Adaptive evolution and effective population size in wild house mice

Estimates of the proportion of amino acid substitutions that have been fixed by selection (α) vary widely among taxa, ranging from zero in humans to over 50% in Drosophila. This wide range may reflect differences in the efficacy of selection due to differences in the effective population size (N(e)). However, most comparisons have been made among distantly related organisms that differ not only in N(e) but also in many other aspects of their biology. Here, we estimate α in three closely related lineages of house mice that have a similar ecology but differ widely in N(e): Mus musculus musculus (N(e) ～ 25,000-120,000), M. m. domesticus (N(e) ～ 58,000-200,000), and M. m. castaneus (N(e) ～ 200,000-733,000). Mice were genotyped using a high-density single nucleotide polymorphism array, and the proportions of replacement and silent mutations within subspecies were compared with those fixed between each subspecies and an outgroup, Mus spretus. There was significant evidence of positive selection in M. m. castaneus, the lineage with the largest N(e), with α estimated to be approximately 40%. In contrast, estimates of α for M. m. domesticus (α = 13%) and for M. m. musculus (α = 12 %) were much smaller. Interestingly, the higher estimate of α for M. m. castaneus appears to reflect not only more adaptive fixations but also more effective purifying selection. These results support the hypothesis that differences in N(e) contribute to differences among species in the efficacy of selection.     

Isolation and sequence analysis of the genomic DNA fragment encoding an aspartic proteinase inhibitor homologue from potato (Solanum tuberosum L.)

A genomic DNA clone encoding an aspartic proteinase inhibitor of potato was isolated from a lambda EMBL3 phage library using the aspartic proteinase inhibitor cDNA as a hybridization probe. The gene has all characteristic sequences normally found in eucaryotic genes. Typical CAAT and TATA box sequences were found in the 5-upstream region. In this part are also two putative regulatory AGGA box sequences located. In the genomic sequence there are no intron sequences interrupting the coding region. An open reading frame of the gene encodes a precursor protein of 217 amino acids which shows high percent identity with the aspartic proteinase inhibitor cDNA.     

Correlation between physico-chemical properties of quaternary ammonium salts of heptacaine and their inhibitory activity against photosynthesizing organisms

Photosynthesis inhibition in algae (Chlorella) and plant (spinach) chloroplasts by quaternary ammonium salts of heptacaine {N-[2-(2-heptyloxyphenylcarbamoyloxy)-ethyl]-N-alkylpiperidinium bromides} depended on the alkyl chain length of the alkyl substituent and showed good correlations with theoretical hydrophobic fragment constants as well as with experimentally determined physico-chemical parameters, namely extraction constants and surface activities. Communicated by. Z. ŠESTáK     

From Mesolithic hunters to Iron Age herders: a unique record of woodland use from eastern central Europe (Czech Republic)

Vegetation History and Archaeobotany - In a continuous, perfectly stratified sedimentary sequence which was discovered under a large sandstone overhang in northern Bohemia, Czech Republic, we...     

Photosynthesis of Cockspur [Echinochloa crus-galli (L.) Beauv.] at Sites of Naturally Elevated CO2 Concentration

High abundance of cockspur (Echinochloa crus-galli) at the geothermal carbon dioxide spring area in Staveinci indicates that this species is able to grow under widely varying CO₂ concentrations. Living cockspur plants can even be found very close to gas-releasing vents where growth is significantly reduced. Plant height correlated well with CO₂ exposure. The ¹³C value of the CO₂ spring air was –3.9 and ¹³C values of high-, medium-, and low-CO₂ plants were –10.14, –10.44, and –11.95 , respectively. Stomatal response directly followed the prevailing CO₂ concentrations, with the highest reduction of stomatal conductance in high CO₂ concentration grown plants. Analysis of the curves relating net photosynthetic rate to intercellular CO₂ concentration (P _N-C_i curves) revealed higher CO₂ compensation concentration in plants growing at higher CO₂ concentration. This indicates adjustment of respiration and photosynthetic carbon assimilation according to the prevailing CO₂ concentrations during germination and growth. There was no difference in other photosynthetic parameters measured.     

Photosynthetic Traits in Wheat Grown under Decreased and Increased CO2 Concentration, and after Transfer to Natural CO2 concentration

Wheat plants were grown from sowing to day 18 in 26-dm³ chambers at three different CO₂ concentrations: 150 (-CO₂), 350 (C, control), 800 (+CO₂) mol mol^-1. Afterwards, plants of the three variants were grown at the same natural CO₂ concentration. Plant characteristics were measured just before the transfer (0 days after CO₂ treatment, DAT), and at 5 – 8 DAT on the 1^st leaf, and at 12 – 22 DAT on the 4^th leaf. Decreased or increased CO₂ concentrations caused acclimations which persisted after transplantation to natural CO₂ concentration. At 5 – 8 DAT, stomatal density, stomatal conductance (g_s), CO₂ saturated net photosynthetic rate (P_Nsat0), radiation saturated net photosynthetic rate (P_Nsat1), and carboxylation efficiency () were higher in -CO₂ plants and lower in +CO₂ plants than in C plants. As compared with C plants, the photochemical efficiency () was lower in -CO₂ and higher in -CO₂ plants, however, chlorophyll (Chl) a, Chl b, Chl a–b and carotenoid contents were lower in both -CO₂ and +CO₂ plants. On the 4^th leaf, which emerged on plant after finishing CO₂ treatments, at 12 – 22 DAT, no differences in stomatal density and g, between treatments were observed. In -CO₂ plants, pigment content and P_Nsat0 were higher, was lower, and P_Nsat1 and were not different from C plants. In contrast, in +CO₂ plants, pigment content, P_Nsat1 and were lower, and P_Nsat0 and were unchanged. Leaf area, dry mass, and tiller development increased in +CO₂ plants and decreased in -CO₂ plants. In the interval between 8 and 22 DAT, lower net assimilation rate in +CO₂ than in -CO₂ plants was observed.     

Cellulosomics, a gene-centric approach to investigating the intraspecific diversity and adaptation of Ruminococcus flavefaciens within the rumen

Background

The bovine rumen maintains a diverse microbial community that serves to break down indigestible plant substrates. However, those bacteria specifically adapted to degrade cellulose, the major structural component of plant biomass, represent a fraction of the rumen microbiome. Previously, we proposed scaC as a candidate for phylotyping Ruminococcus flavefaciens, one of three major cellulolytic bacterial species isolated from the rumen. In the present report we examine the dynamics and diversity of scaC-types both within and between cattle temporally, following a dietary switch from corn-silage to grass-legume hay. These results were placed in the context of the overall bacterial population dynamics measured using the 16S rRNA.

Principal Findings

As many as 117 scaC-types were estimated, although just nineteen were detected in each of three rumens tested, and these collectively accounted for the majority of all types present. Variation in scaC populations was observed between cattle, between planktonic and fiber-associated fractions and temporally over the six-week survey, and appeared related to scaC phylogeny. However, by the sixth week no significant separation of scaC populations was seen between animals, suggesting enrichment of a constrained set of scaC-types. Comparing the amino-acid translation of each scaC-type revealed sequence variation within part of the predicted dockerin module but strong conservation in the N-terminus, where the cohesin module is located.

Conclusions

The R. flavefaciens species comprises a multiplicity of scaC-types in-vivo. Enrichment of particular scaC-types temporally, following a dietary switch, and between fractions along with the phylogenetic congruence suggests that functional differences exist between types. Observed differences in dockerin modules suggest at least part of the functional heterogeneity may be conferred by scaC. The polymorphic nature of scaC enables the relative distribution of R. flavefaciens strains to be examined and represents a gene-centric approach to investigating the intraspecific adaptation of an important specialist population.