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 E . coli and subjecting them to competitive growth. Contrary to expectations, we find that random sequences with bioactivity are not rare. In our experiments we find that up to 25% of the evaluated clones enhance the growth rate of their cells and up to 52% inhibit growth. Testing of individual clones in competition assays confirms their activity and provides an indication that their activity could be exerted either by the transcribed RNA or the translated peptide. This suggests that transcribed and translated random parts of the genome could indeed have a high potential to become functional. The results also suggest that random sequences may become an effective new source of molecules for studying cellular functions, as well as for pharmacological activity screening.

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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 sexual selection is unrelated to the ecological environment. We address this question using grasshopper species of the genus Chorthippus, which have evolved strong assortative mating while lacking noticeable eco-morphological divergence. Mitochondrial genomes suggest that the radiation is relatively recent, dating to the mid-Pleistocene, which leads to extensive incomplete lineage sorting throughout the mitochondrial and the nuclear genomes. Nuclear data show extremely low genomic differentiation among species, yet hybrids are absent in sympatric localities. Demographic analyses shed some light into these seemingly contradictory patterns. The estimated demographic model shows a long period of geographic isolation, followed by secondary contact and extensive introgression. This suggests that an initial period of geographic isolation might favor the coupling of male signaling and female

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. At the 3′ end of introns, the splice signal nearly universally contains the dimer AG, which consists of purines, and the polypyrimidine tract upstream of this 3′ splice signal is characterized by over‐representation of pyrimidines. If the over‐representation of pyrimidines in the polypyrimidine tract is also due to avoidance of a premature splicing signal, we hypothesize that AG should be the most under‐represented dimer. Through the use of DNA‐strand asymmetry patterns, we confirm this prediction in fruit flies of the genus Drosophila and by comparing the asymmetry patterns to a presumably neutrally evolving region, we quantify the selection strength acting on each motif. Moreover, our inference and simulation method revealed that the best explanation for the base composition evolution of the polypyrimidine tract is the joint action of purifying selection against a spurious 3′ splice signal and the selection for pyrimidines. Patterns of asymmetry in other eukaryotes indicate that avoidance of premature splicing similarly affects the nucleotide composition in their polypyrimidine tracts.

Population genetic inference of selection on the nucleotide sequence level often assumes comparison to unconstrained nucleotide sites, 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 favoring GC bases, likely due to GC-biased gene conversion (gBGC), and for the effect of linked selection. Here, we use polymorphism and divergence data of Drosophila melanogaster to detect and describe the forces affecting the evolution the 5SI. We separately analyze mutation classes, compare them between chromosomes, and relate them to recombination rate frequencies. GC-conservative mutations seem to be mainly influenced by mutation and drift, while linked selection mostly causes differences between the central and the peripheral (i.e., telomeric and centromeric) regions of the chromosome arms. Comparing GC-conservative mutation patterns between autosomes and the X chromosome, showed differences in mutation rates, rather than linked selection, in the central chromosomal regions after accounting for differences in autosomal and X chromosomal effective populations sizes. On the other hand, GC-changing mutations show asymmetric site frequency spectra, indicating the presence of gBGC, varying among mutation classes and in amount along chromosomes, but approximately equal in strength in autosomes and the X chromosome.

Among eukaryotes, the major spliceosomal pathway is highly conserved. Long introns may contain additional regulatory sequences, but those in short introns seem to be nearly exclusively related to splicing. While regulatory sequences involved in splicing are well-characterized, little is known about their evolution. At the 3' end of introns, the splice signal nearly universally contains the dimer AG, which consists of purines. The polypyrimidine tract upstream of the 3' splice signal is characterized by over-representation of the pyrimidine bases cytosine and thymine. We hypothesize that the over-representation of pyrimidines in the polypyrimidine tract is caused by avoidance of a premature splicing signal- AG should be most under-represented dimer. DNA-strand asymmetry patterns in fruit flies of the genus Drosophila confirm this prediction. In short introns of Drosophila, a region between the 5' splice signal and the branch point, which at least contains the nucleotides 8-30, is considered to evolve neutrally. Comparing this presumably neutrally evolving region to the polypyrimidine tract, we infer a moderate scaled selection strength below four against 3' splicing signals. Patterns of asymmetry in other eukaryotes indicate that avoidance of premature splicing similarly affects the nucleotide composition in their polypyrimidine tracts.