Inference of genomic landscapes using ordered Hidden Markov Models with emission densities (oHMMed).

Background: Genomes are inherently inhomogeneous, with features such as base composition, recombination, gene density, and gene expression varying along chromosomes. Evolutionary, biological, and biomedical analyses aim to quantify this variation, account for it during inference procedures, and ultimately determine the causal processes behind it. Since sequential observations along chromosomes are not independent, it is unsurprising that autocorrelation patterns have been observed e.

The influence of GC-biased gene conversion on non-adaptive sequence evolution in short introns of Drosophila melanogaster.

Population genetic inference of selection on the nucleotide sequence level often proceeds by comparison to a reference sequence evolving only under mutation and population demography. Among the few candidates for such a reference sequence is the 5' part of short introns (5SI) in Drosophila. In addition to mutation and population demography, however, there is evidence for a weak force favouring GC bases, likely due to GC-biased gene conversion (gBGC), and for the effect of linked selection.

Purifying selection against spurious splicing signals contributes to the base composition evolution of the polypyrimidine tract.

Among eukaryotes, the major spliceosomal pathway is highly conserved. While long introns may contain additional regulatory sequences, the ones in short introns seem to be nearly exclusively related to splicing. Although these regulatory sequences involved in splicing are well-characterized, little is known about their evolution.

Historical isolation facilitates species radiation by sexual selection: Insights from Chorthippus grasshoppers.

Theoretical and empirical studies have shown that species radiations are facilitated when a trait under divergent natural selection is also involved in sexual selection. It is yet unclear how quick and effective radiations are where assortative mating is unrelated to the ecological environment and primarily results from sexual selection. We address this question using sympatric grasshopper species of the genus Chorthippus, which have evolved strong behavioural isolation while lacking noticeable ecomorphological divergence.

Random sequences are an abundant source of bioactive RNAs or peptides.

It is generally assumed that new genes arise through duplication and/or recombination of existing genes. The probability that a new functional gene could arise out of random non-coding DNA is so far considered to be negligible, since it seems unlikely that such a RNA or protein sequence could have an initial function that influences the fitness of an organism. We have here tested this question systematically, by expressing clones with random sequences in and subjecting them to competitive growth.