Statistical method for testing the neutral mutation hypothesis by DNA polymorphism.

So far in this course we have dealt entirely with the evolution of characters that are controlled by simple Mendelian inheritance at a single locus. There are notes on the course website about gametic disequilibrium and how allele frequencies change at two loci simultaneously, but we didn’t discuss them. In every example we’ve considered we’ve imagined that we could understand something about evolution by examining the evolution of a single gene. That’s the domain of classical population genetics. For the next few weeks we’re going to be exploring a field that’s actually older than classical population genetics, although the approach we’ll be taking to it involves the use of population genetic machinery. If you know a little about the history of evolutionary biology, you may know that after the rediscovery of Mendel’s work in 1900 there was a heated debate between the “biometricians” (e.g., Galton and Pearson) and the “Mendelians” (e.g., de Vries, Correns, Bateson, and Morgan). Biometricians asserted that the really important variation in evolution didn’t follow Mendelian rules. Height, weight, skin color, and similar traits seemed to

Human biochemical genetics

KEGG(Kyoto Encyclopedia of Genes and Genomes)〔和文〕 (特集 ゲノム医学の現在と未来--基礎と臨床) -- (データベース)

Genetics and analysis of quantitative traits

http://aerg.canberra.edu.au/library/sex_general/2002_Devlin_Nagahama_sex_determination_in_fish_review.pdf

Sex determination and sex differentiation in fish: an overview of genetic, physiological, and environmental influences

Restriction-site associated DNA sequencing (RADseq) has become a powerful and useful approach for population genomics. Currently, no software exists that utilizes both paired-end reads from RADseq data to efficiently produce population-informative variant calls, especially for non-model organisms with large effective population sizes and high levels of genetic polymorphism. dDocent is an analysis pipeline with a user-friendly, command-line interface designed to process individually barcoded RADseq data (with double cut sites) into informative SNPs/Indels for population-level analyses. The pipeline, written in BASH, uses data reduction techniques and other stand-alone software packages to perform quality trimming and adapter removal, de novo assembly of RAD loci, read mapping, SNP and Indel calling, and baseline data filtering. Double-digest RAD data from population pairings of three different marine fishes were used to compare dDocent with Stacks, the first generally available, widely used pipeline for analysis of RADseq data. dDocent consistently identified more SNPs shared across greater numbers of individuals and with higher levels of coverage. This is due to the fact that dDocent quality trims instead of filtering, incorporates both forward and reverse reads (including reads with INDEL polymorphisms) in assembly, mapping, and SNP calling. The pipeline and a comprehensive user guide can be found at http://dDocent.wordpress.com.

dDocent: a RADseq, variant-calling pipeline designed for population genomics of non-model organisms

Using eight microsatellite loci and a variety of analytical methods, we estimated genetic effective size (N(e)) of an abundant and long-lived marine fish species, the red drum (Sciaenops ocellatus), in the northern Gulf of Mexico (Gulf). The ratio N(e)/N, where short-term variance N(e) was estimated via the temporal method from shifts in allele-frequency data over four cohorts and where N reflected a current estimate of adult census size in the northern Gulf, was approximately 0.001. In an idealized population, this ratio should approximate unity. The extraordinarily low value of N(e)/N appears to arise from high variance in individual reproductive success and perhaps more importantly from variance in productivity of critical spawning and nursery habitats located in spatially discrete bays and estuaries throughout the northern Gulf. An estimate of N(e) based on a coalescent approach, which measures long-term, inbreeding effective size, was four orders of magnitude lower than the estimate of current census size, suggesting that factors presently driving N(e)/N to low values among red drum in the northern Gulf may have operated similarly in the past. Models that predict N(e)/N exclusively from demographic and life-history features will seriously overestimate N(e) if variance in reproductive success and variance in productivity among spatially discrete demes is underestimated. Our results indicate that these variances, especially variance in productivity among demes, must be large for red drum. Moreover, our study indicates that vertebrate populations with enormous adult census numbers may still be at risk relative to decline and extinction from genetic factors.

/pdf/genetic-effective-size-is-three-orders-of-magnitude-smaller-1d2t947sea.pdf

Genetic effective size is three orders of magnitude smaller than adult census size in an abundant, Estuarine-dependent marine fish (Sciaenops ocellatus).

Genetic variation was surveyed at nine microsatellite loci and the mitochondrial control region (868 bp) to test for the presence of genetic stock structure in young-of-the-year Atlantic bluefin tuna (Thunnus thynnus thynnus) from the Mediterranean Sea. Bluefin tuna were sampled over a period of 5 years from the Balearic and Tyrrhenian seas in the western basin of the Mediterranean Sea, and from the southern Ionian Sea in the eastern basin of the Mediterranean Sea. Analyses of multilocus microsatellite genotypes and mitochondrial control region sequences revealed no significant heterogeneity among collections taken from the same location in different years; however, significant spatial genetic heterogeneity was observed across all samples for both microsatellite markers and mitochondrial control region sequences (FST=0.0023, P=0.038 and PhiST=0.0233, P=0.000, respectively). Significant genetic differentiation between the Tyrrhenian and Ionian collections was found for both microsatellite and mitochondrial markers (FST=0.0087, P=0.015 and PhiST=0.0367, P=0.030, respectively). These results suggest the possibility of a genetically discrete population in the eastern basin of the Mediterranean Sea.

/pdf/microsatellite-and-mitochondrial-dna-analyses-of-atlantic-3pxfiinlho.pdf

Microsatellite and mitochondrial DNA analyses of Atlantic bluefin tuna (Thunnus thynnus thynnus) population structure in the Mediterranean Sea.

The number of mitotic chromosomal C-bands, the percent ofthe genome comprised of C-band heterochromatin, and genome size (4C DNA content) were determined for 22 North American inbred and open-pollinated lines of Zea mays. The number of C-bands ranged from 0 in Tama Knobless Flint to 18 in Zapolate Grande. The percent C-band heterochromatin ranged from 0% in Tama Knobless Flint to 16.9% in Tx601. Genome size varied over 23%: Gaspe Flint had the lowest DNA content (9.82 pg), and Zapolate Grande had thehighest (12*12 pg). Genome size and the amount of heterochromatin were significantly correlated. The corn lines were assigned to five maturity zones encompassing a south-to-north range from Mexico to Canada. Significant negative correlations were detected between the amount of C-band heterochromatin and maturity zones, and between DNA content and maturity zones among the lines. It is speculated that the simultaneous selection by man for earlier maturation and plant size may be related to the lower DNA content of corn varieties adapted to higher latitudes. Such selection for larger plants may have been achieved through selection for more cells, which could result from the shorter mitotic cycle time that correlates with reduced DNA amount.

John R. Gold

Papers

dDocent: a RADseq, variant-calling pipeline designed for population genomics of non-model organisms

Genetic effective size is three orders of magnitude smaller than adult census size in an abundant, Estuarine-dependent marine fish (Sciaenops ocellatus).

Microsatellite and mitochondrial DNA analyses of Atlantic bluefin tuna (Thunnus thynnus thynnus) population structure in the Mediterranean Sea.

C band heterochromatin and dna content in zea mays

Chromomycin A 3 Stains Nucleolus Organizer Regions of Fish Chromosomes