Limited influence of local and landscape factors on finescale gene flow in two pond‐breeding amphibians

Dispersal and gene flow within animal populations are influenced by the composition and configuration of the landscape. In this study, we evaluated hypotheses about the impact of natural and anthropogenic factors on genetic differentiation in two amphibian species, the spotted salamander (Ambystoma maculatum) and the wood frog (Lithobates sylvaticus) in a commercial forest in central Maine. We conducted this analysis at two scales: a local level, focused on factors measured at each breeding pond, and a landscape level, focused on factors measured between ponds. We investigated the effects of a number of environmental factors in six categories including Productivity, Physical, Land Composition, Land Configuration, Isolation and Location. Embryos were sampled from 56 spotted salamander breeding ponds and 39 wood frog breeding ponds. We used a hierarchical Bayesian approach in the program GESTE at each breeding pond and a random forest algorithm in conjunction with a network analysis between the ponds. We found overall high genetic connectivity across distances up to 17 km for both species and a limited effect of natural and anthropogenic factors on gene flow. We found the null models best explained patterns of genetic differentiation at a local level and found several factors at the landscape level that weakly influenced gene flow. This research indicates multiscale investigations that incorporate local and landscape factors are valuable for understanding patterns of gene flow. Our findings suggest that dispersal rates in this system are high enough to minimize genetic structuring and that current forestry practices do not significantly impede dispersal.     

Expansion of the canine A blood group system

A detailed study of the canine A blood group system was undertaken, resulting in the expansion of this system into a three-factor, four-allelic one with the recognition of an additional subtype, a3. The serological and extensive family data supported the proposed genetic theory of four alleles with dominance with the order being Aa1, Aa2, Aa3 and A-. Gene frequencies of the alleles were determined in various breeds of dogs with frequencies in the general Brisbane population being 0.244 (Aa1), 0.042 (Aa2), 0.045 (Aa3) and 0.669 (A-).     

What paths do advantageous alleles take during short‐term evolutionary change?

Combining experimental evolution with whole‐genome resequencing is a promising new strategy for investigating the dynamics of evolutionary change. Published studies that have resequenced laboratory‐selected populations of sexual organisms have typically focused on populations sampled at the end of an evolution experiment. These studies have attempted to associate particular alleles with phenotypic change and attempted to distinguish between different theoretical models of adaptation. However, neither the population used to initiate the experiment nor multiple time points sampled during the evolutionary trajectory are generally available for examination. In this issue of Molecular Ecology, Orozco‐terWengel et al. (2012) take a significant step forward by estimating genome‐wide allele frequencies at the start, 15 generations into and at the end of a 37‐generation Drosophila experimental evolution study. The authors identify regions of the genome that have responded to laboratory selection and describe the temporal dynamics of allele frequency change. They identify two common trajectories for putatively adaptive alleles: alleles either gradually increase in frequency throughout the entire 37 generations or alleles plateau at a new frequency by generation 15. The identification of complex trajectories of alleles under selection contributes to a growing body of literature suggesting that simple models of adaptation, whereby beneficial alleles arise and increase in frequency unimpeded until they become fixed, may not adequately describe short‐term response to selection.     

QF-PCR在染色体异常男性不育症诊断中的应用

为评估定量荧光PCR(QF-PCR)方法在男性不育遗传学诊断中的应用价值,文章对78例非梗阻性男性不育患者,采用精液常规检测精子情况,并检测患者性激素水平;采用QF-PCR方法对患者性染色体多态性STR位点及特异性位点进行检测;采用常规染色体G显带方法进行核型分析;PCR检测AZF微缺失。结果显示78例非梗阻性男性不育患者中发现无精子症患者18例,少精子症患者20例,总检出率为48.72%。采用QF-PCR方法检出3例47,XXY患者,2例46,XX(SRY+)性反转患者,1例AZFc区微缺失患者,与细胞培养染色体分析和AZF微缺失PCR检测结果相符。与传统方法相比,QF-PCR技术能更迅速、直接、可靠地检测到男性不育患者的染色体异常区域,及早发现染色体细微结构异常,有助于染色体异常造成的男性不育症的鉴别诊断。     

Evidence for a quantitative trait locus affecting low levels of apolipoprotein B and low density lipoprotein on chromosome 10 in Caucasian families

High plasma apolipoprotein B (apoB) and LDL cholesterol levels increase cardiovascular disease risk. These highly correlated measures may be partially controlled by common genetic polymorphisms. To identify chromosomal regions that contain genes causing low plasma levels of one or both parameters in Caucasian families ascertained for familial hypobetalipoproteinemia (FHBL), we conducted a whole-genome scan using 443 microsatellite markers typed in nine multigenerational families with at least two members with FHBL. Both variance components and regression-based linkage methods were used to identify regions of interest. Common linkage regions were identified for both measures on chromosomes 10q25.1-10q26.11 [maximum log of the odds (LOD) = 4.2 for LDL and 3.5 for apoB] and 6q24.3 (maximum LOD = 1.46 for LDL and 1.84 for apoB). There was also evidence for linkage to apoB on chromosome 13q13.2 (LOD = 1.97) and to LDL on chromosome 3p14.1 at 94 centimorgan (LOD = 1.52). Bivariate linkage analysis provided further evidence for loci contributing to both traits (6q24.3, LOD = 1.43; 10q25.1, LOD = 1.74). We evaluated single nucleotide polymorphisms (SNPs) in genes within our linkage regions to identify variants associated with apoB or LDL levels. The most significant finding was for rs2277205 in the 5' untranslated region of acyl-coenzyme A dehydrogenase short/branched chain and LDL (P = 10(-7)). Three additional SNPs were associated with apoB and/or LDL (P < 0.01). Although only the linkage signal on chromosome 10 reached genome-wide statistical significance, there are likely multiple chromosomal regions with variants that contribute to low levels of apoB and LDL and that may protect against coronary heart disease.     

Pheno2Geno - High-throughput generation of genetic markers and maps from molecular phenotypes for crosses between inbred strains

Background

Genetic markers and maps are instrumental in quantitative trait locus (QTL) mapping in segregating populations. The resolution of QTL localization depends on the number of informative recombinations in the population and how well they are tagged by markers. Larger populations and denser marker maps are better for detecting and locating QTLs. Marker maps that are initially too sparse can be saturated or derived de novo from high-throughput omics data, (e.g. gene expression, protein or metabolite abundance). If these molecular phenotypes are affected by genetic variation due to a major QTL they will show a clear multimodal distribution. Using this information, phenotypes can be converted into genetic markers.

Results

The Pheno2Geno tool uses mixture modeling to select phenotypes and transform them into genetic markers suitable for construction and/or saturation of a genetic map. Pheno2Geno excludes candidate genetic markers that show evidence for multiple possibly epistatically interacting QTL and/or interaction with the environment, in order to provide a set of robust markers for follow-up QTL mapping.We demonstrate the use of Pheno2Geno on gene expression data of 370,000 probes in 148 A. thaliana recombinant inbred lines. Pheno2Geno is able to saturate the existing genetic map, decreasing the average distance between markers from 7.1 cM to 0.89 cM, close to the theoretical limit of 0.68 cM (with 148 individuals we expect a recombination every 100/148=0.68 cM); this pinpointed almost all of the informative recombinations in the population.

Conclusion

The Pheno2Geno package makes use of genome-wide molecular profiling and provides a tool for high-throughput de novo map construction and saturation of existing genetic maps. Processing of the showcase dataset takes less than 30 minutes on an average desktop PC. Pheno2Geno improves QTL mapping results at no additional laboratory cost and with minimum computational effort. Its results are formatted for direct use in R/qtl, the leading R package for QTL studies. Pheno2Geno is freely available on CRAN under “GNU GPL v3”. The Pheno2Geno package as well as the tutorial can also be found at: http://pheno2geno.nl.

Electronic supplementary material

The online version of this article (doi:10.1186/s12859-015-0475-6) contains supplementary material, which is available to authorized users.     

Human temporal bone from the lower Paleolithic site of Castel di Guido, near Rome, Italy

The Castel di Guido site, with an estimated age of approximately 300,000 years, has yielded abundant animal remains, Acheulian stone and bone bifaces, and small tools. On the surface of the original deposit, turned over by agricultural activities, fragments of human remains were discovered between 1980 and 1986, including a temporal bone described here.     

Immunoglobulin (GM and KM) allotypes and relation to population history in native peoples of British Columbia: Haida and Bella Coola

Differences in the frequencies of GM haplotypes among native peoples of the Americas support the hypothesis that there were three distinct waves of migration from northeast Asia into the Americas: Paleo-Indian, Na-Dene, and Inuit (Eskimo)-Aleut (Salzano and Steinberg: Am. J. Hum. Genet. 17:273-279, 1965; Sukernik and Osipova: Hum. Genet. 61:148-153, 1982; Williams et al.:Am. J. Phys. Anthropol. 66:1-19, 1985; Szathmary: In R Kirk and E Szathmary (eds): Out of Asia: Peopling of the Americas and the Pacific. Canberra: The Journal of Pacific History, Canberra Australian National University, pp. 79-104, 1985). We studied GM allotypes in two linguistically unique populations of Canadian west coast native peoples, the Haida and the Bella Coola, and compared them to GM frequencies in populations that are supposed descendants of the three migrations, in order to investigate the possible genetic relationships of these British Columbia (BC) groups to other native populations. We also estimated the amount of European admixture from the frequency of the Caucasian haplotype, Gm3;5. Results showed that the frequencies in both BC populations of the three common native haplotypes (Gm1,17;21, Gm1,2,17;21, and Gm1,17;15,16), were intermediate between the frequencies in supposed descendants of Paleo-Indian and Na-Dene. These genetic findings are consistent with the controversial hypothesis of archeologist C. Borden (Science 203:963-971, 1979) that, following deglaciation about 13,000 years ago, British Columbia was repopulated by peoples from the north (?Na-Dene) and by culturally distinct peoples from the south (?Paleo-Indian). Caucasian admixture estimates suggested that the Haida and Bella Coola have also experienced moderate amounts (12-20%) of genetic input from European-originating peoples.(ABSTRACT TRUNCATED AT 250 WORDS)