How old are bacterial pathogens?

Only few molecular studies have addressed the age of bacterial pathogens that infected humans before the beginnings of medical bacteriology, but these have provided dramatic insights. The global genetic diversity of Helicobacter pylori, which infects human stomachs, parallels that of its human host. The time to the most recent common ancestor (tMRCA) of these bacteria approximates that of anatomically modern humans, i.e. at least 100 000 years, after calibrating the evolutionary divergence within H. pylori against major ancient human migrations. Similarly, genomic reconstructions of Mycobacterium tuberculosis, the cause of tuberculosis, from ancient skeletons in South America and mummies in Hungary support estimates of less than 6000 years for the tMRCA of M. tuberculosis. Finally, modern global patterns of genetic diversity and ancient DNA studies indicate that during the last 5000 years plague caused by Yersinia pestis has spread globally on multiple occasions from China and Central Asia. Such tMRCA estimates provide only lower bounds on the ages of bacterial pathogens, and additional studies are needed for realistic upper bounds on how long humans and animals have suffered from bacterial diseases.     

How old are you now?

Cherkas et al . provide a new, biological approach to a classic problem in anthropology – the estimation of age.     

How old are the extant lineages of Toxoplasma gondii?

Most known isolates of Toxoplasma gondii belong to one of only three lineages, which are presumed to be clonal. Three models have been proposed for the evolutionary relationship of these lineages to the other extant lineages: Model (a) proposing that all lineages are derived from a most recent common ancestor (MRCA) in the distant past, Model (b) that all lineages are derived from a MRCA in the very recent past, and Model (c) that the clonal lineages share a recent MRCA but are related to the other lineages only in the distant past. Here, I test these models using DNA intron and coding-sequence data for loci at 14 genes, using three different methods to calculate the time of the MRCA. All of the calculations agree that the MRCA of the clonal lineages was > 70% of the age of the MRCA of all lineages, thus favouring Model (a). The MRCA may have existed approximately 150,000 years ago, with the clonal lineages expanding in prevalence approximately 10,000 years ago.     

How novel are the chemical weapons of garlic mustard in North American forest understories?

The Novel Weapons Hypothesis predicts that invasive plants excel in their new ranges because they produce novel metabolites to which native species possess little resistance. We examined the novelty of the phytochemistry of the Eurasian invader, Alliaria petiolata, in North America by comparing its phytochemical profile with those of closely related Brassicaceae native to North America. We examined the profile and/or concentrations of glucosinolates, alliarinoside, flavonoids, cyanide, and trypsin inhibitors in cauline leaves of field-collected A. petiolata, Arabis laevigata, Cardamine concatenata, C. bulbosa, and C. douglassii. Cyanide and the glucosinolates and flavonoids produced by A. petiolata were detected only in A. petiolata. Trypsin inhibitor activity was highest in A. laevigata, intermediate in the Cardamine species, and lowest in A. petiolata. The phytochemical profile of A. petiolata was distinct from those of four closely related and/or abundant Brassicaceaeous species native to North America, providing support for the Novel Weapons Hypothesis.     

How old are you? Genet age estimates in a clonal animal

Foundation species such as redwoods, seagrasses and corals are often long‐lived and clonal. Genets may consist of hundreds of members (ramets) and originated hundreds to thousands of years ago. As climate change and other stressors exert selection pressure on species, the demography of populations changes. Yet, because size does not indicate age in clonal organisms, demographic models are missing data necessary to predict the resilience of many foundation species. Here, we correlate somatic mutations with genet age of corals and provide the first, preliminary estimates of genet age in a colonial animal. We observed somatic mutations at five microsatellite loci in rangewide samples of the endangered coral, Acropora palmata (n = 3352). Colonies harboured 342 unique mutations in 147 genets. Genet age ranged from 30 to 838 years assuming a mutation rate of 1.195^?04 per locus per year based on colony growth rates and 236 to 6500 years assuming a mutation rate of 1.542^?05 per locus per year based on sea level changes to habitat availability. Long‐lived A. palmata genets imply a large capacity to tolerate past environmental change, and yet recent mass mortality events in A. palmata suggest that capacity is now being frequently exceeded.     

Evolutionary origins of Gondwanan interactions: How old are Araucaria beetle herbivores?

Studies of a variety of phenomena, ranging from rates of molecular substitution to rates of diversification, draw on estimates of geological age. Studies incorporating estimates of timing from fossils or other geological evidence are largely of relatively young, Tertiary divergences, to which older systems may provide useful comparisons. One apparently old assemblage comprises the beetle groups associated with the ancient genus Araucaria that share comparable, ostensibly Gondwanan distributions with their host. Our previous studies suggested a possibly Cretaceous age for Araucaria associations in bark beetles. However, the absence of confirmed bark beetle fossils earlier than the Tertiary has been taken as evidence of Cretaceous absence, and their confirmed phylogenetic position within the primitively angiosperm-feeding weevil family rules out pre-angiosperm, Jurassic origins. Nevertheless, an early shift from angiosperms to Araucaria seemed plausible in the light of Araucaria fossil history which spans the Mesozoic since the Jurassic. To resolve the phylogenetic affinities and to estimate divergence times of the Australian and South American bark beetle genera affiliated with Araucaria we analysed DNA sequences of nuclear and mitochondrial genes: protein coding elongation factor alpha, enolase and cytochrome oxidase I. The most parsimonious reconstruction of the host relationships of Tomicini from the combined dataset corroborates the ancestral association with the genus Araucaria of both South American and Australian Tomicini. Bayesian estimation of divergence times indicates that the divergence between the Australian and the South American Araucaria-feeding taxa occurred at the very latest in the Cretaceous/Paleocene border and that the age of the first Scolytinae-Araucarsa association would then be during the later stages of the Late Cretaceous, while other known beetle/Araucaria associations are Jurassic.     

How Tough are Sclerophylls?

Fracture toughness was estimated for a 'least tough' path inthe leaves of woody species from three sclerophyllous plantcommunities. Most of the species from Mediterranean, tropicalheath forest and lowland tropical rain forest habitats had verytough leaves, with toughness generally 600-1300 J m^-2, whichis two to four times higher than soft-leaved tropical pioneertrees. The toughest leaf (2032 J m^-2), Parishia insignis, camefrom the canopy of the lowland rain forest. Leaves from theshaded understorey of the rain forest did not appear any lesstough than those from the canopy.Copyright 1993, 1999 AcademicPress Leaf fracture toughness, sclerophylly, Mediterranean vegetation, tropical forest     

How repetitive are genomes?

Background  

Genome sequences vary strongly in their repetitiveness and the causes for this are still debated. Here we propose a novel measure of genome repetitiveness, the index of repetitiveness, I _r, which can be computed in time proportional to the length of the sequences analyzed. We apply it to 336 genomes from all three domains of life.     

How reticulated are species?

Many groups of closely related species have reticulate phylogenies. Recent genomic analyses are showing this in many insects and vertebrates, as well as in microbes and plants. In microbes, lateral gene transfer is the dominant process that spoils strictly tree‐like phylogenies, but in multicellular eukaryotes hybridization and introgression among related species is probably more important. Because many species, including the ancestors of ancient major lineages, seem to evolve rapidly in adaptive radiations, some sexual compatibility may exist among them. Introgression and reticulation can thereby affect all parts of the tree of life, not just the recent species at the tips. Our understanding of adaptive evolution, speciation, phylogenetics, and comparative biology must adapt to these mostly recent findings. Introgression has important practical implications as well, not least for the management of genetically modified organisms in pest and disease control.     

How antigenic are antigenic peptides?

Most of a protein surface is potentially antigenic, consisting of numerous overlapping domains each complementary to antibody-combining sites. These domains may include peptide sequences that are demonstrably antigenic but only when antibodies from the appropriate host individuals and species are used. Methods for locating antigenic peptide sequences are described in which hydrophilic polyamide supports are used for peptide synthesis, then solid-phase radioimmunoassay with antisera and protein A. Most antigenic domains, however, comprise amino acid side chains contributed by two or more nearby polypeptide chains. Such domains can be identified by comparing the cross-reactivities of groups of very closely related proteins towards monoclonal antibodies raised to one of them. Such studies, using myoglobins, have identified a number of residues not previously shown to be antigenic and have provided a guide for the choice of synthetic peptides which are likely to carry several immunodominant side chains. One such peptide corresponding to residues (72–89) of beef myoglobin has been shown, using CD and antibodies to the parent protein, to have interesting conformational and antigenic properties. The peptide (25–55) is also antigenic.