Population structure in an isolated Arctic fox, Vulpes lagopus, population: the impact of geographical barriers

The genetic composition of a population reflects several aspects of the organism and its environment. The Icelandic Arctic fox population exceeds 8000 individuals and is comprised of both coastal and inland foxes. Several factors may affect within-population movement and subsequent genetic population structure. A narrow isthmus and sheep-proof fences may prevent movement between the north-western and central part and glacial rivers may reduce movement between the eastern and central part of Iceland. Moreover, population density and habitat characteristics can influence movement behaviour further. Here, we investigate the genetic structure in the Icelandic Arctic fox population ( n  = 108) using 10 microsatellite loci. Despite large glacial rivers, we found low divergence between the central and eastern part, suggesting extensive movement between these areas. However, both model- and frequency-based analyses suggest that the north-western part is genetically differentiated from the rest of Iceland (F_ST = 0.04, D_S = 0.094), corresponding to 100–200 generations of complete isolation. This suggests that the fences cannot be the sole cause of divergence. Rather, the isthmus causes limited movement between the regions, implying that protection in the Hornstrandir Nature Reserve has a minimal impact on Arctic fox population size in the rest of Iceland.  © 2009 The Linnean Society of London, Biological Journal of the Linnean Society , 2009, 97 , 18–26.     

Improved profile HMM performance by assessment of critical algorithmic features in SAM and HMMER

Background  

Profile hidden Markov model (HMM) techniques are among the most powerful methods for protein homology detection. Yet, the critical features for successful modelling are not fully known. In the present work we approached this by using two of the most popular HMM packages: SAM and HMMER. The programs' abilities to build models and score sequences were compared on a SCOP/Pfam based test set. The comparison was done separately for local and global HMM scoring.