Mitochondrial phylogeography of the moor frog, Rana arvalis
The geographical distribution and genealogical relationships between haplotypes from the AI lineage indicate that this group had two glacial refugia, one located in the eastern part of the CB and the other probably in southern Russia.
Does reduced MHC diversity decrease viability of vertebrate populations?
New generation sequencers as a tool for genotyping of highly polymorphic multilocus MHC system
The parallel 454 sequencing can be an efficient genotyping platform for MHC and provides an alternative to classical genotypesing methods, and procedures to identify the threshold that can be used to reduce number of genotyped errors by eliminating most of artefactual alleles (AA).
Methods for MHC genotyping in non‐model vertebrates
- W. Babik
- BiologyMolecular Ecology Resources
- 1 March 2010
This review addresses the well established typing methods such as the Single Strand Conformation Polymorphism (SSCP), Denaturing Gradient Gel Electrophoresis (DGGE), ReferenceStrand Conformational Analysis (RSCA) and cloning of PCR products and includes the intriguing possibility of direct amplicon sequencing followed by the computational inference of alleles and also next generation sequencing (NGS) technologies.
Phylogeography of two European newt species — discordance between mtDNA and morphology
Patterns of sequence variation within clades suggested long‐term demographic stability in the southern groups, moderate and relatively old demographic growth in the populations inhabiting central Europe, and high growth in some of the groups that colonized northern parts of Europe after the last glacial maximum.
454 sequencing reveals extreme complexity of the class II Major Histocompatibility Complex in the collared flycatcher
- M. Zagalska‐Neubauer, W. Babik, M. Stuglik, L. Gustafsson, M. Cichoń, J. Radwan
- BiologyBMC Evolutionary Biology
- 31 December 2010
Next generation sequencing offers a universal, affordable method for the characterization and, in perspective, genotyping of MHC systems of virtually any complexity and is an effective tool for advancing the understanding of the MHC class II structure and evolutionary patterns in Passeriformes.
Detecting balancing selection in genomes: limits and prospects
The results of recent theoretical studies suggest that balancing selection may be ubiquitous but transient, leaving few signatures detectable by existing methods, and novel solutions, recently developed model‐based approaches and good practices that should be implemented in future studies looking for signals of balancing selection are emphasized.
Phylogeography of the fire‐bellied toads Bombina: independent Pleistocene histories inferred from mitochondrial genomes
- S. Hofman, C. Spolsky, T. Uzzell, D. Cogǎlniceanu, W. Babik, J. Szymura
- BiologyMolecular Ecology
- 1 June 2007
Deep divergence among European Bombina lineages suggests their preglacial origin, and implies long and largely independent evolutionary histories of the species, as well as drastic reductions of population sizes during the last glacial period, and significant demographic growth related to postglacial colonization.
Effects of an MHC‐DRB genotype and allele number on the load of gut parasites in the bank vole Myodes glareolus
The finding of two significant associations between MHC alleles and the intensity of the infection with the most prevalent nematode, Aspiculuris tetraptera, suggests that the directions of selection can differ between populations connected by a low level of gene flow, which may contribute to the maintenance of high DRB allele diversity.
Evaluation of two approaches to genotyping major histocompatibility complex class I in a passerine—CE‐SSCP and 454 pyrosequencing
- M. Promerová, W. Babik, J. Bryja, T. Albrecht, M. Stuglik, J. Radwan
- BiologyMolecular Ecology Resources
- 1 March 2012
In systems with highly duplicated MHC, 454 provides more reliable information on individual diversity than CE‐SSCP, and numbers of alleles detected by both methods are significantly correlated, although the correlation is weak.