DNA microenvironments and the molecular clock

Summary A few years ago we presented a stationary Markov model of gene evolution according to which only homologous genes from not too divergent species obeying the condition of being stationary may behave as reliable molecular clocks. A compartmentalized model of the nuclear genome in which the genes are distributed in compartments, the isochores, defined by their G+C content has been proposed recently. We have found that only homologous gene pairs that are stationary, and belong to the same isochore, can be used consistently for the determination of phylogeny and base substitution rate. In particular, for the rodent-human couple, only about half of the homologous gene pairs are stationary. Stationary genes evolve at the third silent codon position with the same velocity independent of the genes and base composition. By contrast, nonstationary genes display apparent rate values (pseudovelocities) that are significantly higher. Our results cast doubt upon recent claims of a large acceleration in the rate of molecular evolution in rodents.     

Predicting variability in catch-per-effort in Atlantic cod, Gadus morhua, trap and gillnet fisheries

The relationships between catch rates and fish abundance, hydrographic conditions and fishing effort, for Atlantic cod caught by trapnets (fixed gear) and gillnets (non-fixed gear) in the northern Gulf of St Lawrence have been quantified. Daily changes in trap catch rates were accounted for by changes in salinity, currents and mean local cod densities in 1985 ( R ²= 0.78), and predicted 1986 trap catch rate changes (by 1985 model) were correlated significantly with those observed ( r = 0.60, P < 0.05). In contrast, the daily changes in 1985 gillnet catch rates were determined by currents, maximum (not mean) local cod densities, and fishing effort (negative) ( R ²= 0.68), while predicted 1986 gillnet catch rates (by 1985 model) were significantly correlated with those observed ( r = 0.35, P < 0.05). Seasonal catchability coefficients of the traps were similar in 1985 and 1986, but for gillnets this index was an order of magnitude higher in 1986 than in 1985.     

Why fly? The possible benefits for lower mortality

In adult endotherms—birds and mammals—mortality rates are lower in flying than non-flying species. Rates vary with size, but allowing for this they are higher in penguins than flying birds, and in rodents than bats. These observations are most simply explained in terms of predation since flight, allowing movement in three dimensions, increases the chances of escape.
There are various problems in obtaining and comparing data on rates of mortality and this partly explains a wide scattering of points. Nevertheless the main results are statistically significant, mostly at P<0.001. Amongst birds, there are several other significant differences. Mortality rates are lower at lower latitudes, and in aquatic compared to terrestrial species, with cliff-nesters having lower rates than other aquatic birds and co-operative breeders than other terrestrial ones. No latitudinal effect was detected in mammals. The exceptionally low rates of mortality in bats and swifts are attributed to their being particularly hard to catch.     

Sexual differences in survival rates of adult pipistrelle bats (Pipistrellus pipistrellus) in South Sweden

Summary A pipistrelle bat (Pipistrellus pipistrellus) population in southernmost Sweden was studied for eight consecutive breeding seasons by means of bat boxes. Survival rates were calculated using Cormack's stochastic technique. The mean survival rate of adult females exceeded that of territorial males. Annual variations in survival rates were most evident in males, low rates being observed in years following wet autumns. Energy constraints imposed on territorial males by the mating system, a resource defence polygyny, were assumed to account for the differences obtained in survival rates between the sexes.     

Wall extensibility and gravitropic curvature of sunflower hypocotyls: correlation between timing of curvature and changes in extensibility

Abstract. Gravitropic curvature results from unequal growth rates on the upper and lower sides of horizontal stems. These unequal growth rates cold be due to differences in wall extensibility between the two sides. To test this, the time course of curvature of horizontal sunflower ( Helianthus anmus L.) hypocotyls was determined and compared with the time courses of changes in Instron-measured wall extensibility (PEx) of the upper and lower epidermal layers. As gravicurvature developed, so did the difference in PEx between the upper and lower epidermis. The enhanced growth rate on the lower side during the period of maximum increase in curvature was matched by PEx values greater than those of the vertical control, while the inhibited growth rate on the upper side was accompanied by PEx values below that of the control. The close correlation between changes in growth rates and alterations in PEx demonstrates that changes in wall extensibility play a major role in controlling gravicurvature.     

Analysis of inbreeding in a colonizing population of Drosophila subobscura

An analysis of the effects of inbreeding on the genetic structure of a colonizing population of Drosophila subobscura has been carried out. Species of Drosophila, particularly D. subobscura, may have lethal alleles associated with chromosomal inversions and our aim was to assess the extent to which the genome is balanced in this way. The frequencies of chromosomal inversions were compared between a large population and a set of 72 lines that were maintained by brother-sister mating for 10 generations. Fisher's matrix method was used to calculate the expected homozygosity in these inbred lines for 5 allozyme loci (Aph, Hk-1, Lap, Odh, and Pept-1) used as markers of large chromosomal segments. Furthermore, the expected rates of fixation corresponding to these allozyme loci were also calculated. The results show that the amount of homozygosis observed did not differ significantly from expectations (with the corresponding loss of lines as a consequence of the reduction in viability). However, two deviations from strict neutrality were observed: there was a heterozygote excess at the Lap locus, and the frequency of the O ₅ inversion (always associated with a lethal gene in colonizing populations) was higher than expected.     

Sex allocation in a simultaneous hermaphrodite, the zebra goby Lythrypnus zebra: insights gained through a comparison with its sympatric congener, Lythrypnus dalli

Synopsis The sexual pattern of the zebra goby Lythrypnus zebra, is an apparent exception to sex allocation theory. Most L. zebra are simultaneous hermaphrodites (i.e., have active female and male gonadal tissue), yet it appears they do not reproduce as males and females simultaneously. Understanding the maintenance of simultaneous hermaphroditism in L. zebra could expand sex allocation theory. In this study, I used a comparison with the blue-banded goby, Lythrypnus dalli, a sympatric congener with a qualitatively similar sexual pattern, to investigate the role of male spawning rate, body size and sexual flexibility in determining the sexual pattern of L. zebra and to isolate differences between the species that might explain their differing sexual patterns. Using field measurements of male nesting success, I found no differences between the species in the body size of nesting males suggesting that large size is associated with successful male reproduction in both species. In addition, nesting males spawned at approximately three times the rate of females in both species; thus, reproduction via male function can be equally advantageous relative to adopting the female role. However, the nest longevity of L. zebra males was shorter than that of L. dalli males, suggesting reproduction via male function may be less reliable in L. zebra. Finally, under laboratory conditions, L. zebra females tended to prefer large mates, and L. zebra were able to re-allocate in both directions, exhibiting a greater capacity to switch than L. dalli. Given these results, I suggest that switching between the sexes plays a greater role in maintaining simultaneous hermaphroditism in L. zebra than L. dalli, perhaps because male reproduction is not as consistent in L. zebra. Sexual flexibility may be an important factor affecting patterns of sex allocation, generally.     

The origin and recycling of sedimented biogenic debris in a subalphine eutrophic lake (Lake Bled, Slovenia)

The areal distribution of organic C contents, ¹³C values, total N and P and biogenic Si contents in surficial sediments were used to study the distribution, origin and diagenetic transformations of sedimented biogenic debris in the eutrophic subalpine Lake Bled (Slovenia), which for most of the yearhas an anoxic hypolimnion. The influence of an allochthonous input, restricted to the western basin, was clearly traced by higher organic C and total N and P contents, higher ¹³C values, and higher sedimentation rate in comparison to the eastern basin. The low ¹³C values of sedimentary organic matter in the major part of the lake, lower than the ¹³C values of different types of organic matter, suggest that this sedimentary organic matter is most probably the product of a microbial community and not a residue of primary production.The temporal variation of benthic diffusive fluxes of NH₄, Si and PO₄, derived from modelling the pore water profiles, was related to sedimentation of phytoplanktonic blooms, while the PO₄ fluxes were also dependent on changing redox conditions at the sediment-water interface in the period of the winter-spring overtum. The removal of PO₄ in pore waters is probably due to the adsorption of phosphate and precipitation of apatite and vivianite. The budget of C, N and P at the sediment-water interface revealed a high recycling efficiency (>70%), also confirmed by the rather uniform (or only slightly decreasing) vertical profiles of organic C, total N and P in sediment cores and C/N and C/P ratios. The percentage of biogenic Si recycling is low (<10%), suggesting its removal in sediments.     

Soil nitrogen dynamics along a gradient of long-term soil development in a Hawaiian wet montane rainforest

I analyzed the rates of net N mineralization and nitrification of soils from seven sites in a Hawaiian wet montane forest. The sites differ in age, ranging from 400 to 4,100,000 yr, but are comparable in other variables (all at 1200 miasl with 4000 mm or more mean annual rainfall), and the chronosequence simulated a development of soils from basaltic lava. Soils were incubated for 20 days at 17.5 °C, which is nearly equivalent to a mean field air temperature of the sites, and at an elevated temperature of 25.5 °C under three treatments: 1) field-wet without amendments, 2) air dried to a permanent wilting point, and 3) fertilized with phosphate (NaH₂PO₄) at the rate of 50 g P per g dry soil. Both mineralization and nitrification rates varied significantly among the sites at the field temperature (p<.00001). Fractions of the mineralized organic matter (indexed by the N produced per g organic C) increased sharply from the youngest to the 5000-yr site before declining abruptly to a near constant value from the 9000 to the 1,400,000-yr sites. Total organic C in the top soils (<15 cm deep) increased almost linearly with age across the sites. Consequently, net NH₄- and NO₃-N produced on an area basis (g m^-2 20 d^-1) increased sharply from 0.2 in the youngest site to 1.2 in the 5000-yr site, then both became depressed once but steadily increased again. The fraction of organic matter mineralized, and the net N turnover rates were outstandingly high in the oldest site where a large amount of organic matter was observed; the topsoil organic matter which was used in this analysis appeared to be highly labile, whereas the subsurface organic matter could be relatively recalcitrant. As suggested by earlier workers, the initial increase in N turnover seemed to correspond to the increasing quantity of N in the soils through atmospheric deposition and biological fixation. The later decline in fraction of organic matter mineralized seemed to relate to increasing soil C/N ratios, increasingly recalcitrant organic matter, and poorer soil drainage with age. The elevated temperature treatment produced significantly higher amounts of N mineralization, except for the youngest site where N was most limiting, and for two sites where soil waterlogging might be severe. P fertilization invariably resulted in slower N turnovers, suggesting that soil microbes responded to added P causing N immobilization. The youngest site did not significantly respond to added P. The magnitude of immobilization was higher in older than in younger soils, suggesting that P more strongly limits microbial populations in the older soils.