Statistical method for testing the neutral mutation hypothesis by DNA polymorphism.

As more complete genomes are sequenced, phylogenetic analysis is entering a new era — that of phylogenomics. One branch of this expanding field aims to reconstruct the evolutionary history of organisms on the basis of the analysis of their genomes. Recent studies have demonstrated the power of this approach, which has the potential to provide answers to several fundamental evolutionary questions. However, challenges for the future have also been revealed. The very nature of the evolutionary history of organisms and the limitations of current phylogenetic reconstruction methods mean that part of the tree of life might prove difficult, if not impossible, to resolve with confidence.

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Phylogenomics and the reconstruction of the tree of life.

The mitochondrial (mt) genome is, to date, the most extensively studied genomic system in insects, outnumbering nuclear genomes tenfold and representing all orders versus very few. Phylogenomic analysis methods have been tested extensively, identifying compositional bias and rate variation, both within and between lineages, as the principal issues confronting accurate analyses. Major studies at both inter- and intraordinal levels have contributed to our understanding of phylogenetic relationships within many groups. Genome rearrangements are an additional data type for defining relationships, with rearrangement synapomorphies identified across multiple orders and at many different taxonomic levels. Hymenoptera and Psocodea have greatly elevated rates of rearrangement offering both opportunities and pitfalls for identifying rearrangement synapomorphies in each group. Finally, insects are model systems for studying aberrant mt genomes, including truncated tRNAs and multichromosomal genomes. Greater integration of nuclear and mt genomic studies is necessary to further our understanding of insect genomic evolution.

Insect Mitochondrial Genomics: Implications for Evolution and Phylogeny

Germ cells play a unique role in gamete production, heredity and evolution. Therefore, to understand the mechanisms that specify germ cells is a central challenge in developmental and evolutionary biology. Data from model organisms show that germ cells can be specified either by maternally inherited determinants (preformation) or by inductive signals (epigenesis). Here we review existing data on 28 metazoan phyla, which indicate that although preformation is seen in most model organisms, it is actually the less prevalent mode of germ cell specification, and that epigenetic germ cell specification may be ancestral to the Metazoa.

/pdf/mechanisms-of-germ-cell-specification-across-the-metazoans-30rvm8f91n.pdf

Mechanisms of germ cell specification across the metazoans: epigenesis and preformation

DNA data has been widely used in animal phylogenetic studies over the past 15 years. Here we review how these studies have used advances in knowledge of molecular evolutionary processes to create more realistic models of evolution, evaluate the information content of data, test phylogenetic hypotheses, attach time to phylogenies, and understand the relative usefulness of mitochondrial and nuclear genes. We also provide a new compilation of conserved polymerase chain reaction (PCR) primers for mitochondrial genes that complements our earlier compilation.

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Incorporating molecular evolution into phylogenetic analysis, and a new compilation of conserved polymerase chain reaction primers for animal mitochondrial DNA

Recent morphological and molecular evidence has changed interpretations of arthropod phylogeny and evolution. Here we compare complete mitochondrial genomes to show that Collembola, a wingless group traditionally considered as basal to all insects, appears instead to constitute a separate evolutionary lineage that branched much earlier than the separation of many crustaceans and insects and independently adapted to life on land. Therefore, the taxon Hexapoda, as commonly defined to include all six-legged arthropods, is not monophyletic.

http://science.sciencemag.org/content/sci/299/5614/1887.full.pdf

Hexapod Origins: Monophyletic or Paraphyletic?

Adequate stress response is a critical factor during athlete horses' training and is central to our capacity to obtain better performances while safeguarding animal welfare. In order to investigate the molecular mechanisms underlying this process, several studies have been conducted that take advantage of microarray and quantitative real-time PCR (qRT-PCR) technologies to analyse the expression of candidate genes involved in the cellular stress response. Appropriate application of qRT-PCR, however, requires the use of reference genes whose level of expression is not affected by the test, by general physiological conditions or by inter-individual variability. The expression of nine potential reference genes was evaluated in lymphocytes of ten endurance horses during strenuous exercise. These genes were tested by qRT-PCR and ranked according to the stability of their expression using three different methods (implemented in geNorm, NormFinder and BestKeeper). Succinate dehydrogenase complex subunit A (SDHA) and hypoxanthine phosphoribosyltransferase (HPRT) always ranked as the two most stably expressed genes. On the other hand, glyceraldehyde-3-phosphate dehydrogenase (GAPDH), transferrin receptor (TFRC) and ribosomal protein L32 (RPL32) were constantly classified as the less reliable controls. This study underlines the importance of a careful selection of reference genes for qRT-PCR studies of exercise induced stress in horses. Our results, based on different algorithms and analytical procedures, clearly indicate SDHA and HPRT as the most stable reference genes of our pool.

/pdf/exercise-induced-stress-in-horses-selection-of-the-most-41c126yqze.pdf

Exercise induced stress in horses: Selection of the most stable reference genes for quantitative RT-PCR normalization

Background
Odontocete cetaceans occupy the top position of the marine food-web and are particularly sensitive to the bioaccumulation of lipophilic contaminants. The effects of environmental pollution on these species are highly debated and various ecotoxicological studies have addressed the impact of xenobiotic compounds on marine mammals, raising conservational concerns. Despite its sensitivity, quantitative real-time PCR (qRT-PCR) has never been used to quantify gene induction caused by exposure of cetaceans to contaminants. A limitation for the application of qRT-PCR is the need for appropriate reference genes which allow the correct quantification of gene expression. A systematic evaluation of potential reference genes in cetacean skin biopsies is presented, in order to validate future qRT-PCR studies aiming at using the expression of selected genes as non-lethal biomarkers.

/pdf/selection-of-reference-genes-for-quantitative-rt-pcr-studies-4de8mnsi54.pdf

Selection of reference genes for quantitative RT-PCR studies in striped dolphin (Stenella coeruleoalba) skin biopsies

Background
Besides functioning as chemosensors for a broad range of endogenous and synthetic ligands, transient receptor potential vanilloid (TRPV) 1–4 channels have also been related to capsaicin (TRPV1), pain, and thermal stimuli perception, and itching sensation (TRPV1–4). While the expression of the TRPV1–4 genes has been adequately proved in skin, sensory fibres and keratinocytes, less is known about TRPV3 and TRPV4 expression in human blood cells.

/pdf/quantitative-real-time-pcr-detection-of-trpv1-4-gene-5fbxjfoo2v.pdf

Quantitative Real-Time PCR detection of TRPV1–4 gene expression in human leukocytes from healthy and hyposensitive subjects

We carried out a phylogeographic study using mtDNA (COII) for the endemic springtail Desoria klovstadi (formerly Isotoma klovstadi) from northern Victoria Land, Antarctica. Low levels of sequence divergence (≤ 1.6%) across 26 unique haplotypes (from 69 individuals) were distributed according to geographic location. Cape Hallett and Daniell Peninsula contained the highest nucleotide (both > 0.004) and haplotype (both > 0.9) diversity with 10 (of 16) and 8 (of 12) unique haplotypes, respectively. All other populations (Football Saddle, Crater Cirque, Cape Jones) had lower diversity with 2–4 unique haplotypes. Across the 69 individuals from five populations there was only a single haplotype shared between two populations (Daniell Peninsula and Football Saddle). Furthermore, nested clade analyses revealed that some of the Daniell Peninsula haplotypes were more closely related to Football Saddle haplotypes than to any other population. Such discrete haplotype groupings suggest historical (rare) dispersal across the Pleistocene (1.8 mya−11 kya) and Holocene (11 kya–present), coupled with repeated extinction, range contraction and expansion events, and/or incomplete sampling across the species range. The nested clade analyses reveal that a common pattern of climatic and geological history over long-term glacial habitat fragmentation has determined the geographic and haplotype distributions found for D. klovstadi.

Phylogeographic structure suggests multiple glacial refugia in northern Victoria Land for the endemic Antarctic springtail Desoria klovstadi (Collembola, Isotomidae)

Giacomo Spinsanti

Papers

Hexapod Origins: Monophyletic or Paraphyletic?

Exercise induced stress in horses: Selection of the most stable reference genes for quantitative RT-PCR normalization

Selection of reference genes for quantitative RT-PCR studies in striped dolphin (Stenella coeruleoalba) skin biopsies

Quantitative Real-Time PCR detection of TRPV1–4 gene expression in human leukocytes from healthy and hyposensitive subjects

Phylogeographic structure suggests multiple glacial refugia in northern Victoria Land for the endemic Antarctic springtail Desoria klovstadi (Collembola, Isotomidae)