Analysis of gene-trap Ds rice populations in Korea

Insertional mutagen-mediated gene tagging populations have been essential resources for analyzing the function of plant genes. In rice, maize transposable elements have been successfully utilized to produce transposant populations. However, many generations and substantial field space are required to obtain a sufficiently sized transposant population. In rice, the japonica and indica subspecies are phenotypically and genetically divergent. Here, callus cultures with seeds carrying Ac and Ds were used to produce 89,700 lines of Dongjin, a japonica cultivar, and 6,200 lines of MGRI079, whose genome is composed of a mixture of the genetic backgrounds of japonica and indica. Of the more than 3,000 lines examined, 67% had Ds elements. Among the Ds-carrying lines, 81% of Dongjin and 63% of MGRI079 contained transposed Ds, with an average of around 2.0 copies. By examining more than 15,000 lines, it was found that 12% expressed the reporter gene GUS during the early-seedling stage. GUS was expressed in root hairs and crown root initials at estimated frequencies of 0.78% and 0.34%, respectively. The 5,271 analyzed Ds loci were found to be randomly distributed over all of the rice chromosomes. Electronic supplementary material The online version of this article (doi:) contains supplementary material, which is available to authorized users. Sung Han Park, Nam Soo Jun, Chul Min Kim are contributed equally to this paper     

Coalescent theory for a completely random mating monoecious population

Consider a large random mating monoecious diploid population that has N individuals in each generation. Let us assume that at time 0 a random sample of ninfinity. It is then possible to obtain a generalization of coalescent theory for haploid populations if the distribution of G1 has a finite second moment and E[G(1)(3)]/N-->0 as N-->infinity.     

Asymptotic behaviour of solutions to abstract logistic equations

We analyze the asymptotic behaviour of solutions of the abstract differential equation u'(t)=Au(t)-F(u(t))u(t)+f. Our results are applicable to models of structured population dynamics in which the state space consists of population densities with respect to the structure variables. In the equation the linear term A corresponds to internal processes independent of crowding, the nonlinear logistic term F corresponds to the influence of crowding, and the source term f corresponds to external effects. We analyze three separate cases and show that for each case the solutions stabilize in a way governed by the linear term. We illustrate the results with examples of models of structured population dynamics -- a model for the proliferation of cell lines with telomere shortening, a model of proliferating and quiescent cell populations, and a model for the growth of tumour cord cell populations.     

Warming and free-air CO2 enrichment alter demographics in four co-occurring grassland species

Species differ in their responses to global changes such as rising CO(2) and temperature, meaning that global changes are likely to change the structure of plant communities. Such alterations in community composition must be underlain by changes in the population dynamics of component species. Here, the impact of elevated CO(2) (550 micromol mol(-1)) and warming (+2 degrees C) on the population growth of four plant species important in Australian temperate grasslands is reported. Data collected from the Tasmanian free-air CO(2) enrichment (TasFACE) experiment between 2003 and 2006 were analysed using population matrix models. Population growth of Themeda triandra, a perennial C(4) grass, was largely unaffected by either factor but population growth of Austrodanthonia caespitosa, a perennial C(3) grass, was reduced substantially in elevated CO(2) plots. Warming and elevated CO(2) had antagonistic effects on population growth of two invasive weeds, Hypochaeris radicata and Leontodon taraxacoides, with warming causing population decline. Analysis of life cycle stages showed that seed production, seedling emergence and establishment were important factors in the responses of the species to global changes. These results show that the demographic approach is very useful in understanding the variable responses of plants to global changes and in elucidating the life cycle stages that are most responsive.     

Introduction of Trojan sex chromosomes to boost population growth

Conservation programs that deal with small or declining populations often aim at a rapid increase of population size to above-critical levels in order to avoid the negative effects of demographic stochasticity and genetic problems like inbreeding depression, fixation of deleterious alleles, or a general loss of genetic variability and hence of evolutionary potential. In some situations, population growth is determined by the number of females available for reproduction, and manipulation of family sex ratios towards more daughters has beneficial effects. If sex determination is predominantly genetic but environmentally reversible, as is the case in many amphibia, reptiles, and fish, Trojan sex chromosomes could be introduced into populations in order to change sex ratios towards more females. We analyse the possible consequences for the introduction of XX-males (XX individuals that have been changed to phenotypic males in a XY/XX sex determination system) and ZW males, WW males, or WW females (in a ZZ/ZW sex determination system). We find that the introduction of WW individuals can be most effective for an increase of population growth, especially if the induced sex change has little or no effect on viability.     

Population dynamical consequences of gregariousness in a size-structured consumer-resource interaction

Many animal species live in groups. Group living may increase exploitation competition within the group, and variation among groups in intra-group competition intensity could induce life-history variability among groups. Models of physiologically structured populations generally predict single generation cycles, driven by exploitation competition within and between generations. We expect that life-history variability and habitat heterogeneity induced by group living may affect such competition-driven population dynamics. In this study, we vary the gregariousness (the tendency to aggregate in groups) of a size-structured consumer population in a spatially explicit environment. The consumer has limited mobility, and moves according to a probabilistic movement process. We study the effects on the population dynamics, as mediated through the resource and the life-history of the consumer. We find that high gregariousness leads to large spatial resource variation, and highly variable individual life-history, resulting in highly stochastic population dynamics. At reduced gregariousness, life-history of consumers synchronizes, habitat heterogeneity is reduced, and single generation cycles appear. We expect this pattern to occur for any group living organism with limited mobility. Our results indicate that constraints set by population dynamical feedback may be an important aspect in understanding group living in nature.     

Tit-for-tat or win-stay, lose-shift?

The repeated Prisoner's Dilemma is usually known as a story of tit-for-tat (TFT). This remarkable strategy has won both of Robert Axelrod's tournaments. TFT does whatever the opponent has done in the previous round. It will cooperate if the opponent has cooperated, and it will defect if the opponent has defected. But TFT has two weaknesses: (i) it cannot correct mistakes (erroneous moves) and (ii) a population of TFT players is undermined by random drift when mutant strategies appear which play always-cooperate (ALLC). Another equally simple strategy called 'win-stay, lose-shift' (WSLS) has neither of these two disadvantages. WSLS repeats the previous move if the resulting payoff has met its aspiration level and changes otherwise. Here, we use a novel approach of stochastic evolutionary game dynamics in finite populations to study mutation-selection dynamics in the presence of erroneous moves. We compare four strategies: always-defect (ALLD), ALLC, TFT and WSLS. There are two possible outcomes: if the benefit of cooperation is below a critical value then ALLD is selected; if the benefit of cooperation is above this critical value then WSLS is selected. TFT is never selected in this evolutionary process, but lowers the selection threshold for WSLS.     

Patterns of nucleotide sequence variation in <Emphasis Type="Italic">ICAM1</Emphasis> and <Emphasis Type="Italic">TNF</Emphasis> genes in twelve ethnic groups of India: roles of demographic history and natural selection

We have studied DNA sequence variation in and around the genes ICAM1 and TNF, which play functional and correlated roles in inflammatory processes and immune cell responses, in 12 diverse ethnic groups of India, with a view to investigating the relative roles of demographic history and natural selection in shaping the observed patterns of variation. The total numbers of single nucleotide polymorphisms (SNPs) detected at the ICAM1 and TNF loci were 29 and 12, respectively. Haplotype and allele frequencies differed significantly across populations. The site frequency spectra at these loci were significantly different from those expected under neutrality, and showed an excess of intermediate-frequency variants consistent with balancing selection. However, as expected under balancing selection, there was no significant reduction of F _ST values compared to neutral autosomal loci. Mismatch distributions were consistent with population expansion for both loci. On the other hand, the phylogenetic network among haplotypes for the TNF locus was similar to expectations under population expansion, while that for the ICAM1 was as expected under balancing selection. Nucleotide diversity at the ICAM1 locus was an order of magnitude lower in the promoter region, compared to the introns or exons, but no such difference was noted for the TNF gene. Thus, we conclude that the pattern of nucleotide variation in these genes has been modulated by both demographic history and selection. This is not surprising in view of the known allelic associations of several polymorphisms in these genes with various diseases, both infectious and noninfectious.     

Modeling the Western Arctic Caribou Herd During a Positive Growth Phase: Potential Effects of Wolves and Radiocollars

ABSTRACT Population modeling exercises can lead to both expected and unexpected results useful for wildlife research and management, even though inferences must often be qualitative, given underlying assumptions. Our main objective was to use empirical data on wolf (Canis lupus) kill rates and growth of the Western Arctic caribou (Rangifer tarandus) herd (WAH) of Alaska, USA, to assess the potential for predator regulation. We used available data and published literature to construct a deterministic density-dependent population model fitted to trends of the WAH from 1976 through 2003. By increasing wolf densities in the baseline model, we failed to reject the hypothesis that wolves at a density of 6.5 wolves per 1,000 km² could regulate a caribou herd at a density of 0.4 caribou per km². In addition, our model may be conservative by underestimating the regulatory potential of wolves. We suggest that this relatively simple predator-preysystem shows signs of a predation—food 2-state model. Elasticities from matrix models may be deceiving. Although herd growth is most sensitive to changes in adult female survival, survival of younger cohorts may be more easily influenced by natural conditions or management action. Management of the WAH near maximum sustained yield may not be attainable if desired, but modeling exercises such as this elucidate options. In conducting this research, we also discovered by Monte Carlo simulation that survival and productivity data from radiocollared females and calves were negatively biased and failed to predict herd growth. Thus, researchers should consider potential effects of neck collars on vital rates of female tundra caribou and concomitant offspring when using sample data to model population dynamics or test hypotheses.