Does your species have memory? Analyzing capture–recapture data with memory models

We examine memory models for multisite capture–recapture data. This is an important topic, as animals may exhibit behavior that is more complex than simple first‐order Markov movement between sites, when it is necessary to devise and fit appropriate models to data. We consider the Arnason–Schwarz model for multisite capture–recapture data, which incorporates just first‐order Markov movement, and also two alternative models that allow for memory, the Brownie model and the Pradel model. We use simulation to compare two alternative tests which may be undertaken to determine whether models for multisite capture–recapture data need to incorporate memory. Increasing the complexity of models runs the risk of introducing parameters that cannot be estimated, irrespective of how much data are collected, a feature which is known as parameter redundancy. Rouan et al. (JABES, 2009, pp 338–355) suggest a constraint that may be applied to overcome parameter redundancy when it is present in multisite memory models. For this case, we apply symbolic methods to derive a simpler constraint, which allows more parameters to be estimated, and give general results not limited to a particular configuration. We also consider the effect sparse data can have on parameter redundancy and recommend minimum sample sizes. Memory models for multisite capture–recapture data can be highly complex and difficult to fit to data. We emphasize the importance of a structured approach to modeling such data, by considering a priori which parameters can be estimated, which constraints are needed in order for estimation to take place, and how much data need to be collected. We also give guidance on the amount of data needed to use two alternative families of tests for whether models for multisite capture–recapture data need to incorporate memory.     

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.     

Dietary fat saturation produces lipid modifications in peritoneal macrophages of mouse

We investigated the effects of a saturated fat diet on mice lipid metabolism in resident peritoneal macrophages. Male C57BL/6 mice were weaned at 21 days of age and assigned to either the experimental diet, containing coconut oil (COCO diet), or the control diet, containing soybean oil as fat source. Fat content of each diet was 15% (w/w). Mice were fed for 6 weeks until sacrifice. In plasma of mice fed the COCO diet, the concentration of triglyceride, total cholesterol, HLD- and (LDL+VLDL)-cholesterol, and thiobarbituric acid-reactive substances (TBARS) increased, without changes in phospholipid concentration, compared with the controls. In macrophages of COCO-fed mice, the concentration of total (TC), free and esterified cholesterol, triglyceride, phospholipid (P) and TBARS increased, while the TC/P ratio did not change. The phospholipid compositions showed an increase of phosphatidylcholine and phosphatidylserine + phosphadytilinositol, a decrease of phosphatidylethanolamine, and no change in phosphatidylglycerol. (3)H(2)O incorporation into triglyceride and phospholipid fractions of macrophages increased, while its incorporation into free cholesterol decreased. Incorporation of [(3)H]cholesterol into macrophages of COCO-fed mice and the fraction of [(3)H]cholesterol ester increased. COCO diet produced an increase in myrystic, palmitic and palmitoleic acids proportion, a decrease in linoleic and arachidonic acids and no changes in stearic and oleic acids, compared with the control. Also, a higher relative percentage of saturated fatty acid and a decrease in unsaturation index (p <0.001) were observed in macrophages of COCO-fed mice. These results indicate that the COCO-diet, high in saturated fatty acids, alters the lipid metabolism and fatty acid composition of macrophages and produces a significant degree of oxidative stress.     

MDR1A (ABCB1)-deficient CF-1 mutant mice are susceptible to cerebral malaria induced by Plasmodium berghei ANKA

Under experimental conditions, Plasmodium berghei infection causes cerebral malaria (CM) in susceptible strains of mice such as C57BL/6 and CBA/Ca, whereas BALB/c or DBA/2J strains serve as a model for CM-resistant mice. The aim of the present study was to investigate the susceptibility of the CF1 mouse strain, carrying a spontaneous mutation of the mdr1a gene, to infection with Plasmodium berghei ANKA (PbA). The mdr1a gene codes for P-glycoprotein (P-gp/ABCB1), an efflux pump that is one of the major components of the blood-brain barrier. P-gp effluxes a broad range of xenobiotics from the brain to blood, preventing accumulation and toxicity in the central nervous system. CFI mdr1a (-/-) mice are used to investigate drug transport by efflux pumps. Because many antimalarial agents are effluxed by P-gp (mefloquine, quinine), it was important to determine whether CF1 mice can develop cerebral malaria to predict drug toxicity during cerebral malaria. Our work showed that CF1 mdr1a (-/-) mice are susceptible to PbA. CF1 and C57BL/6N mice (the reference strain) infected with PbA have similar profiles with regard to clinical signs, brain histological lesions, and brain macrophagic activation observed by immunohistological methods.     

Sulfadiazine/hydroxypropyl-beta-cyclodextrin host-guest system: Characterization, phase-solubility and molecular modeling

In this work we prepared and characterized an inclusion complex of the dihydropteroate synthase inhibitor sulfadiazine (SDZ) in 2-hydroxypropyl-beta-cyclodextrin (HPBCD). From the phase-solubility diagram we observed an increase in the water solubility of the drug, calculating a binding constant of 1879M(-1). The inclusion mode involves a NH(2)-in orientation of the drug in the HPBCD cavity, according to the 2D NMR (ROESY) data and confirmed by molecular modeling using the semiempirical PM6 and RM1 methods.     

COMPARE, a multi-organism system for cross-species data comparison and transfer of information

MOTIVATION: COMPARE is a multi-organism web-based resource system designed to easily retrieve, correlate and interpret data across species. The COMPARE interface provides access to a wide array of information including genomic structure, expression data, annotations, pathways and literature links for human and three widely studied animal models (zebrafish, Drosophila and mouse). A consensus ortholog-finding pipeline combining several ortholog prediction methods allows accurate comparisons of data across species and has been utilized to transfer information from well studied organisms to more poorly annotated ones. AVAILABILITY: http://compare.ibdml.univ-mrs.fr.     

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     

Assessment of individual and conspecific reproductive success as determinants of breeding dispersal of female tree swallows: A capture–recapture approach

Breeding dispersal is a key process of population structure and dynamics and is often triggered by an individual's breeding failure. In both colonial and territorial birds, reproductive success of conspecifics (RSc) can also lead individuals to change breeding sites after a failure on a site. Yet, few studies have simultaneously investigated the independent contribution of individual reproductive success (RSi) and of RSc on dispersal decision. Here, we develop a modeling framework to disentangle the effects of RSi and RSc on demographic parameters, while accounting for imperfect individual detection and other confounding factors such as age or dispersal behavior in the previous year. Using a 10‐year capture–recapture dataset composed of 1,595 banded tree swallows, we assessed the effects of nonmanipulated RSi and RSc on female breeding dispersal in this semicolonial passerine. Dispersal was strongly driven by RSi, but not by RSc. Unsuccessful females were 9.5–2.5 times more likely to disperse than successful ones, depending if they had dispersed or not in the previous year, respectively. Unsuccessful females were also three times less likely to be detected than successful ones. Contrary to theoretical and empirical studies, RSc did not drive the decision to disperse but influenced the selection of the following breeding site once dispersal had been initiated. Because detection of individuals was driven by RSi, which was positively correlated to RSc, assuming a perfect detection as in previous studies may have lead us to conclude that RSc affected dispersal patterns, yet our approach corrected for this bias. Overall, our results suggest that the value and use of RSc as public information to guide dispersal decisions are likely dictated by multiple ecological determinants, such as landscape structure and extent, if this cue is indeed used.