ABC as a flexible framework to estimate demography over space and time: some cons,many pros

The analysis of genetic variation to estimate demographic and historical parameters and to quantitatively compare alternative scenarios recently gained a powerful and flexible approach: the Approximate Bayesian Computation (ABC). The likelihood functions does not need to be theoretically specified, but posterior distributions can be approximated by simulation even assuming very complex population models including both natural and human‐induced processes. Prior information can be easily incorporated and the quality of the results can be analysed with rather limited additional effort. ABC is not a statistical analysis per se, but rather a statistical framework and any specific application is a sort of hybrid between a simulation and a data‐analysis study. Complete software packages performing the necessary steps under a set of models and for specific genetic markers are already available, but the flexibility of the method is better exploited combining different programs. Many questions relevant in ecology can be addressed using ABC, but adequate amount of time should be dedicated to decide among alternative options and to evaluate the results. In this paper we will describe and critically comment on the different steps of an ABC analysis, analyse some of the published applications of ABC and provide user guidelines.     

Spatial distribution of chitinases and β-1,3-glucanase transcripts in bean arbuscular mycorrhizal roots under low and high soil phosphate conditions

Arbuscular mycorrhizal (AM) fungi extensively colonize the root cortex under low-soil-phosphate (P) conditions, whereas infection is limited under high-P conditions. Fungal growth under both P conditions might be influenced by plant defence-related gene expression. In this study, we used in situ hybridization methods to compare the cellular localization of three defence-related mRNAs in non-infected bean roots and in relation to fungal infection units. In non-infected and infected roots, mRNAs encoding acidic and basic endochitinases were generally most abundant in the vascular cylinder. High-P-grown mycorrhizal roots showed localized accumulation of the acidic endochitinase mRNA in cortical cells containing arbuscules and in their immediate vicinity (one to five cell layers). The pattern of accumulation of the basic endochitinase mRNA was not affected by P or AM fungal infection. At the low P concentration, the β-1,3-glucanase mRNA accumulated predominantly in the vascular cylinder of non-infected roots. Suppression of β-1,3-glucanase mRNA accumulation in these tissues was observed in non-infected roots at the high-P and in mycorrhizal roots at both P concentrations. The observed suppression extends at least several mm from fungal infection units, characterizing a systemic effect. Beta-1,3-glucanase mRNA accumulated also around a number of cortical cells containing arbuscules only at the low P concentration. The localized accumulations of the endochitinase and β-1,3-glucanase mRNAs suggest that the encoded proteins might be involved in the control of intraradical fungal growth.     

Tropical zooplankton: phenotypic and spatial analyses of polymorphic Ceriodaphnia cornuta (Crustacea: Cladocera)

SUMMARY. 1. The predation-balanced polymorphism of Ceriodaphnia cornuta (a small-eyed horned form and a large-eyed unhorned form) in Lake Gatun, Panama, is re-examined approximately 12 years after the original study (Zaret, 1972a). We consider morphological variability, distribution and fecundity of the population inhabiting Laboratory Bay.
2. The two morphological characters emphasized by Zaret, eye size and horn length, are studied in detail. The C. cornuta population exhibits wide, yet continuous variation; coefficients of variation are 28% or eye diameter and range from 114% to 136% for horn and spine lengths. Phenotypic variation in the population is characterized by: (1) negative correlations between spine lengths and eye size; (2) positive correlations among spines from different body regions (anterior horn, lateral spines, and tail spine); and (3) weak correlations between body length and spine lengths.
3. While the horned and unhorned forms continue to coexist in Laboratory Bay. the frequencies of horned forms have increased in the open water areas since the time of the original study. The increase in horned form frequencies may be due to changes in fish predation intensity. Did vertical distribution patterns of the forms remain very similar to each other.
4. In contrast to previous laboratory findings, egg ratio calculations from field samples revealed similar clutch sizes for the horned and unhorned forms. The egg development time of the horned form, however, was found to be approximately 30% longer than that of the unhorned form, perhaps because of increased moulting difficulties produced by the presence of spines.     

Prevalence of common <Emphasis Type="Italic">MEFV</Emphasis> mutations and carrier frequencies in a large cohort of Iranian populations

Familial Mediterranean fever (FMF) is a hereditary autoinflammatory disorder caused by mutations in the MEFV gene. The disease is especially common among Armenian, Turkish, Jewish and Middle East Arab populations. To identify the frequency and the spectrum of common MEFV mutations in different Iranian populations, we investigated a cohort of 208 unselected asymptomatic individuals and 743 FMF patients. Nine hundred and fifty-one samples were analysed for the presence of 12 MEFV mutations by PCR and reverse-hybridization (FMF StripAssay, ViennaLab, Vienna, Austria). Confirmatory dideoxy sequencing of all MEFV gene exons was performed for 39 patients. Fifty-seven (27.4%) healthy individual carried mutant MEFV alleles. Three hundred and ninety-one (52.6%) FMF patients were found positive for either one (172/743; 23.1%), two or three MEFV mutations. Using dideoxy sequencing, three novel variants, A66P, R202W and H300Q, could be identified. Our analysis revealed an allele frequency and carrier rate of 15.6 and 27.4%, respectively, among healthy Iranians. Still moderate compared to neighbouring Armenia, but higher than in Turkey or Iraq, these data suggest that FMF is remarkably common among Iranian populations. E148Q was most frequent in the group of healthy individuals, whereas M694V was the most common mutation among FMF patients, thereby corroborating previous studies on MEFV mutational spectra in the Middle East. Accordingly, MEFV mutations are frequent in healthy Iranian individuals across different ethnic groups. Based on this finding, the awareness for FMF and the implementation of augmented carrier screening programmes considering the multiethnic nature of the Iranian population should be promoted.     

Disentangling the effects of recombination,selection, and demography on the genetic variation at a major histocompatibility complex class II gene in the alpine chamois

The major histocompatibility complex (MHC) harbours some of the most polymorphic loci in vertebrate genomes. MHC genes are thought to be subject to some form of balancing selection, most likely pathogen‐mediated selection. Hence, MHC genes are excellent candidates for exploring adaptive processes. In this study, we investigated the genetic variation at exon 2 of the DRB class II MHC locus in 191 alpine chamois (Rupicapra rupicapra) from 10 populations in the eastern Alps of Italy. In particular, we were interested in distinguishing and estimating the relative impact of selective and demographic factors, while taking into account the confounding effect of recombination. The extremely high d_n/d_s ratio and the presence of trans‐species polymorphisms suggest that a strong long‐term balancing selection effect has been operating at this locus throughout the evolutionary history of this species. We analysed patterns of genetic variation within and between populations, and the mitochondrial D‐loop polymorphism patterns were analysed to provide a baseline indicator of the effects of demographic processes. These analyses showed that (i) the chamois experienced a demographic decline in the last 5000–30 000 years, most likely related to the postglacial elevation in temperature; (ii) this demographic process can explain the results of neutrality tests applied to MHC variation within populations, but cannot justify the much weaker divergence between populations implied by MHC as opposed to mitochondrial DNA; (iii) similar sets of divergent alleles are probably maintained with similar frequencies by balancing selection in different populations, and this mechanism is also operating in small isolated populations, which are strongly affected by drift.     

Molecular Phylogeny of Parvilucifera prorocentri (Alveolata, Myzozoa): Insights into Perkinsid Character Evolution

ABSTRACT. Perkinsids and colpodellids are lineages that diverged near the origins of dinoflagellates and apicomplexans, respectively, and provide compelling insights into the earliest stages of alveolate evolution. Perkinsids, including Perkinsus and Parvilucifera , are intracellular parasites of animals and dinoflagellates and possess traits also known in syndineans, dinokaryotes (mainly free living dinoflagellates), and colpodellids. An improved understanding of perkinsid biodiversity and phylogeny is expected to shed considerable light on the evolutionary origins of syndineans and dinokaryotes as well as the cellular identities of environmental sequences derived from marine and freshwater habitats. Accordingly, the small subunit (SSU) rDNA sequence from Parvilucifera prorocentri , a tube-forming intracellular parasite of the marine benthic dinoflagellate Prorocentrum fukuyoi , was determined. Molecular phylogenetic analyses demonstrated, with very high statistical support, that P. prorocentri branched as a sister lineage to a divergent clade consisting of Parvilucifera infectans and Parvilucifera sinerae . The entire Parvilucifera clade was nested within a more inclusive and modestly supported clade consisting of Perkinsus and several environmental sequences. Because P. prorocentri possessed a novel combination of ultrastructural features known in Perkinsus, Parvilucifera , and/or syndineans (i.e. germ tubes, trichocysts, and a syndinean-like nucleus), establishing the molecular phylogenetic position of this species enabled us to build a more comprehensive framework for understanding the earliest stages in the evolution of myzozoans.     

The Uptake of Pyrimidine Nucleosides in Tetrahymena. I. Uridine*

SYNOPSIS. Uridine uptake was examined in Tetrahymena pyriformis GL-7 in defined medium under conditions where food vacuole formation is not a significant factor in solute acquisition by the cell. The results indicate the presence of a saturable mechanism which follows Michaelis-Menten kinetics. When corrected for diffusion the apparent K_m for the carrier is 2.3 ± 0.6 μM and the V_max is 7.3 ± 0.2 × 10^?7 nmoles/cell/min. It is evident from nucleotide pool analysis that most of the radioactivity of externally supplied [³H]uridine appears in UMP with the remainder in UTP. Uridine is apparently phosphorylated immediately upon entry into the cell and neither uridine-cytidine kinase activity nor RNA synthesis are rate-limiting in the uptake process. Uridine transport is competitively inhibited by a variety of ribo- and deoxyribonucleosides as well as several nucleoside analogs. Neither uracil nor ribose or deoxyribose are effective inhibitors of uridine transport indicating the carrier is specific for the nucleoside. There is little difference between the K_i values for ribo- as opposed to deoxyribonucleosides except in the case of deoxyguanosine which is much less effective as an inhibitor under the conditions of this study, than all the other nucleosides, including guanosine.     

Trypanosoma acomys (Wenyon, 1909): Continuous Culturing with a Mouse Fibroblast Cell-Line (A9)

The continuous culturing of Trypanosoma acomys in the presence of a murine areolar-adipose cell line (A9) was possible for the 1st time. The trypanosomes were cultured at 37° C with A9 in DMEM supplemented with 20% heat inactivated fetal bovine serum, using an initial inoculum from primary cultures of lung or blood clots from infected spiny mice. The cultures were maintained for 115 days and underwent 15 passages before termination and cryopreservation. Using this culture system T. acomys subcultures were initiated from 3 different initial inocula (3 × 10⁴, 1.5 × 10⁵ and 7.4 × 10⁵ parasites/ml) and growth curves revealed that the lowest inoculum gave the best growth pattern. This inoculum yielded a population doubling time of less than 12 h for 4 days, a high peak density of 7 × 10⁶ parasites/ml and the most gradual decline compared to the other 2 inocula. Rosetting epimastigotes and nests of amastigotes were observed in close association with the feeder layer cells. Epimastigotes were the most predominant form in culture supernatants but other morphological forms observed included trypomastigotes and sphaeromastigotes.