of the simulation and compare anharmonic motions with harmonic ones, previously obtained from a coarse-grained normal mode analysis performed on the same structural model. Significant similarities exist between low-frequency harmonic motions and those observed with essential dynamics in DMPE. In summary, change in membrane thickness permits to accelerate the conformational changes involved in the mechanics of the E. coli channel, providing a closed structural intermediate en route to the open state. These results give clues for better understanding why the channel activation energy is lowered in a thinner membrane.     

The scent of your enemy is my friend? The acquisition of large carnivore scent by a smaller carnivore

Scent marking is critical to intraspecific communication in many mammal species, but little is known regarding its role in communication among different species. We used 4 years of motion-triggered video to document the use of scent marking areas—termed “community scrapes”—by pumas (Puma concolor) (http://www.momo-p.com/showdetail-e.php?movieid=momo160812pc01a) and other carnivore species. We found that gray foxes (Urocyon cinereoargenteus) routinely rubbed their cheeks on puma scrapes (http://www.momo-p.com/showdetail-e.php?movieid=momo160812uc01a), and tested a series of hypotheses to determine its function. We found that gray foxes selected puma scrapes over other objects, and cheek rubbing by foxes was also correlated with how recently a puma had visited the scrape, suggesting that foxes were intent upon accumulating fresh puma scent. Cheek rubbing by foxes was not correlated with their breeding season or with how recently another fox had visited the site. Finally we found a cascading pattern in the occurrence of pumas, coyotes (Canis latrans) and gray foxes at community scrapes, suggesting that gray foxes may use puma scent to deter predation. This is the first published study to find evidence of a subordinate species using the scent of a dominant species to communicate with heterospecifics. The behavioral cascade we found in scent marking patterns also suggests that scent marking could be a mechanism that impacts the distribution and abundance of species. Additional videos pertaining to this article include http://www.momo-p.com/showdetail-e.php?movieid=momo160812uc02a, and http://www.momo-p.com/showdetail-e.php?movieid=momo160812uc03a.     

Microbial production of glutathione

World Journal of Microbiology and Biotechnology - The present work aims to identify the microbial diversity associated with six Indian Drosophila species using next generation sequencing (NGS)...     

LAT displacement from lipid rafts as a molecular mechanism for the inhibition of T cell signaling by polyunsaturated fatty acids

Polyunsaturated fatty acids (PUFAs) suppress immune responses and inhibit T cell activation through largely unknown mechanisms. The displacement of signaling proteins from membrane lipid rafts has recently been suggested as underlying PUFA-mediated T cell inhibition. We show here that PUFA treatment specifically interferes with T cell signal transduction by blocking tyrosine phosphorylation of LAT (linker for activation of T cells) and phospholipase Cgamma1. A significant fraction of LAT was displaced from rafts by PUFA treatment along with other signaling proteins. However, retaining LAT alone in lipid rafts effectively restored phospholipase Cgamma1/calcium signaling in PUFA-treated T cells. These data reveal LAT displacement from lipid rafts as a molecular mechanism by which PUFAs inhibit T cell signaling and underline the predominant importance of LAT localization in rafts for efficient T cell activation.     

Nonneutral admixture of immigrant genotypes in African Drosophila melanogaster populations from Zimbabwe

Drosophila melanogaster originated in Africa and colonized the rest of the world only recently (approximately 10,000 to 15,000 years ago). Using 151 microsatellite loci, we investigated patterns of gene flow between African D. melanogaster populations representing presumptive ancestral variation and recently colonized European populations. Although we detected almost no evidence for alleles of non-African ancestry in a rural D. melanogaster population from Zimbabwe, an urban population from Zimbabwe showed evidence for admixture. Interestingly, the degree of admixture differed among chromosomes. X chromosomes of both rural and urban populations showed almost no non-African ancestry, but the third chromosome in the urban population showed up to 70% of non-African alleles. When chromosomes were broken into contingent microsatellite blocks, even higher estimates of admixture and significant heterogeneity in admixture was observed among these blocks. The discrepancy between the X chromosome and the third chromosome is not consistent with a neutral admixture hypothesis. The higher number of European alleles on the third chromosome could be due to stronger selection against foreign alleles on the X chromosome or to more introgression of (beneficial) alleles on the third chromosome.     

<Emphasis Type="Italic">SONIC HEDGEHOG</Emphasis> mutations causing human holoprosencephaly impair neural patterning activity

Holoprosencephaly (HPE) is a common forebrain malformation associated with mental retardation and craniofacial anomalies. Multiple lines of evidence indicate that loss of ventral neurons is associated with HPE. The condition is etiologically heterogeneous, and abnormalities in any of several genes can cause human HPE. Among these genes, mutations in SONIC HEDGEHOG ( SHH) are the most commonly identified single gene defect causing human HPE. SHH mediates a number of processes in central nervous system development and is required for the normal induction of ventral cell types in the brain and spinal cord. Although a number of missense mutations in SHH have been identified in patients with HPE, the functional significance of these mutations has not yet been determined. We demonstrate that two SHH mutations that cause human HPE result in decreased in vivo activity of SHH in the developing nervous system. These mutant forms of SHH fail to regulate genes properly that are normally responsive to SHH signaling and do not induce ventrally expressed genes. In addition, the immunoreactivity of the mutant proteins is altered, suggesting that the conformation of the SHH protein has been disrupted. These studies are the first demonstration that mutations in SHH associated with human HPE perturb the in vivo patterning function of SHH in the developing nervous system.