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Open AccessA burst of genomic innovation at the origin of placental mammals mediated embryo implantation
The origin of embryo implantation in mammals ~148 million years ago was a dramatic shift in reproductive strategy, yet the molecular changes that established mammal implantation are largely unknown. Although p...
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Pangenomes and Selection: The Public Goods Hypothesis
The evolution and structure of prokaryotic genomes are largely shaped by horizontal gene transfer. This process is so prevalent that DNA can be seen as a public good—a resource that is shared across individua...
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Open AccessStrigolactone synthesis is ancestral in land plants, but canonical strigolactone signalling is a flowering plant innovation
Strigolactones (SLs) are an important class of carotenoid-derived signalling molecule in plants, which function both as exogenous signals in the rhizosphere and as endogenous plant hormones. In flowering plant...
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Reply to ‘The population genetics of pangenomes’
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Open AccessErratum to: Positive selection neighboring functionally essential sites and disease-implicated regions of mammalian reproductive proteins
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Open AccessErratum to: Surface layer proteins from virulent Clostridium difficile ribotypes exhibit signatures of positive selection with consequences for innate immune response
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Why prokaryotes have pangenomes
The existence of large amounts of within-species genome content variability is puzzling. Population genetics tells us that fitness effects of new variants—either deleterious, neutral or advantageous—combined w...
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Open AccessSurface layer proteins from virulent Clostridium difficile ribotypes exhibit signatures of positive selection with consequences for innate immune response
Clostridium difficile is a nosocomial pathogen prevalent in hospitals worldwide and increasingly common in the community. Sequence differences have been shown to be present in the Surf...
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Mind the gaps in cellular evolution
Eukaryotic cells, with complex features such as membrane-bound nuclei, evolved from prokaryotic cells that lack these components. A newly identified prokaryotic group reveals intermediate steps in eukaryotic-c...
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Mitochondrial data are not suitable for resolving placental mammal phylogeny
Mitochondrial data have traditionally been used in reconstructing a variety of species phylogenies. The low rates of recombination and thorough characterization of mitochondrial data across vertebrate species ...
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Ghost locus appears
The sequences of two sponge genomes provide evidence that the ParaHox developmental genes are older than previously thought. This has implications for animal taxonomy and for developmental and evolutionary bio...
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The hybrid nature of the Eukaryota and a consilient view of life on Earth
McInerney and colleagues summarize the phylogenetic, cell biological, population biology, biochemical and paleontological evidence that cellular life consists of two primary, paraphyletic, prokaryotic groups a...
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Open AccessMolecular adaptation of telomere associated genes in mammals
Placental mammals display a huge range of life history traits, including size, longevity, metabolic rate and germ line generation time. Although a number of general trends have been proposed between these trai...
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Open AccessCucurbitacin I blocks cerebrospinal fluid and platelet derived growth factor-BB stimulation of leptomeningeal and meningioma DNA synthesis
Currently, there are no consistently effective chemotherapies for recurrent and inoperable meningiomas. Recently, cucurbitacin I (JSI-124), a naturally occurring tetracyclic triterpenoid compound used as folk ...
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Open AccessSimultaneous miRNA and mRNA transcriptome profiling of human myoblasts reveals a novel set of myogenic differentiation-associated miRNAs and their target genes
miRNA profiling performed in myogenic cells and biopsies from skeletal muscles has previously identified miRNAs involved in myogenesis.
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Open AccessIn Arabidopsis thaliana codon volatility scores reflect GC3 composition rather than selective pressure
Synonymous codon usage bias has typically been correlated with, and attributed to translational efficiency. However, there are other pressures on genomic sequence composition that can affect codon usage patter...
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Open AccessColon cancer associated genes exhibit signatures of positive selection at functionally significant positions
Cancer, much like most human disease, is routinely studied by utilizing model organisms. Of these model organisms, mice are often dominant. However, our assumptions of functional equivalence fail to consider t...
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Open AccessThe public goods hypothesis for the evolution of life on Earth
It is becoming increasingly difficult to reconcile the observed extent of horizontal gene transfers with the central metaphor of a great tree uniting all evolving entities on the planet. In this manuscript we ...
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Analysis of transforming growth factor β receptor expression and signaling in higher grade meningiomas
TGF-β receptors (TGF-βRs) inhibit growth of many cell types. Loss of TGF-βRs or its signaling components have been found in several human malignancies. The expression and the role of TGF-βRs in regulating anap...
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Selection and the Cell Cycle: Positive Darwinian Selection in a Well-Known DNA Damage Response Pathway
Cancer is a common occurrence in multi-cellular organisms and is not strictly limited to the elderly in a population. It is therefore possible that individuals with genotypes that protect against early onset c...
