Updating the evolutionary history of Carnivora (Mammalia): a new species-level supertree complete with divergence time estimates

Background

Although it has proven to be an important foundation for investigations of carnivoran ecology, biology and evolution, the complete species-level supertree for Carnivora of Bininda-Emonds et al. is showing its age. Additional, largely molecular sequence data are now available for many species and the advancement of computer technology means that many of the limitations of the original analysis can now be avoided. We therefore sought to provide an updated estimate of the phylogenetic relationships within all extant Carnivora, again using supertree analysis to be able to analyze as much of the global phylogenetic database for the group as possible.

Results

In total, 188 source trees were combined, representing 114 trees from the literature together with 74 newly constructed gene trees derived from nearly 45,000 bp of sequence data from GenBank. The greater availability of sequence data means that the new supertree is almost completely resolved and also better reflects current phylogenetic opinion (for example, supporting a monophyletic Mephitidae, Eupleridae and Prionodontidae; placing Nandinia binotata as sister to the remaining Feliformia). Following an initial rapid radiation, diversification rate analyses indicate a downturn in the net speciation rate within the past three million years as well as a possible increase some 18.0 million years ago; numerous diversification rate shifts within the order were also identified.

Conclusions

Together, the two carnivore supertrees remain the only complete phylogenetic estimates for all extant species and the new supertree, like the old one, will form a key tool in helping us to further understand the biology of this charismatic group of carnivores.     

Red antenna states of photosystem I from Synechococcus sp. PCC 7002

Absorption, fluorescence and single-molecule spectroscopy at low temperatures were used to elucidate spectral properties, heterogeneities and dynamics of the red-shifted chlorophyll a (Chla) molecules responsible for the fluorescence in photosystem I (PSI) from the cyanobacterium Synechoccocus sp. PCC 7002. The 77 K absorption spectrum indicates the presence of 2–3 red-shifted Chla’s absorbing at about 708 nm. The fluorescence emission spectrum is dominated by a broad band at 714 nm. The emission spectra of single PSI complexes show zero-phonon lines (ZPLs) as well as a broad intensity distribution without ZPLs. The spectral region below 710 nm often shows ZPLs, they form a spectral band with a maximum at 698 nm (F698). The region above 710 nm is dominated by broad intensity distributions and the observation of ZPLs is less frequent. The broad distributions are due to the emission of the C708 Chla’s and the emission from F698 stems from a Chla species absorbing at the blue side of P700. The properties of these two emissions show a close relation to those of the C708 and C719 pools observed in T. elongatus. Therefore an assignment of F698 and C708 to Chla-species with similarities to C708 and C719 in T. elongatus is proposed.     

Fermentation characterization and flux analysis of recombinant strains of Clostridium acetobutylicum with an inactivated solR gene

The effect of solR inactivation on the metabolism of Clostridium acetobutylicum was examined using fermentation characterization and metabolic flux analysis. The solR-inactivated strain (SolRH) of this study had a higher rate of glucose utilization and produced higher solvent concentrations (by 25%, 14%, and 81%, respectively, for butanol, acetone, and ethanol) compared to the wild type. Strain SolRH(pTAAD), carrying a plasmid-encoded copy of the bifunctional alcohol/aldehyde dehydrogenase gene (aad) used in butanol production, produced even higher concentrations of solvents (by 21%, 45%, and 62%, respectively, for butanol, acetone, and ethanol) than strain SolRH. Clarithromycin used for strain SolRH maintenance during SolRH(pTAAD) fermentations did not alter product formation; however, tetracycline used for pTAAD maintenance resulted in 90% lower solvent production. Journal of Industrial Microbiology & Biotechnology (2001) 27, 322–328. Received 12 September 2000/ Accepted in revised form 21 July 2001     

京郊典型集约化"农田-畜牧"生产系统氮素流动特征

城郊畜牧业的集约化发展在满足人们日益增长的肉蛋奶等动物性产品需求的同时,也带来了巨大的环境压力。本文利用养分流动和模型分析的方法,分析北京市郊区某村三种不同类型"农田-畜牧"生产系统(大型集约化种猪场、种养结合小规模生态养殖园和集约化单一种植区)的氮素流动特征。结果表明:饲料是集约化种猪场和生态养殖园氮素输入的主要来源,饲料投入氮量分别为12469.0和9268.5 kg.hm-.2a-1);集约化种猪场农牧体系间生产脱节,致使农田氮素输入主要依赖于化肥投入,化肥氮输入量(435.0 kg.hm-.2a-1)占农田氮素输入量的82.7%。相反,生态养殖园农牧体系结合紧密,猪粪尿氮还田比例达28.6%,这使得园区化肥氮输入量仅为135.0 kg.hm-.2a-1,因此畜禽粪尿的合理循环利用可作为减少化肥投入的有效途径;集约化种猪场、生态养殖园和单一种植区农牧生产系统氮素利用效率分别为18.8%、20.6%和17.3%,均处于较低水平;集约化种猪场猪粪尿在猪舍和储藏处理过程的氮素损失率为15.8%和25.4%,分别低于小规模生态养殖园相应损失率约8.7和4.8个百分点;生态养殖园粪肥氮还田量高,导致农田氮素盈余量高达1962.8 kg.hm-.2a-1,未能实现生态型养殖的理想效果,优化氮素管理、确定合理的消纳畜禽粪尿的农田面积和调整畜禽养殖密度是解决该问题的关键。     

Significance of nitrate leaching and long term N immobilization after deepening the plough layers for the N regime of arable soils in N.W. Germany

Field studies were conducted to assess the turnover and the leaching of nitrogen in arable soils of Lower Saxony (NW Germany). The mean surplus N (difference between N inputs by fertilization and N export by the yield; 146 field plots) from 1985–1988 amounted to 38 kg ha^-1 yr^-1 in fine textured (clay, loam, silt) and to 98 kg ha^-1 yr^-1 in coarse (sandy) soils. Leaching of nitrate calculated by a simple functional model for simulation of the N regime over the winter period (i.e. mineralization and leaching) was 16 kg ha^-1 in the fine and 63 kg N ha^-1 in coarse soils (mean values of the winter periods 1985–1988 from 256 plots).Before the 1960s, the depth of the A_p horizons rarely exceeded 25 cm in arable soils of the former FRG. During the last three decades, ploughing depth has increased to at least 35 cm. The mass balance calculations for total N after ploughing to 35 cm in loess soils of southern Lower Saxony (105 farm plots) yielded a mean increase in total N by about 900 kg ha^-1 in 20 years. With respect to soil organic matter equilibria, N accumulation will continue for at least another 10 years on 67% of the examined farm plots. This study suggests that long term N immobilization is one of the most important sinks for nitrogen in arable soils of Germany. For simulation of the N dynamics over the growing season and for long time periods total nitrogen dynamics need to be considered.     

Deep ploughing increases agricultural soil organic matter stocks

Subsoils play an important role within the global C cycle, since they have high soil organic carbon (SOC) storage capacity due to generally low SOC concentrations. However, measures for enhancing SOC storage commonly focus on topsoils. This study assessed the long‐term storage and stability of SOC in topsoils buried in arable subsoils by deep ploughing, a globally applied method for breaking up hard pans and improving soil structure to optimize crop growing conditions. One effect of deep ploughing is translocation of SOC formed near the surface into the subsoil, with concomitant mixing of SOC‐poor subsoil material into the ‘new’ topsoil. Deep‐ploughed croplands represent unique long‐term in situ incubations of SOC‐rich material in subsoils. In this study, we sampled five loamy and five sandy soils that were ploughed to 55–90 cm depth 35–50 years ago. Adjacent, similarly managed but conventionally ploughed subplots were sampled as reference. The deep‐ploughed soils contained on average 42 ± 13% more SOC than the reference subplots. On average, 45 years after deep ploughing, the ‘new’ topsoil still contained 15% less SOC than the reference topsoil, indicating long‐term SOC accumulation potential in the topsoil. In vitro incubation experiments on the buried sandy soils revealed 63 ± 6% lower potential SOC mineralisation rates and also 67 ± 2% lower SOC mineralisation per unit SOC in the buried topsoils than in the reference topsoils. Wider C/N ratio in the buried sandy topsoils than in the reference topsoils indicates that deep ploughing preserved SOC. The SOC mineralisation per unit SOC in the buried loamy topsoils was not significantly different from that in the reference topsoils. However, 56 ± 4% of the initial SOC was preserved in the buried topsoils. It can be concluded that deep ploughing contributes to SOC sequestration by enlarging the storage space for SOC‐rich material.     

Seeing more than meets the eye: processing of illusory contours in animals

This review article illustrates that mammals, birds and insects are able to perceive illusory contours. Illusory contours lack a physical counterpart, but monkeys, cats, owls and bees perceive them as if they were real borders. In all of these species, a neural correlate for such perceptual completion phenomena has been described. The robustness of neuronal responses and the abundance of cells argue that such neurons might indeed represent a neural correlate for illusory contour perception. The internal state of an animal subject (i.e., alert and behaving) seems to be an important factor when correlating neural activity with perceptual phenomena. The fact that the neural network necessary for illusory contour perception has been found in relatively early visual brain areas in all tested animals suggests that bottom-up processing is largely sufficient to explain such perceptual abilities. However, recent findings in monkeys indicate that feedback loops within the visual system may provide additional modulation. The detection of illusory contours by independently evolved visual systems argues that processing of edges in the absence of contrast gradients reflects fundamental visual constraints and not just an artifact of visual processing.     

Multi-Scale Controls on Water Quality Effects of Submerged Aquatic Vegetation in the Tidal Freshwater Hudson River

Patches of submerged vegetation can be important sites of primary production and habitat for organisms in many aquatic ecosystems. In the tidal freshwater Hudson River they make up about 6% of the river bottom area. Direct sampling of water masses passing through patches of vegetation and week-long continuous monitoring of water characteristics were used to determine plant effects on dissolved oxygen and suspended sediments. Vegetated areas could have dissolved oxygen concentrations substantially higher than in the main channel and suspended sediments and turbidity were frequently higher in vegetated areas. Patches of Vallisneria americana had variable capacity to maintain super-saturated oxygen concentrations; patch size accounted for some of the variability whereas larger-scale differences in main-channel influent water also contributed. Differences in turbidity among sites were harder to account for; width of plant beds and abundance of neighboring vegetated areas contributed weakly to predictions of local turbidity. Functional heterogeneity within ecosystems is common and attempts to explain variability may require understanding different controlling factors for different functions and appreciating that factors operate at multiple scales.