Gene Sampling Strategies for Multi-Locus Population Estimates of Genetic Diversity (θ)

BACKGROUND: Theoretical work suggests that data from multiple nuclear loci provide better estimates of population genetic parameters than do single loci, but just how many loci are needed and how much sequence is required from each has been little explored. METHODOLOGY/PRINCIPLE FINDINGS: To investigate how much data is required to estimate the population genetic parameter θ (4N(e)μ) accurately under ideal circumstances, we simulated datasets of DNA sequences under three values of θ per site (0.1, 0.01, 0.001), varying in both the total number of base pairs sequenced per individual and the number of equal-length loci. From these datasets we estimated θ using the maximum likelihood coalescent framework implemented in the computer program Migrate. Our results corroborated the theoretical expectation that increasing the number of loci impacted the accuracy of the estimate more than increasing the sequence length at single loci. However, when the value of θ was low (0.001), the per-locus sequence length was also important for estimating θ accurately, something that has not been emphasized in previous work. CONCLUSIONS/SIGNIFICANCE: Accurate estimation of θ required data from at least 25 independently evolving loci. Beyond this, there was little added benefit in terms of decreasing the squared coefficient of variation of the coalescent estimates relative to the extra effort required to sample more loci

Historical divergence and gene flow: Coalescent analyses of mitochondrial, autosomal and sex-linked loci in passerina buntings

Quantifying the role of gene flow during the divergence of closely related species is crucial to understanding the process of speciation. We collected DNA sequence data from 20 loci (one mitochondrial, 13 autosomal, and six sex-linked) for population samples of Lazuli Buntings (Passerina amoena) and Indigo Buntings (Passerina cyanea) (Aves: Cardinalidae) to test explicitly between a strict allopatric speciation model and a model in which divergence occurred despite postdivergence gene flow. Likelihood ratio tests of coalescent-based population genetic parameter estimates indicated a strong signal of postdivergence gene flow and a strict allopatric speciation model was rejected. Analyses of partitioned datasets (mitochondrial, autosomal, and sex-linked) suggest the overall gene flow patterns are driven primarily by autosomal gene flow, as there is no evidence of mitochondrial gene flow and we were unable to reject an allopatric speciation model for the sex-linked data. This pattern is consistent with either a parapatric divergence model or repeated periods of allopatry with gene flow occurring via secondary contact. These results are consistent with the low fitness of female avian hybrids under Haldane\u27s rule and demonstrate that sex-linked loci likely are important in the initial generation of reproductive isolation, not just its maintenance. © 2010 The Author(s). Journal compilation © 2010 The Society for the Study of Evolution

Prospectus, March 24, 1993

https://spark.parkland.edu/prospectus_1993/1004/thumbnail.jp

Effect of Corn Processing in Finishing Diets Containing Wet Distillers Grains on Feedlot Performance and Carcass Characteristics of Finishing Steers

Three-hundred sixty calf-fed steers (BW = 318 ± 15 kg) were used in a completely randomized design to evaluate corn processing methods in finishing diets containing wet distillers grains plus solubles (WDGS). Whole corn (WC) was compared with corn processed by different methods, consisting of dryrolled corn (DRC), high-moisture corn (HMC), a 1:1 DRC:HMC combination (DM basis), steam-flaked corn (SFC), and finely-ground corn (FGC). The SFC with a flake density of 0.33 kg/L was obtained from a commercial feedlot. Basal dietary ingredients consisted of ground alfalfa hay (5.6% of DM) and dry supplement (3.0% of DM), with the balance being WDGS (30% of DM) and corn (61.4% of DM). Final BW and ADG were greater (P \u3c 0.05) for the cattle fed DRC (1.84 kg/d) compared with cattle fed FGC (1.53 kg/d), SFC (1.63 kg/d), and WC (1.75 kg/d), but was not different (P = 0.11) from cattle fed DRC:HMC (1.78 kg/d). Cattle fed HMC (0.185) had greater (P \u3c 0.05) G:F compared with cattle fed FGC (0.166), SFC (0.176), and WC (0.166). No differences (P \u3e 0.30) were detected between cattle fed HMC and DRC:HMC for ADG and G:F; however, cattle fed DRC tended to have greater (P = 0.08) ADG, yet lower (P = 0.08) G:F than cattle fed HMC. Carcass characteristics reflected performance. These data indicate that steam flaked and finely ground corn processing methods, or no processing, are not as effective as high-moisture or dry-rolled corn processing methods in finishing diets containing 30% WDGS

Effect of Corn Processing in Finishing Diets Containing Wet Distillers Grains on Feedlot Performance and Carcass Characteristics of Finishing Steers

An experiment evaluated the effects of six corn processing methods in feedlot diets containing 30% (DM basis) wet distillers grains plus solubles (WDGS). Treatments consisted of whole corn, dry-rolled corn, a dry-rolled/ high-moisture corn mix, high-moisture corn, steam flaked corn, and fine ground corn. The ADG was highest for steers receiving dry-rolled corn, high-moisture corn, or a 50:50 blend of dry-rolled and high-moisture corn. Feed conversion was best for steers receiving high-moisture corn. Interestingly, cattle fed finely ground corn or steam-flaked corn did not gain or convert as well as expected. Results indicate that there is a performance advantage obtained by processing corn as either dry-rolled or high-moisture when included with WDGS in finishing diets