3,134 publications from this institution
Our results highlight the need for more accurate phylogenetic network methods and the importance of detecting and accounting for recombination in phylogenetic studies. Furthermore, we provide useful information for choosing a network algorithm and a framework in which to evaluate improvements to existing methods and novel algorithms developed in the future.
Abstract Motivation: Models of molecular evolution aim at describing the evolutionary processes at the molecular level. However, current models rarely incorporate information from protein structure. Conversely, structure-based models of protein evolution have not been commonly applied to simulate sequence evolution in a phylogenetic framework, and they often ignore relevant evolutionary processes such as recombination. A simulation evolutionary framework that integrates substitution models that account for protein structure stability should be able to generate more realistic in silico evolved proteins for a variety of purposes. Results: We developed a method to simulate protein evolution that combines models of protein folding stability, such that the fitness depends on the stability of the native state both with respect to unfolding and misfolding, with phylogenetic histories that can be either specified by the user or simulated with the coalescent under complex evolutionary scenarios, including recombination, demographics and migration. We have implemented this framework in a computer program called ProteinEvolver. Remarkably, comparing these models with empirical amino acid replacement models, we found that the former produce amino acid distributions closer to distributions observed in real protein families, and proteins that are predicted to be more stable. Therefore, we conclude that evolutionary models that consider protein stability and realistic evolutionary histories constitute a better approximation of the real evolutionary process. Availability: ProteinEvolver is written in C, can run in parallel and is freely available from http://code.google.com/p/proteinevolver/. Contact: marenas@cbm.uam.es Supplementary information: Supplementary data are available at Bioinformatics online.
Abstract The populations of Atlantic salmon in the Ulla and Lérez rivers, located in Galicia in northwestern Spain, were close to extinction early in the 1990s. A restoration programme involving supportive breeding has been conducted since 1995, using a mixture of salmon populations from several Galician rivers. The programme utilizes progeny of adults returning to the rivers and wild parr reared in fresh water until maturity. Five microsatellite loci were used to compare genetic variability in the restored populations with that in populations before their collapse in the 1950s. DNA samples were obtained from scale collections (old samples) and from tissue samples of live fish caught in the rivers (modern samples). Average heterozygosities and allelic richness are very similar in modern and old samples. Populations inhabiting the Ulla and Lérez rivers today are more similar than they were in the past, possibly because they originated in the same stock mixture.
Hermida, R. C.1; Calvo, C.2; Ayala, D. E.1; Dominguez, M. J.2; Covelo, M.2; Mojon, A.1; Fernandez, J. R.1; Fontao, M. J.1; Soler, R.1; Lopez, J. E.2 Author Information
Omega-9 fatty acids represent some of the main mono-unsaturated fatty acids (MUFA) found in plant and animal sources.
On behalf of the editorial board, we are proud to announce the launching of the open access journal Sustainable Food Production (SFP) published and owned by the Publishing house SciPress Ltd, Switzerland.
We studied the relative role of genetic determination versus plastic response for traits involved in ecological adaptation of two ecotypes of Littorina saxatilis living at different shore levels. To investigate the magnitude of the plastic response across ontogeny, we compared morphological data from individuals grown in the laboratory and taken from the wild at three developmental stages: shelled embryos, juveniles, and adults. The results indicate that most shell shape variation (72-99%) in adaptive traits (globosity and aperture of the shell) is explained by the ecotype irrespective of the growth environment, suggesting that direct genetic determination is the main factor responsible for the process of adaptation in the wild. There was a tendency for the contribution of plasticity to increase over ontogeny but, in general, the direction of the plastic response did not suggest that this was adaptive.
