Demographic processes in the montane Atlantic rainforest: Molecular and cytogenetic evidence from the endemic frog Proceratophrys boiei

Historical climatic refugia predict genetic diversity in lowland endemics of the Brazilian Atlantic rainforest. Yet, available data reveal distinct biological responses to the Last Glacial Maximum (LGM) conditions across species of different altitudinal ranges. We show that species occupying Brazil's montane forests were significantly less affected by LGM conditions relative to lowland specialists, but that pre-Pleistocene tectonics greatly influenced their geographic variation. Our conclusions are based on palaeoclimatic distribution models, molecular sequences of the cytochrome b, 16S, and RAG-1 genes, and karyotype data for the endemic frog Proceratophrys boiei. DNA and chromosomal data identify in P. boiei at least two broadly divergent phylogroups, which have not been distinguished morphologically. Cytogenetic results also indicate an area of hybridization in southern Sao Paulo. The location of the phylogeographic break broadly matches the location of a NW-SE fault, which underwent reactivation in the Neogene and led to remarkable landscape changes in southeastern Brazil. Our results point to different mechanisms underpinning diversity patterns in lowland versus montane tropical taxa, and help us to understand the processes responsible for the large number of narrow endemics currently observed in montane areas of the southern Atlantic forest hotspot. (C) 2011 Elsevier Inc. All rights reserved.

A rigorous approach to facilitate and guarantee the correctness of the genetic testing management in human genome information systems

Abstract Background Recent medical and biological technology advances have stimulated the development of new testing systems that have been providing huge, varied amounts of molecular and clinical data. Growing data volumes pose significant challenges for information processing systems in research centers. Additionally, the routines of genomics laboratory are typically characterized by high parallelism in testing and constant procedure changes. Results This paper describes a formal approach to address this challenge through the implementation of a genetic testing management system applied to human genome laboratory. We introduced the Human Genome Research Center Information System (CEGH) in Brazil, a system that is able to support constant changes in human genome testing and can provide patients updated results based on the most recent and validated genetic knowledge. Our approach uses a common repository for process planning to ensure reusability, specification, instantiation, monitoring, and execution of processes, which are defined using a relational database and rigorous control flow specifications based on process algebra (ACP). The main difference between our approach and related works is that we were able to join two important aspects: 1) process scalability achieved through relational database implementation, and 2) correctness of processes using process algebra. Furthermore, the software allows end users to define genetic testing without requiring any knowledge about business process notation or process algebra. Conclusions This paper presents the CEGH information system that is a Laboratory Information Management System (LIMS) based on a formal framework to support genetic testing management for Mendelian disorder studies. We have proved the feasibility and showed usability benefits of a rigorous approach that is able to specify, validate, and perform genetic testing using easy end user interfaces.