The evolution of noncoding DNA: how much junk, how much func?

Comparative sequence analysis on a genomic scale has opened the door for the systematic analysis of cis-acting regulatory DNA. It is now possible to begin to answer basic questions such as, how much meaningful noncoding sequence is in the genome? How strong is natural selection on functional noncoding sequences in different species? Two recent articles have capitalized on the comparative genomic approach in an attempt to answer these questions with surprising results.     

How much should reproduction cost?

The ultimate goal of investigating costs of reproduction isto see whether evolutionary tradeoffs are important determinantsof observed variation in fecundity. However, the current empiricalapproach to studying costs of reproduction, manipulation ofbrood size, is only capable of demonstrating the existence ofa cost of reproduction. Little attention has been paid to thebiological significance of a cost of reproduction, when oneis found. In this paper, I outline an analytical framework thatcan be used in conjunction with brood manipulation experimentsto determine whether an observed cost of reproduction is capableof limiting clutch sizes at observed levels. In addition, thisframework can be used to determine whether patterns of variationin fecundity within a population are caused by evolutionarytrade-offs between present and future reproduction. Two patternsused as examples are increase in clutch size with female ageand intraseasonal decline in clutch size in birds. Because increasingbrood size can have several effects on adults (e.g., decreasedadult survival, decreased future fecundity of surviving adults,decreased care given to offspring in the enlarged brood), thereis a need to understand how all these effects are interrelated.The analytical framework outlined in this paper allows one toexpress a cost of reproduction (i.e., a decrease in future fecundityof parents) and decreases in the rate of survival of offspringfrom the current nesting attempt in a common "currency." Thispaper also suggests how brood manipulation experiments can distinguishbetween variation in clutch size resulting from life-historytrade-offs and variation that results from differences in parentalability or territory quality. The analytical methods can bereadily applied to other taxa.     

How much pollen can thrips destroy?

ABSTRACT. 1. A laboratory technique for measuring the number of pollen grains consumed by thrips is described.
2. Thrips imaginis Bagnall and Thrips obscuratus (Crawford) (Thripidae) were studied particularly on pollen of the kiwifruit Actinidia deliciosa (A. Chevalier) Liang & Ferguson in New Zealand, and Echium plantagineum L. in Australia.
3. Mean daily feeding rates (in grains per thrips per day) ranged from 29 to 843, with an individual rate as high as 1626 for T.imaginis larvae II on E. plantagineum.
4. The time taken to feed on a single grain was proportional to grain volume, and decreased with temperature.
5. Daily feeding rates were significantly different between pollens, and were higher for smaller grains. The total volume of pollen contents consumed and the total time spent ingesting this volume per thrips per day may be constant with respect to pollen species.
6. Daily feeding rates were equivalent to 0.2–0.7% of the average total pollen production of a flower per thrips per day.
7. Extrapolation of the daily feeding rates suggests that pollen damage by thrips could sometimes be reducing crop yield or plant fitness.     

How much evolutionary advantage does sex confer?

In discussing the long term advantage of sex, Crow & Kimura (1965) andMaynard Smith (1971) have argued that the advantage of a reproductive system allowing recombination (sex) is greatest for large populations. However the validity of this conclusion depends upon the model used for evolution. We propose two simple models: the bootstrap model, where the number of loci at which favourable mutations may take place remains constant over long time periods; and the environment-led model, where evolution is at a constant rate dictated by the environment (and does not depend on the organism's ability to evolve). While the bootstrap model leads to conclusions similar to those mentioned above, the conclusions for environment-led evolution are the opposite: as the size of the population decreases the advantage for sex increases.     

Too much linoleic acid promotes inflammation-doesn't it?

Controversy exists over how much linoleic acid (LA) should be consumed in a healthy diet. Some claim that high LA intake promotes inflammation through accumulation of tissue arachidonic acid (AA) and subsequent production of pro-inflammatory lipid mediators. Here the author reviews the current available evidence from human studies that address this issue. The data indicate that high LA in the diet or circulation is not associated with higher in vivo or ex vivo pro-inflammatory responses. Surprisingly, several studies showed that those individuals consuming the highest level of LA had the lowest inflammatory status. Recent findings suggest that LA and AA are involved in both pro- and anti-inflammatory signaling pathways. Thus, within the ranges of intake that are achievable for most human populations, the evidence do not support reducing LA intake below current consumption levels.     

How much non-coding DNA do eukaryotes require?

Despite tremendous advances in the field of genomics, the amount and function of the large non-coding part of the genome in higher organisms remains poorly understood. Here we report an observation, made for 37 fully sequenced eukaryotic genomes, which indicates that eukaryotes require a certain minimum amount of non-coding DNA (ncDNA). This minimum increases quadratically with the amount of DNA located in exons. Based on a simple model of the growth of regulatory networks, we derive a theoretical prediction of the required quantity of ncDNA and find it to be in excellent agreement with the data. The amount of additional ncDNA (in basepairs) which eukaryotes require obeys N_DEF=1/2 (N_C/N_P) (N_C−N_P), where N_C is the amount of exonic DNA, and N_P is a constant of about 10 Mb. This value N_DEF corresponds to a few percent of the genome in Homo sapiens and other mammals, and up to half the genome in simpler eukaryotes. Thus, our findings confirm that eukaryotic life depends on a substantial fraction of ncDNA and also make a prediction of the size of this fraction, which matches the data closely.