Testing Introgressive Hybridization Hypotheses Using Statistical Network Analysis of Nuclear and Cytoplasmic Haplotypes in the Leaf Beetle Timarcha goettingensis Species Complex

Previous studies of leaf beetles (Chrysomelidae) in the Timarcha goettingensis species complex using mitochondrial (cox2) and nuclear (ITS-2 rRNA) markers revealed two main clades confined to the Iberian Peninsula and the rest of Europe but showing incongruent distributions indicative of gene exchange between both groups. Because of the anastomosing nature of hybridization, which disrupts the cladistic structure of character variation, phylogenetic trees might be inappropriate to represent and study this process. Here we test for evidence of hybridization in the T. goettingensis complex by analyzing the extra homoplasy arising in hybrid genomes from the simultaneous analysis of genetically independent markers. Haplotype networks obtained by Templeton’s statistical parsimony analysis were generated for combined (concatenated) cox2 and ITS-2 sequences from 167 individuals of the T. goettingensis complex. Networks were used to detect runs of homoplasious characters physically clustered along a nucleotide sequence, as evidence for recombination between both gene partitions. A hypergeometric tail probability for the chance occurrence of physically clustered character changes on the connections linking networks of genotypes was applied. The test recognized two instances of statistically significant clustering, indicating the presence of cox2–ITS-2 mosaic genotypes and reticulation of both main T. goettingensis clades, supporting the reticulate origin of samples of T. maritima in southwestern France and T. sinuatocollis/T. monserratensis in the eastern Pyrenees. Although the assessment of reticulation in DNA sequences does not provide direct proof for hybridization, the geographical distribution of mosaic genotypes in the vicinity of “pure” genotypes supports the effect of gene flow between the two divergent lineages. The study demonstrates the utility of statistical parsimony networks for the detection of hybrids in the growing number of phylogeographic studies based on multiple gene markers. [Reviewing Editor: Dr. Rafael Zardoya]     

玉米杂种优势分子基础研究进展

当今作物改良中杂种优势的广泛应用得益于杂交玉米的首先培育成功,对其分子基础的探讨已历经近一个世纪却尚未达成共识。关于杂种优势的经典解释曾聚焦于显性和超显性假说,现在看来似乎是借喻遗传学分子概念而无实际分子基础的实用性概念,籍此导致了一些研究结果的不一致是可以理解的。随着基因组时代的到来和相关分子技术的出现,文章回顾了过去的研究结果,分析了杂种优势分子机制研究的现状和问题,针对两亲本及其后代杂交后基因组构架和基因表达变化的研究趋势及方向进行了评价,并提出了由此资讯引发的SNPs单倍型用于玉米杂种优势分子基础研究的新策略。     

Polymorphisms of DNA repair genes are associated with renal cell carcinoma

DNA repair gene alterations have been shown to cause a reduction in DNA repair capacity and may influence an individual's susceptibility to carcinogenesis. Single nucleotide polymorphisms (SNPs) of DNA repair genes have been shown to cause a reduction in repair activity. We hypothesized that SNPs of DNA repair genes may be a risk factor for renal cell carcinoma (RCC). To test this hypothesis, DNA samples from 112 cases of renal cell cancer and healthy controls (n=180) were analyzed by PCR-RFLP to determine the genotypic frequency of six different polymorphic loci on five DNA repair genes (XRCC1, XPC, ERCC1, XRCC3, and XRCC7). The chi(2) test was applied to compare the genotype frequency between patients and controls. We found that the frequency of 399Gln variant at XRCC1 Arg399Gln was significantly higher in RCC cases than in controls (OR=2.83, 95%CI=1.24-6.49, P=0.01). The frequency of T-A haplotype of XRCC1 194 Trp and XRCC1 399Gln was significantly higher in RCC than controls. No differences in genotypes were observed at the other sites. This is the first report on SNPs of DNA repair genes in renal cell carcinoma that suggests XRCC1 399Gln polymorphism may be a risk factor for RCC. Our present data suggest that the XRCC1 399Gln allele may be linked to susceptibility for RCC.     

In-gel multiple displacement amplification of long DNA fragments diluted to the single molecule level

The isolation and multiple genotyping of long individual DNA fragments are needed to obtain haplotype information for diploid organisms. Limiting dilution of sample DNA followed by multiple displacement amplification is a useful technique but is restricted to short (<5 kb) DNA fragments. In the current study, a novel modification was applied to overcome these problems. A limited amount of cellular DNA was carefully released from intact cells into a mildly heated alkaline agarose solution and mixed thoroughly. The solution was then gently aliquoted and allowed to solidify while maintaining the integrity of the diluted DNA. Exogenously provided Phi29 DNA polymerase was used to perform consistent genomic amplification with random hexameric oligonucleotides within the agarose gels. Simple heat melting of the gel allowed recovery of the amplified materials in a solution of the polymerase chain reaction (PCR)-ready form. The haplotypes of seven SNPs spanning 240 kb of the DNA surrounding the human ATM gene region on chromosome 11 were determined for 10 individuals, demonstrating the feasibility of this new method.     

Intraspecific diversity matters in bryophyte conservation – internal transcribed spacer and rpl16 G2 intron variation in some European mosses

Intraspecific diversity and molecular relations among regional populations were studied for 16 moss species in three European regions, Central Europe, Southern Scandinavia, and Northern Scandinavia, based on internal transcribed spacer and rpl16 G2 intron. The range of nuclear diversity values found is mainly similar to that of other organisms, and to that found in bryophytes from other regions, but higher diversity was found in Isothecium alopecuroides (Dubois) Isov. No correlations were found between diversity values or number of haplotypes unique to a region and morphological diversity, geographical distribution range, or regional frequency, possibly since this study did not include sufficiently rare species to reflect the factors affecting such species. Finally, no general differences in diversity levels were found among the three studied regions. When haplotype composition is considered, differences were found among the regions for some species, but again no general inter-regional pattern of intraspecific relationships exists. While it is clear that intraspecific variation is crucial to consider in biodiversity conservation contexts since a high proportion of the total diversity is found below the species level, it is also evident that it is necessary to investigate each individual species rather than to rely on what has been found for other taxa.     

Polymorphism and Haplotype Structure in River Buffalo (Bubalus bubalis) Toll-Like Receptor 5 (TLR5) Coding Sequence

Most of the 160 million river buffalo in the world are in Asia where they are used extensively, both as a food source and for draught power. Only recently have investigations begun exploring the buffalo genome for variation that might influence health and productivity of these economically important animals. This paper describes the sequence variability of the toll-like receptor 5 (TLR5) gene, which recognizes bacterial flagellin and is a key player in the immune system. TLR5 is comprised of a single exon that is 2577 bp and codes 858 amino acids. We examined single-nucleotide polymorphisms (SNPs) located within the coding region. Overall, 17 SNPs were discovered, seven of which are non-synonymous. Our study population yielded four different haplotypes. We examined predicted protein domain structure and found that river buffalo, swamp buffalo, and African Forest buffalo shared the same protein domain structure and are more similar to each other than they are to cattle and American bison, which are similar to each other. PolyPhen 2 analysis revealed one amino acid substitution in the river buffalo population with potential functional significance.     

Mathematical properties and bounds on haplotyping populations by pure parsimony

Although the haplotype data can be used to analyze the function of DNA, due to the significant efforts required in collecting the haplotype data, usually the genotype data is collected and then the population haplotype inference (PHI) problem is solved to infer haplotype data from genotype data for a population. This paper investigates the PHI problem based on the pure parsimony criterion (HIPP), which seeks the minimum number of distinct haplotypes to infer a given genotype data. We analyze the mathematical structure and properties for the HIPP problem, propose techniques to reduce the given genotype data into an equivalent one of much smaller size, and analyze the relations of genotype data using a compatible graph. Based on the mathematical properties in the compatible graph, we propose a maximal clique heuristic to obtain an upper bound, and a new polynomial-sized integer linear programming formulation to obtain a lower bound for the HIPP problem.     

A putative disease-associated haplotype within the SCN1A gene in Dravet syndrome

Dravet syndrome (DS), previously known as severe myoclonic epilepsy of infancy, is one of the most severe forms of childhood epilepsy. DS is caused by a mutation in the neuronal voltage-gated sodium-channel alpha-subunit gene (SCN1A). However, 25–30% of patients with DS are negative for the SCN1A mutation screening, suggesting that other molecular mechanisms may account for these disorders. Recently, the first case of DS caused by a mutation in the neuronal voltage-gated sodium-channel beta-subunit gene (SCN1B) was also reported. In this report we aim to make the molecular analysis of the SCN1A and SCN1B genes in two Tunisian patients affected with DS. The SCN1A and SCN1B genes were tested for mutations by direct sequencing. No mutation was revealed in the SCN1A and SCN1B genes by sequencing analyses. On the other hand, 11 known single nucleotide polymorphisms were identified in the SCN1A gene and composed a putative disease-associated haplotype in patients with DS phenotype. One of the two patients with putative disease-associated haplotype in SCN1A had also one known single nucleotide polymorphism in the SCN1B gene. The sequencing analyses of the SCN1A gene revealed the presence of a putative disease-associated haplotype in two patients affected with Dravet syndrome.