Biology subjects

Lopez, D.

Publications and source records attributed to Lopez, D..

2 recordsLinked to original sources

bioRxiv2017

A Phylogenomic Study Quantifies Competing Mechanisms for Pseudogenization in Prokaryotes

BackgroundPseudogenes are non-functional sequences in the genome with homologous sequences that are functional (i.e. genes). They are abundant in eukaryotes where they have been extensively investigated, while in prokaryotes they are significantly scarcer and less well studied. Here we conduct a comprehensive analysis of the evolution of pseudogenes in prokaryotes. For this analysis we consider a broad range of bacteria, but also focus on the leprosy pathogen Mycobacterium leprae, which contains an unusually large number of pseudogenes which comprise approximately 40% of its entire genome.\n\nResultsWe have developed an informatics-based approach to characterize the evolution of pseudogenes. This approach combines tools from phylogenomics, genomics, and transcriptomics. The results we obtain suggest the presence of two mechanisms for pseudogene formation: failed horizontal gene transfer events and disruption of native genes.\n\nConclusionsWe conclude that while in most bacteria the former is most likely responsible for the majority of pseudogenization events, in mycobacteria, and in particular in M. leprae with its exceptionally high pseudogene numbers, the latter predominates. We believe that our study sheds new light on the evolution of pseudogenes in bacteria, by utilizing new methodologies that are applied to the unusually abundant M. leprae pseudogenes and their orthologs. As such, we anticipate that it will be of broad interest to both evolutionary biologists as well as microbiologists.

evolutionary biology↗

bioRxiv2017

Food Webs Over Time: Evaluating The Variability Of Degree Distribution On Ecological Networks

Although networks analysis has moved from static to dynamic, ecological networks are still analyzed as time-aggregated units where time-specific interactions are aggregated into one single network. As a result, several questions arise such as what is the functional form of and how variable is the topology of time-specific versus time-aggregated ecological networks? Furthermore, it is yet unknown to what extent the structure of time-aggregated networks is representative of the dynamics of the community. Here, we compared the topology of time-specific and time-aggregated networks by analyzing a set of intertidal networks containing more than 1,000 interactions, and assessed the spatiotemporal dynamics of their degree distributions. By fitting different distribution models, we found that the out-degree distributions of seasonal and time-aggregated networks were best described by an exponential model while the in-degree distributions were best described by a discrete generalized beta model. The degree distributions of the seasonal networks were highly temporally variable and are significantly different from those of time-aggregated networks. We observed that seasonal degree distributions converged toward time-aggregated network distributions after 1.5 years of sampling. Our results highlight the importance of understanding the dynamics of ecological networks, which can show topological characteristics significantly different from those of time-aggregated networks.

ecology↗