The Variance of Coalescent Time Estimates from DNA Sequences

A method for estimating the variance of a simple estimate of the time of the most recent common ancestor of a sample of sequences is described. [Reviewing Editor: Dr. Rasmus Nielson]     

PCA and Clustering Reveal Alternate mtDNA Phylogeny of N and M Clades

Phylogenetic trees based on mtDNA polymorphisms are often used to infer the history of recent human migrations. However, there is no consensus on which method to use. Most methods make strong assumptions which may bias the choice of polymorphisms and result in computational complexity which limits the analysis to a few samples/polymorphisms. For example, parsimony minimizes the number of mutations, which biases the results to minimizing homoplasy events. Such biases may miss the global structure of the polymorphisms altogether, with the risk of identifying a "common" polymorphism as ancient without an internal check on whether it either is homoplasic or is identified as ancient because of sampling bias (from oversampling the population with the polymorphism). A signature of this problem is that different methods applied to the same data or the same method applied to different datasets results in different tree topologies. When the results of such analyses are combined, the consensus trees have a low internal branch consensus. We determine human mtDNA phylogeny from 1737 complete sequences using a new, direct method based on principal component analysis (PCA) and unsupervised consensus ensemble clustering. PCA identifies polymorphisms representing robust variations in the data and consensus ensemble clustering creates stable haplogroup clusters. The tree is obtained from the bifurcating network obtained when the data are split into k = 2,3,4,...,kmax clusters, with equal sampling from each haplogroup. Our method assumes only that the data can be clustered into groups based on mutations, is fast, is stable to sample perturbation, uses all significant polymorphisms in the data, works for arbitrary sample sizes, and avoids sample choice and haplogroup size bias. The internal branches of our tree have a 90% consensus accuracy. In conclusion, our tree recreates the standard phylogeny of the N, M, L0/L1, L2, and L3 clades, confirming the African origin of modern humans and showing that the M and N clades arose in almost coincident migrations. However, the N clade haplogroups split along an East-West geographic divide, with a "European R clade" containing the haplogroups H, V, H/V, J, T, and U and a "Eurasian N subclade" including haplogroups B, R5, F, A, N9, I, W, and X. The haplogroup pairs (N9a, N9b) and (M7a, M7b) within N and M are placed in nonnearest locations in agreement with their expected large TMRCA from studies of their migrations into Japan. For comparison, we also construct consensus maximum likelihood, parsimony, neighbor joining, and UPGMA-based trees using the same polymorphisms and show that these methods give consistent results only for the clade tree. For recent branches, the consensus accuracy for these methods is in the range of 1-20%. From a comparison of our haplogroups to two chimp and one bonobo sequences, and assuming a chimp-human coalescent time of 5 million years before present, we find a human mtDNA TMRCA of 206,000 +/- 14,000 years before present.     

Molecular evolution and multilocus sequence typing of 145 strains of SARS-CoV

In this study, we have identified 876 polymorphism sites in 145 complete or partial genomes of SARS-CoV available in the NCBI GenBank. One hundred and seventy-four of these sites existed in two or more SARS-CoV genome sequences. According to the sequence polymorphism, all SARS-CoVs can be divided into three groups: (I) group 1, animal-origin viruses (such as SARS-CoV SZ1, SZ3, SZ13 and SZ16); (II) group 2, all viruses with clinical origin during first epidemic; and (III) group 3, SARS-CoV GD03T0013. According to 10 special loci, group 2 again can be divided into genotypes C and T, which can be further divided into sub-genotypes C1-C4 and T1-T4. Positive Darwinian selections were identified between any pair of these three groups. Genotype C gives neutral selection. Genotype T, however, shows negative selection. By comparing the death rates of SARS patients in the different regions, it was found that the death rate caused by the viruses of the genotype C was lower than that of the genotype T. SARS-CoVs might originate from an unknown ancestor.     

Studies of the ADP/ATP carrier of mitochondria with fluorescent ADP analogue formycin diphosphate

The ADP/ATP carrier was studied by a fluorescent substrate, formycin diphosphate which is the only fluorescent ADP analogue to bind. Its low quantum yield, short decay time and spectral overlap with tryptophan has as yet prevented its wider use.By incorporating fluorescent acceptors of formycin diphosphate fluorescence, anthracene-maleimide and vinylanthracene, into the membrane, these difficulties were circumvented. Only bound formycin diphosphate transfers energy to the probes so that the secondary emission of these probes is a measure for membrane-bound formycin diphosphate.The fluorescent transfer is inhibited by ADP, bongkrekate and carboxy-atractylate whether added before or after incubation of formycin diphosphate showing that only binding to the adenine nucleotide carrier is measured. It also shows directly that the earlier demonstrated ADP fixation by bongkrekate is indeed a displacement into the matrix.The fluorescence decay time of the bound formycin diphosphate is measured as 1.95 ns compared to 0.95 ns of the free formycin diphosphate, indicating that formycin diphosphate is bound at the carrier in a non-polar environment.The depolarization decay time was found to be larger than 15 ns, indicating that carrier-bound formycin diphosphate is immobile within this time period.     

The adenylate energy charge in marine phytoplantkon: The effect of temperature on the physiological state of Skeletonema costatum (Grev.) Cleve

The adenylate energy charge $\text{([ATP] +}\text{1}\text{2}\text{[ADP])}\text{[0ATP+ADP+AMP]}$ was measured in axenic batch cultures of Skeletonema costatum (Grev.) Cleve at 2°, 10°, 15°, 20°, 24° and 30°C. The results suggest that this eurythermal diatom is physiologically capable of adapting to the 28 °C range of temperature with little apparent difference in the potential energy available to the cell. In N-limited continuous cultures at 15 °C, the energy charge values were lower than those observed in batch culture by 0.2, implying nutrient stress may result in decreased intracellular chemical energy. The utilization of the adenylate energy charge as an indicator of physiological state is suggested.     

Meeting the challenges of on-host and off-host water balance in blood-feeding arthropods

In this review, we describe water balance requirements of blood-feeding arthropods, particularly contrasting dehydration tolerance during the unfed, off-host state and the challenges of excess water that accompany receipt of the bloodmeal. Most basic water balance characteristics during the off-host stage are applicable to other terrestrial arthropods, as well. A well-coordinated suite of responses enable arthropods to conserve water resources, enhance their desiccation tolerance, and increase their water supplies by employing a diverse array of molecular, structural and behavioral responses. Water loss rates during the off-host phase are particularly useful for generating a scheme to classify vectors according to their habitat requirements for water, thus providing a convenient tool with potential predictive power for defining suitable current and future vector habitats. Blood-feeding elicits an entirely different set of challenges as the vector responds to overhydration by quickly increasing its rate of cuticular water loss and elevating the rate of diuresis to void excess water and condense the bloodmeal. Immature stages that feed on blood normally have a net increase in water content at the end of a blood-feeding cycle, but in adults the water content reverts to the pre-feeding level when the cycle is completed. Common themes are evident in diverse arthropods that feed on blood, particularly the physiological mechanisms used to respond to the sudden influx of water as well as the mechanisms used to counter water shortfalls that are encountered during the non-feeding, off-host state.     

Effects of the herbicide atrazine on adenine nucleotide levels in Zostera marina L. (eelgrass)

Response of adenine nucleotides (ATP, ADP, AMP) and adenylate energy charge (EC) to atrazine, a triazine herbicide, was evaluated as an indicator of metabolic state in Zostera marina L. (eelgrass), a submerged marine angiosperm. Short-term (6 h) atrazine stress reduced ATP and total adenylates (AT) at both 10 and 100 ppb, but EC remained constant. Net productivity decreased at 100, but not at 10 ppb atrazine over 6 h. Long-term (21 day) atrazine stress was evidenced by growth inhibition and 50% mortality near 100 ppb. EC was reduced at 0.1, 1.0 and 10 ppb atrazine, but ATP and EC increased with physiological response to severe stress (100 ppb) after 21 days. Apparently, ATP and AT decrease over the short-term but rebound over the long-term with severe atrazine stress, increasing beyond control levels before plant death results. Supplementing adenine nucleotide and EC results with more conventional quantitative analyses should afford greater knowledge of physiological response to environmental variation.     

On the Origin of Operons and Their Possible Role in Evolution Toward Thermophily

We present a hypothesis suggesting that close linkage of functionally related anabolic genes and their ultimate integration into operons developed under selective pressure as a molecular strategy which contributed to the viability of ancestral thermophilic cells. Cotranslation of functionally related proteins is viewed as having facilitated the formation of multienzyme complexes channeling thermolabile substrates and the mutual stabilization of inherently thermolabile proteins. In this perspective, the evolutionary scheme considered the most probable is the evolution of both Bacteria and Archaea by thermoreduction (Forterre 1995) from a mesophilic, protoeukaryotic last common ancestor (LCA) endowed with appreciable genetic redundancy.     

Control of the Mitochondrial Permeability Transition Pore by High-Affinity ADP Binding at the ADP/ATP Translocase in Permeabilized Mitochondria

Low levels of ADP binding at the ADP/ATP translocase caused inhibition of the Ca²⁺-inducedpermeability transition of the mitochondrial inner membrane, when measured using the shrinkage assay on mitochondria, which have already undergone a transition. Inhibition was preventedby carboxyatractyloside, but potentiated by bongkrekic acid, which increased the affinity forinhibition by ADP. This suggests that inhibition was related to the conformation of thetranslocase. Ca²⁺ addition was calculated to remove most of the free ADP. Ca²⁺ added after ADPinduced a slow decay of the inhibition, which probably reflected the dissociation of ADP fromthe translocator. We conclude that the probability of forming a permeability transition pore(PTP) is much greater when the translocase is in the CAT conformation than in the BKAconformation, and, in the absence of CAT and BKA, the translocator is shifted between theBKA and CAT conformations by ADP binding and removal, even in deenergized mitochondria with no nucleotide gradients.     

Energy status in the fat body of Trichoplusia ni parasitized by the insect parasite Hyposoter exiguae

The levels of adenylate nucleotides were examined in 4th-instar Trichoplusia ni larvae 3 days after parasitization by the insect parasite Hyposoter exiguae. In general, parasitization caused a decrease in the level of ATP and increased ADP and AMP levels. These changes resulted in alteration of the adenylate kinase mass-action ratio. The overall energy status of parasitized larvae, however, as indicated by energy ratios, including the “energy charge,” was affected only slightly. The result demonstrates that the host maintained an active and viable metabolic state despite extensive alterations in physiology which occur at this stage of the parasite-host association.