Assessing the Applicability of the GTR Nucleotide Substitution Model Through Simulations

The General Time Reversible (GTR) model of nucleotide substitution is at the core of many distance-based and character-based phylogeny inference methods. The procedure described by Waddell and Steel (1997), for estimating distances and instantaneous substitution rate matrices, R, under the GTR model, is known to be inapplicable under some conditions, ie, it leads to the inapplicability of the GTR model. Here, we simulate the evolution of DNA sequences along 12 trees characterized by different combinations of tree length, (non-)homogeneity of the substitution rate matrix R, and sequence length. We then evaluate both the frequency of the GTR model inapplicability for estimating distances and the accuracy of inferred alignments. Our results indicate that, inapplicability of the Waddel and Steel’s procedure can be considered a real practical issue, and illustrate that the probability of this inapplicability is a function of substitution rates and sequence length

Reptilian-transcriptome v1.0, a glimpse in the brain transcriptome of five divergent Sauropsida lineages and the phylogenetic position of turtles

<p>Abstract</p> <p>Background</p> <p>Reptiles are largely under-represented in comparative genomics despite the fact that they are substantially more diverse in many respects than mammals. Given the high divergence of reptiles from classical model species, next-generation sequencing of their transcriptomes is an approach of choice for gene identification and annotation.</p> <p>Results</p> <p>Here, we use 454 technology to sequence the brain transcriptome of four divergent reptilian and one reference avian species: the Nile crocodile, the corn snake, the bearded dragon, the red-eared turtle, and the chicken. Using an in-house pipeline for recursive similarity searches of >3,000,000 reads against multiple databases from 7 reference vertebrates, we compile a reptilian comparative transcriptomics dataset, with homology assignment for 20,000 to 31,000 transcripts per species and a cumulated non-redundant sequence length of 248.6 Mbases. Our approach identifies the majority (87%) of chicken brain transcripts and about 50% of <it>de novo </it>assembled reptilian transcripts. In addition to 57,502 microsatellite loci, we identify thousands of SNP and indel polymorphisms for population genetic and linkage analyses. We also build very large multiple alignments for Sauropsida and mammals (two million residues per species) and perform extensive phylogenetic analyses suggesting that turtles are not basal living reptiles but are rather associated with Archosaurians, hence, potentially answering a long-standing question in the phylogeny of Amniotes.</p> <p>Conclusions</p> <p>The reptilian transcriptome (freely available at <url>http://www.reptilian-transcriptomes.org</url>) should prove a useful new resource as reptiles are becoming important new models for comparative genomics, ecology, and evolutionary developmental genetics.</p

Liver antioxidant and plasmatic immune responses in juvenile golden grey mullet (Liza aurata) exposed to dispersed crude oil

International audienceDispersant application is an oil spill response technique. To evaluate the environmental cost of this operation in nearshore habitats, the experimental approach conducted in this study exposed juvenile golden grey mullets (Liza aurata) for 48 hours to chemically dispersed oil (simulating, in vivo, dispersant application), to dispersant alone in sea water (as an internal control of chemically dispersed oil), to mechanically dispersed oil (simulating, in vivo, natural dispersion), to the water-soluble fraction of oil (simulating, in vivo, an oil slick confinement response technique) and to sea water alone (control condition). Biomarkers such as fluorescence of biliary polycyclic aromatic hydrocarbon (PAH) metabolites, total glutathione liver content, EROD (7-ethoxy-resorufin-O-deethylase) activity, liver antioxidant enzyme activity, liver lipid peroxidation and an innate immune parameter (haemolytic activity of the alternative complement pathway) were measured to assess the toxicity of dispersant application. Significant responses of PAH metabolites and total glutathione liver content to chemically dispersed oil were found, when compared to water-soluble fraction of oil. As it was suggested in other studies, these results highlight that priority must be given to oil slick confinement instead of dispersant application. However, since the same patterns of biomarkers responses were observed for both chemically and mechanically dispersed oil, the results also suggest that dispersant application is no more toxic than the natural dispersion occurring in nearshore areas (e.g. waves). The results of this study must, nevertheless, be interpreted cautiously since other components of nearshore habitats must be considered to establish a framework for dispersant use in nearshore areas

The anatomical placode in reptile scale morphogenesis indicates shared ancestry among skin appendages in amniotes

Most mammals, birds, and reptiles are readily recognized by their hairs, feathers, and scales, respectively. However, the lack of fossil intermediate forms between scales and hairs and substantial differences in their morphogenesis and protein composition have fueled the controversy pertaining to their potential common ancestry for decades. Central to this debate is the apparent lack of an “anatomical placode” (that is, a local epidermal thickening characteristic of feathers’ and hairs’ early morphogenesis) in reptile scale development. Hence, scenarios have been proposed for the independent development of the anatomical placode in birds and mammals and parallel co-option of similar signaling pathways for their morphogenesis. Using histological and molecular techniques on developmental series of crocodiles and snakes, as well as of unique wild-type and EDA (ectodysplasin A)–deficient scaleless mutant lizards, we show for the first time that reptiles, including crocodiles and squamates, develop all the characteristics of an anatomical placode: columnar cells with reduced proliferation rate, as well as canonical spatial expression of placode and underlying dermal molecular markers. These results reveal a new evolutionary scenario where hairs, feathers, and scales of extant species are homologous structures inherited, with modification, from their shared reptilian ancestor’s skin appendages already characterized by an anatomical placode and associated signaling molecules.Peer reviewe

2× genomes - depth does matter

The use of low coverage genomes in comparative evolutionary analyses skews estimates of gene gains and losses

Somitic positional information guides self-organized patterning of snake scales

Two influential concepts in tissue patterning are Wolpert’s positional information and Turing’s self-organized reaction–diffusion (RD). The latter establishes the patterning of hair and feathers. Here, our morphological, genetic, and functional—by CRISPR-Cas9–mediated gene disruption—characterization of wild-type versus “scaleless” snakes reveals that the near-perfect hexagonal pattern of snake scales is established through interactions between RD in the skin and somitic positional information. First, we show that ventral scale development is guided by hypaxial somites and, second, that ventral scales and epaxial somites guide the sequential RD patterning of the dorsolateral scales. The RD intrinsic length scale evolved to match somite periodicity, ensuring the alignment of ribs and scales, both of which play a critical role in snake locomotion

Molecular identification of small cetacean samples from Peruvian fish markets

In the last 60years, incidental entanglement in fishing gears (so called by-catch) became the main cause of mortality worldwide for small cetaceans and is pushing several populations and species to the verge of extinction. Thus, monitoring and quantifying by-catches is an important step towards proper and sustainable management of cetacean populations. Continuous studies indicated that by-catches and directed takes of small cetaceans in Peru greatly increased since 1985. Legal measures banning cetacean takes, enforced in 1994 and 1996, ironically made monitoring highly problematic as fishers continue catching these animals but utilize or dispose of carcasses clandestinely. Hence, in locations where cetaceans are landed covertly or already butchered, molecular genetic methods can provide the only means of identification of the species, sex, and sometimes the population of each sample. Here, we generate and analyse a fragment of the mitochondrial DNA cytochrome b gene and 5 nuclear microsatellite markers from 182 meat and skin samples of unidentified small cetaceans collected at three Peruvian markets between July 2006 and April 2007. Our results, compared to past surveys, indicate that Lagenorhynchus obscurus, Phocoena spinipinnis, Tursiops truncatus, Delphinus capensis, and D. delphis continue to be caught and marketed, but that the relative incidence of P. spinipinnis is highly reduced, possibly because of population depletion. The small number of possible sampling duplicates demonstrates that a high monitoring frequency is required for a thorough evaluation of incidental catches in the area. A wide public debate on by-catch mitigation measures is greatly warranted in Per