Leveraging whole genome sequencing data for demographic inference with approximate Bayesian computation

Accounting for historical demographic features, such as the strength and timing of gene flow and divergence times between closely related lineages, is vital for many inferences in evolutionary biology. Approximate Bayesian computation (ABC) is one method commonly used to estimate demographic parameters. However, the DNA sequences used as input for this method, often microsatellites or RADseq loci, usually represent a small fraction of the genome. Whole genome sequencing (WGS) data, on the other hand, have been used less often with ABC, and questions remain about the potential benefit of, and how to best implement, this type of data; we used pseudo‐observed data sets to explore such questions. Specifically, we addressed the potential improvements in parameter estimation accuracy that could be associated with WGS data in multiple contexts; namely, we quantified the effects of (a) more data, (b) haplotype‐based summary statistics, and (c) locus length. Compared with a hypothetical RADseq data set with 2.5 Mbp of data, using a 1 Gbp data set consisting of 100 Kbp sequences led to substantial gains in the accuracy of parameter estimates, which was mostly due to haplotype statistics and increased data. We also quantified the effects of including (a) locus‐specific recombination rates, and (b) background selection information in ABC analyses. Importantly, assuming uniform recombination or ignoring background selection had a negative effect on accuracy in many cases. Software and results from this method validation study should be useful for future demographic history analyses.     

pathmatrix: a geographical information system tool to compute effective distances among samples

pathmatrix is a tool used to compute matrices of effective geographical distances among samples using a least‐cost path algorithm. This program is dedicated to the study of the role of the environment on the spatial genetic structure of populations. Punctual locations (e.g. individuals) or zones encompassing sample data points (e.g. demes) are used in conjunction with a species‐specific friction map representing the cost of movement through the landscape. Matrices of effective distances can then be exported to population genetic software to test, for example, for isolation by distance. pathmatrix is an extension to the geographical information system (GIS) software arcview 3.x.     

Uncoupling of mitochondrial oxidative phosphorylation by thallium.

The mechanism of integration of λ$\text{bio}$ll, which is deleted of all the known λ recombination genes, was studied using $\text{bio}$ deleted hosts as recipients. The presence of $\text{rec}$BC DNase and $\text{exo}$I in the recipient cells affected the fate of λ$\text{bio}$ll DNA. In nine of ten $\text{imm}\text{λ}{}^{\mathrm{+}}$ transductants, insertion of the λ$\text{bio}$ll genome took place somewhere between J and N and the remaining one had abnormally permuted prophage λ. In this lysogen (#42), the sequence of prophage genes was similar to that of vegetative phage λ. The properties of lysogen #42 were compared with those of other lysogens.     

Stonefly nymphs use hydrodynamic cues to discriminate between prey

Summary Playback experiments conducted in a Rocky Mountain, USA, stream determined whether predatory stonefly nymphs (Kogotus modestus; Plecoptera: PerlodiMae) used hydrodynamic cues to discriminate prey species from nonprey species. In the laboratory we recorded pressure wave patterns associated with swimming escape behavior of Baetis bicaudatus (Baetidae), the favored mayfly prey species, and those of a nonprey mayfly, Ephemerella infrequens (Ephemerellidae). We video taped the responses of 24-h starved Kogotus to Baetis playbacks, Ephemerella playbacks or no playbacks made by oscillating (or not) live mayflies (Ephemerella) or clear plastic models placed within in situ flow-through observation boxes. The probability of attacks per encounter with Baetis playbacks was highest and independent of the model type used, but Kogotus also showed an unexpected high probability of attacks per encounter when Ephemerella playbacks were made through live Ephemerella. Thus, Kogotus discriminated between Baetis and Ephemerella swimming patterns but only when playbacks were made through the plastic model. Kogotus never attacked motionless mayflies or motionless plastic models. We allowed some Kogotus to successfully capture one small Baetis immediately before playbacks, which resulted in a much higher probability of attacks per encounter with Baetis playbacks on either model and a heightened discrimination of prey versus nonprey playbacks. The probability of attacks per encounter by Kogotus with live Baetis swimming under similar experimental conditions was strikingly similar to its response to Baetis playbacks made by oscillating the plastic model after a successful capture. Order of playback presentation (Baetis first or Ephemerella first) did not influence predatory responses to mayfly swimming patterns. This study is the first to document the use of hydrodynamic cues by stream-dwelling predators for discrimination of prey from nonprey and provides a mechanism to explain selective predation by stoneflies on Baetis in nature.     

Induction of hepatic metallothionein by salicylate in adult rats

Application of salicylate increased the concentration of metallothionein (MT) in liver of pregnant rats as well as of adult male rats, whereas in fetal liver, MT was reduced by salicylate. Induction of MT synthesis by salicylate is an indirect effect because in cultured hepatocytes salicylate did not induce MT synthesis. Salicylate increased MT also in adrenalectomized rats. Indomethacin induced the same concentration of MT in maternal liver as salicylate. However, indomethacin had no effect on MT in fetal liver. Induction of MT in adult liver by salicylate and indomethacin was independent of zinc.     

Induction of hepatic drug metabolizing enzymes by DL-methionine in rats

A single intraperitoneal injection of DL-methionine (500 mg/kg body wt.) to adult male Wistar rats was shown to significantly induce all the components of the hepatic microsomal mixed function oxidase system such as NADPH cytochrome C reductase activity, cytochromes P-450 and b₅, as well as activities of drug metabolizing enzymes such as aminopyrine demethylase and uridine 5′ -diphosphate-glucuronosyltransferase. Combined administration of nicotinamide (250 mg/kg body wt.) and DL-methionine (500 mg/kg body wt.) was shown to bring about an additional increase (25-30%) in the activities of these enzymes as compared to their induction on independent administration of the two endobiotics. In rats bearing Yoshida sarcoma (ascites) tumour as well as in normal rats injected with serum from tumour bearing animals, the decreased activities of hepatic mixed function oxidases could be restored to their normal levels by administration of DL-methionine (500 mg/kg body wt.) to these rats. Whereas actinomycin D (1 mg/kg body wt.) had no effect on the increased incorporation of [¹⁴C] labelled leucine into microsomal proteins following administration of nicotinamide, the enhanced incorporation of the label following DL-methionine administration was completely inhibited by the same dose of actinomycin D. Administration of cycloheximide (0·5 mg/kg body wt.) to rats could completely inhibit the increased incorporation of [¹⁴C] leucine into hepatic microsomal proteins following independent administration of nicotinamide and DL-methionine. Similar inhibitory pattern with actinomycin D and cycloheximide was also demonstrated in case of induction of NADPH cytochromeC reductase activity by both these endobiotics.     

Analysis of the Escherichia coli glycogen gene cluster suggests that catabolic enzymes are encoded among the biosynthetic genes

The nucleotide sequences of the Escherichia coli genome between the glycogen biosynthetic genes glgB and glgC, and 1170 bp of DNA which follows glgA have been determined. The region between glgB and glgC contains an open reading frame (ORF) of 1521 bp which we call glgX. This ORF is capable of coding for an M_r 56 684 protein. The deduced amino acid (aa) sequence for the putative product shows significant similarity to the E. coli glycogen branching enzyme, and to several different glucan hydrolases and transferases. The regions of sequence similarity include residues which have been reported to be involved in substrate binding and catalysis by taka-amylase. This suggests that the proposed product may catalyze hydrolysis or glycosyltransferase reactions. The cloned region which follows glgA contains an incomplete ORF (1149 bp), glgY, which appears to encode 383 aa of the N terminus of glycogen phosphorylase, based upon sequence similarity with the enzyme from rabbit muscle (47% identical aa residues) and with maltodextrin phosphorylase from E. coli (37% identical aa residues). Results suggest that neither ORF is required for glycogen biosynthesis. The localization of glycogen biosynthetic and degradative genes together in a cluster may facilitate the regulation of these systems in vivo.     

The major light-harvesting complex of Photosystem II: aspects of its molecular and cell biology

The light-harvesting complex of photosystem II (LHC II) contains one major (LHC IIb) and at least three minor chlorophyll-protein components. The apoproteins of LHC IIb (LHCP) are encoded by nuclear genes and synthesized in the cytoplasm as a higher molecular weight precursor(s) (pLHCP). Several genes coding for pLHCP have been cloned from various higher plant species. The expression of these genes is dependent upon a variety of factors such as light, the developmental stage of the plastids and the plant. After its synthesis in the cytoplasm, pLHCP is imported into plastids, inserted into thylakoids, processed to its mature form, and assembled into LHC IIb. The pathway of assembly of LHC IIb in the thylakoid membranes is currently being investigated in several laboratories. We present a model that gives some details of the steps in the assembly process. Many of the steps involved in the synthesis and assembly are dependent on light and the stage of plastid development.Abbreviations PS Photosystem - LHC II Light-harvesting complex of PS II - LHCP Apoproteins of LHC IIb - pLHCP Precursor of LHCP - PAGE Polyacrylamide gel electrophoresis