BioMed Research International: Evolutionary Biology http://www.hindawi.com The latest articles from Hindawi Publishing Corporation © 2014 , Hindawi Publishing Corporation . All rights reserved. Genetic Diversity and Distribution of Human Norovirus in China (1999–2011) Tue, 21 Jan 2014 12:34:18 +0000 http://www.hindawi.com/journals/bmri/2014/196169/ Noroviruses (NoVs) are a leading cause of epidemic and sporadic acute gastroenteritis worldwide. However, the genetic diversity and geographical distribution of NoV isolates from China have not been well described thus far. In this study, all NoV sequences obtained in China from 1999 to 2011 (), both partial and complete genomes, were downloaded from GenBank. Genotyping and phylogenetic and recombination analyses were performed in order to gain a better understanding of the distribution and genetic diversity of NoVs in China. The results indicated that approximately 90% of NoV sequences were obtained from the coastal regions of China, and most of the NoV sequences from distinct geographical regions appeared to be closely related. GII.4 was the most prevalent genotype, accounting for 64.4% of all genotypes, followed by GII.12 (13.9%) and GII.3 (7.0%). Over the last decade, the GII.4 variants were dominated by successive circulation of GII.4/2002, GII.4/2004, GII.4/2006b, and GII.4/2008, with GII.4/2006b continuing to date. A relatively high frequency of NoV intergenotype recombinants was identified. The most common ORF1/ORF2 intergenotype recombinant was GII.12/GII.4 (), and the relative frequency was up to 30% among all the recombinant strains (). These findings may aid in the evaluation and implementation of appropriate measures for monitoring NoV infectious diseases in China. Yongxin Yu, Shuling Yan, Bailin Li, Yingjie Pan, and Yongjie Wang Copyright © 2014 Yongxin Yu et al. All rights reserved. Genetic Structure and Preliminary Findings of Cryptic Diversity of the Malaysian Mahseer (Tor tambroides Valenciennes: Cyprinidae) Inferred from Mitochondrial DNA and Microsatellite Analyses Thu, 26 Dec 2013 14:27:42 +0000 http://www.hindawi.com/journals/bmri/2013/170980/ This study examines the population genetic structure of Tor tambroides, an important freshwater fish species in Malaysia, using fifteen polymorphic microsatellite loci and sequencing of 464 base pairs of the mitochondrial cytochrome c oxidase I (COI) gene. A total of 152 mahseer samples were collected from eight populations throughout the Malaysia river system. Microsatellites results found high levels of intrapopulation variations, but mitochondrial COI results found high levels of interpopulations differentiation. The possible reasons for their discrepancies might be the varying influence of genetic drift on each marker or the small sample sizes used in most of the populations. The Kelantan population showed very low levels of genetic variations using both mitochondrial and microsatellite analyses. Phylogenetic analysis of the COI gene found a unique haplotype (ER8*), possibly representing a cryptic lineage of T. douronensis, from the Endau-Rompin population. Nevertheless, the inclusion of nuclear microsatellite analyses could not fully resolve the genetic identity of haplotype ER8* in the present study. Overall, the findings showed a serious need for more comprehensive and larger scale samplings, especially in remote river systems, in combination with molecular analyses using multiple markers, in order to discover more cryptic lineages or undescribed “genetic species” of mahseer. Yuzine Esa and Khairul Adha Abdul Rahim Copyright © 2013 Yuzine Esa and Khairul Adha Abdul Rahim. All rights reserved. CpGislandEVO: A Database and Genome Browser for Comparative Evolutionary Genomics of CpG Islands Wed, 25 Sep 2013 13:19:42 +0000 http://www.hindawi.com/journals/bmri/2013/709042/ Hypomethylated, CpG-rich DNA segments (CpG islands, CGIs) are epigenome markers involved in key biological processes. Aberrant methylation is implicated in the appearance of several disorders as cancer, immunodeficiency, or centromere instability. Furthermore, methylation differences at promoter regions between human and chimpanzee strongly associate with genes involved in neurological/psychological disorders and cancers. Therefore, the evolutionary comparative analyses of CGIs can provide insights on the functional role of these epigenome markers in both health and disease. Given the lack of specific tools, we developed CpGislandEVO. Briefly, we first compile a database of statistically significant CGIs for the best assembled mammalian genome sequences available to date. Second, by means of a coupled browser front-end, we focus on the CGIs overlapping orthologous genes extracted from OrthoDB, thus ensuring the comparison between CGIs located on truly homologous genome segments. This allows comparing the main compositional features between homologous CGIs. Finally, to facilitate nucleotide comparisons, we lifted genome coordinates between assemblies from different species, which enables the analysis of sequence divergence by direct count of nucleotide substitutions and indels occurring between homologous CGIs. The resulting CpGislandEVO database, linking together CGIs and single-cytosine DNA methylation data from several mammalian species, is freely available at our website. Guillermo Barturen, Stefanie Geisen, Francisco Dios, E. J. Maarten Hamberg, Michael Hackenberg, and José L. Oliver Copyright © 2013 Guillermo Barturen et al. All rights reserved. Gradient Evolution of Body Colouration in Surface- and Cave-Dwelling Poecilia mexicana and the Role of Phenotype-Assortative Female Mate Choice Tue, 24 Sep 2013 15:41:42 +0000 http://www.hindawi.com/journals/bmri/2013/148348/ Ecological speciation assumes reproductive isolation to be the product of ecologically based divergent selection. Beside natural selection, sexual selection via phenotype-assortative mating is thought to promote reproductive isolation. Using the neotropical fish Poecilia mexicana from a system that has been described to undergo incipient ecological speciation in adjacent, but ecologically divergent habitats characterized by the presence or absence of toxic H2S and darkness in cave habitats, we demonstrate a gradual change in male body colouration along the gradient of light/darkness, including a reduction of ornaments that are under both inter- and intrasexual selection in surface populations. In dichotomous choice tests using video-animated stimuli, we found surface females to prefer males from their own population over the cave phenotype. However, female cave fish, observed on site via infrared techniques, preferred to associate with surface males rather than size-matched cave males, likely reflecting the female preference for better-nourished (in this case: surface) males. Hence, divergent selection on body colouration indeed translates into phenotype-assortative mating in the surface ecotype, by selecting against potential migrant males. Female cave fish, by contrast, do not have a preference for the resident male phenotype, identifying natural selection against migrants imposed by the cave environment as the major driver of the observed reproductive isolation. David Bierbach, Marina Penshorn, Sybille Hamfler, Denise B. Herbert, Jessica Appel, Philipp Meyer, Patrick Slattery, Sarah Charaf, Raoul Wolf, Johannes Völker, Elisabeth A. M. Berger, Janis Dröge, Konstantin Wolf, Rüdiger Riesch, Lenin Arias-Rodriguez, Jeanne R. Indy, and Martin Plath Copyright © 2013 David Bierbach et al. All rights reserved. Genome Diversification Mechanism of Rodent and Lagomorpha Chemokine Genes Wed, 07 Aug 2013 16:01:00 +0000 http://www.hindawi.com/journals/bmri/2013/856265/ Chemokines are a large family of small cytokines that are involved in host defence and body homeostasis through recruitment of cells expressing their receptors. Their genes are known to undergo rapid evolution. Therefore, the number and content of chemokine genes can be quite diverse among the different species, making the orthologous relationships often ambiguous even between closely related species. Given that rodents and rabbit are useful experimental models in medicine and drug development, we have deduced the chemokine genes from the genome sequences of several rodent species and rabbit and compared them with those of human and mouse to determine the orthologous relationships. The interspecies differences should be taken into consideration when experimental results from animal models are extrapolated into humans. The chemokine gene lists and their orthologous relationships presented here will be useful for studies using these animal models. Our analysis also enables us to reconstruct possible gene duplication processes that generated the different sets of chemokine genes in these species. Kanako Shibata, Hisayuki Nomiyama, Osamu Yoshie, and Sumio Tanase Copyright © 2013 Kanako Shibata et al. All rights reserved. Evaluating Phylogenetic Informativeness as a Predictor of Phylogenetic Signal for Metazoan, Fungal, and Mammalian Phylogenomic Data Sets Wed, 26 Jun 2013 18:00:44 +0000 http://www.hindawi.com/journals/bmri/2013/621604/ Phylogenetic research is often stymied by selection of a marker that leads to poor phylogenetic resolution despite considerable cost and effort. Profiles of phylogenetic informativeness provide a quantitative measure for prioritizing gene sampling to resolve branching order in a particular epoch. To evaluate the utility of these profiles, we analyzed phylogenomic data sets from metazoans, fungi, and mammals, thus encompassing diverse time scales and taxonomic groups. We also evaluated the utility of profiles created based on simulated data sets. We found that genes selected via their informativeness dramatically outperformed haphazard sampling of markers. Furthermore, our analyses demonstrate that the original phylogenetic informativeness method can be extended to trees with more than four taxa. Thus, although the method currently predicts phylogenetic signal without specifically accounting for the misleading effects of stochastic noise, it is robust to the effects of homoplasy. The phylogenetic informativeness rankings obtained will allow other researchers to select advantageous genes for future studies within these clades, maximizing return on effort and investment. Genes identified might also yield efficient experimental designs for phylogenetic inference for many sister clades and outgroup taxa that are closely related to the diverse groups of organisms analyzed. Francesc López-Giráldez, Andrew H. Moeller, and Jeffrey P. Townsend Copyright © 2013 Francesc López-Giráldez et al. All rights reserved. In Situ Gene Mapping of Two Genes Supports Independent Evolution of Sex Chromosomes in Cold-Adapted Antarctic Fish Tue, 12 Feb 2013 10:11:23 +0000 http://www.hindawi.com/journals/bmri/2013/243938/ Two genes, that is, 5S ribosomal sequences and antifreeze glycoprotein (AFGP) genes, were mapped onto chromosomes of eight Antarctic notothenioid fish possessing a X1X1X2X2/X1X2Y sex chromosome system, namely, Chionodraco hamatus and Pagetopsis macropterus (family Channichthyidae), Trematomus hansoni, T. newnesi, T. nicolai, T. lepidorhinus, and Pagothenia borchgrevinki (family Nototheniidae), and Artedidraco skottsbergi (family Artedidraconidae). Through fluorescence in situ hybridization (FISH), we uncovered distinct differences in the gene content of the Y chromosomes in the eight species, with C. hamatus and P. macropterus standing out among others in bearing 5S rDNA and AFGP sequences on their Y chromosomes, respectively. Both genes were absent from the Y chromosomes of any analyzed species. The distinct patterns of Y and non-Y chromosome association of the 5S rDNA and AFGP genes in species representing different Antarctic fish families support an independent origin of the sex heterochromosomes in notothenioids with interesting implications for the evolutionary/adaptational history of these fishes living in a cold-stable environment. Laura Ghigliotti, C.-H. Christina Cheng, Céline Bonillo, Jean-Pierre Coutanceau, and Eva Pisano Copyright © 2013 Laura Ghigliotti et al. All rights reserved.