Counting the founders: the matrilineal genetic ancestry of the Jewish Diaspora

The history of the Jewish Diaspora dates back to the Assyrian and Babylonian conquests in the Levant, followed by complex demographic and migratory trajectories over the ensuing millennia which pose a serious challenge to unraveling population genetic patterns. Here we ask whether phylogenetic analysis, based on highly resolved mitochondrial DNA (mtDNA) phylogenies can discern among maternal ancestries of the Diaspora. Accordingly, 1,142 samples from 14 different non-Ashkenazi Jewish communities were analyzed. A list of complete mtDNA sequences was established for all variants present at high frequency in the communities studied, along with high-resolution genotyping of all samples. Unlike the previously reported pattern observed among Ashkenazi Jews, the numerically major portion of the non-Ashkenazi Jews, currently estimated at 5 million people and comprised of the Moroccan, Iraqi, Iranian and Iberian Exile Jewish communities showed no evidence for a narrow founder effect, which did however characterize the smaller and more remote Belmonte, Indian and the two Caucasus communities. The Indian and Ethiopian Jewish sample sets suggested local female introgression, while mtDNAs in all other communities studied belong to a well-characterized West Eurasian pool of maternal lineages. Absence of sub-Saharan African mtDNA lineages among the North African Jewish communities suggests negligible or low level of admixture with females of the host populations among whom the African haplogroup (Hg) L0-L3 sub-clades variants are common. In contrast, the North African and Iberian Exile Jewish communities show influence of putative Iberian admixture as documented by mtDNA Hg HV0 variants. These findings highlight striking differences in the demographic history of the widespread Jewish Diaspora.     

Single bioreactor gastrointestinal tract simulator for study of survival of probiotic bacteria

The aim of the present study was to design an in vitro model system to evaluate the probiotic potential of food. A single bioreactor system-gastrointestinal tract simulator (GITS) was chosen for process simulation on account of its considerable simplicity compared to multi-vessel systems used in previous studies. The bioreactor was evaluated by studying the viability of four known probiotic bacteria (Lactobacillus acidophilus La-5, Lactobacillus johnsonii NCC 533, Lactobacillus casei strain Shirota, and Lactobacillus rhamnosus GG) as a function of their physiological state. L. acidophilus and L. johnsonii survived in GITS better when introduced at an early stationary or exponential phase compared to being previously stored for 2 weeks at 4 degrees C. These two species were more resistant to bile salts and survived better than L. casei and L. rhamnosus GG. The latter two species gave large losses (up to 6 log) in plate counts independent of growth state due to the bile. However, experiments with some commercial probiotic products containing Lb. GG bacteria showed much better survival compared with model food (modified deMan-Rogosa-Sharpe growth medium), thus demonstrating the influence of the food matrix on the viability of bacteria. The study demonstrated that GITS can be successfully used for evaluation of viability of probiotic bacteria and functionality of probiotic food.     

Maternal footprints of Southeast Asians in North India

We have analyzed 7,137 samples from 125 different caste, tribal and religious groups of India and 99 samples from three populations of Nepal for the length variation in the COII/tRNA(Lys) region of mtDNA. Samples showing length variation were subjected to detailed phylogenetic analysis based on HVS-I and informative coding region sequence variation. The overall frequencies of the 9-bp deletion and insertion variants in South Asia were 1.9 and 0.6%, respectively. We have also defined a novel deep-rooting haplogroup M43 and identified the rare haplogroup H14 in Indian populations carrying the 9-bp deletion by complete mtDNA sequencing. Moreover, we redefined haplogroup M6 and dissected it into two well-defined subclades. The presence of haplogroups F1 and B5a in Uttar Pradesh suggests minor maternal contribution from Southeast Asia to Northern India. The occurrence of haplogroup F1 in the Nepalese sample implies that Nepal might have served as a bridge for the flow of eastern lineages to India. The presence of R6 in the Nepalese, on the other hand, suggests that the gene flow between India and Nepal has been reciprocal.     

Oviposition in an eruptive moth species, Yponomeuta evonymellus, is insensitive to the population density experienced during the larval period

We studied if the population density experienced during larval development affects the reproductive schedule of Yponomeuta evonymellus L. (Lepidoptera, Yponomeutidae), a moth species characterized by outbreak population dynamics. More specifically, we predicted that reproduction would be delayed to facilitate emigration from sites with suboptimally high densities of conspecifics. We manipulated larval densities in the laboratory, as well as in those pupae collected from the extremes of natural densities. As the response, we also recorded the timing and sizes of egg clutches laid. The results did not support our initial predictions: the timing of oviposition was not dependent on larval growth conditions. This apparent lack of adaptation might be related to the loss of ‘memory’ during metamorphosis in holometabolous insects. However, oviposition schedules were also only minimally sensitive to elevated adult density. An inability to respond to high larval densities may contribute to the outbreak dynamics in this species.     

Carotenoid-based colour polyphenism in a moth species: search for fitness correlates

Carotenoid‐based integumental coloration is often associated with individual performance in various animals. This is because the limited amount of the pigment has to be allocated to different vital functions. However, most of the evidence for the carotenoid‐based trade‐off comes from vertebrate studies, and it is unclear if this principle can be applied to insects. This possibility was investigated in Orgyia antiqua L. (Lepidoptera: Lymantriidae). The larvae of this species are polyphenic in their coloration, varying from a highly conspicuous combination of yellow hair tufts on black background to cryptic appearance with brown hair tufts. The conspicuous larvae are aposematic, advertising their aversive hairiness. The maintenance of different colour morphs in O. antiqua requires explanation, as an aposematic signal is expected to evolve towards monomorphism. Chromatographic analysis showed that the yellow coloration of the hair is based on the carotenoid pigment lutein (α‐carotene‐3,3’‐diol). The colour of hair tufts was dependent on their carotenoid content. This justifies an expectation of carotenoid‐based physiological trade‐offs between aposematic coloration and individual performance. To test this hypothesis, we monitored life histories of differently coloured larvae reared on various host plants, recording their body sizes, growth rates, and mortalities in each instar. There was a significant but relatively low heritability of tuft coloration, which allowed us to expect environmental effects. We found no phenotypic associations between hair tuft colour and performance indices in O. antiqua larvae, neither did the quality of host plant affect the frequency of colour morphs. However, the frequency of colour morphs differed between larval instars. Our results suggest that carotenoid‐mediated physiological trade‐offs are not involved in the maintenance of colour morphs in O. antiqua larvae, and factors other than individual condition should be responsible for the observed variability.     

Evaluating the role and measures of juvenile growth rate: latitudinal variation in insect life histories

Latitudinal and elevational trends in body size are found in numerous animal taxa, with various adaptive explanations proposed. It is however debatable whether geographic trends in adult body size are accompanied by corresponding differences in juvenile growth rate (= mass gain per unit time). Respective studies have been complicated by conceptual and methodological problems related to defining and measuring this variable, particularly in organisms with discontinuous growth like arthropods. Using an original method for estimating differential (instantaneous) juvenile growth rates, we compared geographically distant European populations of six insect species in a common garden experiment. We found no among population differences in differential growth rate in any of the species. This result is in concert with concurrent increase in both adult size and developmental time towards the south. While opposite examples exist, we interpret our results as challenging the view that growth rate is a trait that readily responds to environmentally based selective pressures. Our results thus advocate the more classical view of growth rate maximisation within its physiological limits. We discuss the advantages of using differential (rather than integral) measures of growth rate in evolutionary ecological studies and evaluate the reasons for the detected latitudinal trends in life history traits.     

Seasonal variability in the grazing potential of the invasive amphipod Gammarus tigrinus and the native amphipod Gammarus salinus (Amphipoda: Crustacea) in the northern Baltic Sea

Mesograzers are known to reduce the biomass of their host plant and modify the structure of the whole macrophyte community in many ecosystems. Thus, the introduction of an efficient mesograzer may destabilize macrophyte community and also affect the native grazers. We estimated how large proportion of macrophyte production are consumed by the alien gammarid G. tigrinus and the native gammarid G. salinus in the species poor ecosystem of the northern Baltic Sea. We analysed whether G. tigrinus consumes different diet as the native G. salinus and whether the effect of G. tigrinus on the survival of the native G. salinus is macrophyte species specific. Grazing experiments showed that there was a clear difference in the grazing rates of gammarids among the studied macrophyte species in summer and autumn but not in spring. The grazing rates were significantly higher in the prevailing macrophyte Pilayella littoralis as compared to other macrophytes. The grazing was inversely related to the diurnal net photosynthetic values of macrophytes. The gammarid amphipods potentially removed only a minor part of plant primary production except for summer and autumn when grazing of a few perennial species exceeded macrophyte production. Macrophyte species and presence of G. salinus had no effect on the survival of G. tigrinus. The presence of G. tigrinus, however, reduced the survival of the native gammarids within P. littoralis in summer. To conclude it is likely that both native and alien gammarid amphipods do not exert significant pressure on the macroalgal communities in the northern Baltic Sea. Competitive interactions between G. tigrinus and G. salinus within the prevailing macrophyte P. littoralis is the likely explanation of the decline of the native gammarid amphipods after the establishment of G. tigrinus in the northern Baltic Sea.     

Decreased Rate of Evolution in Y Chromosome STR Loci of Increased Size of the Repeat Unit

Background

Polymorphic Y chromosome short tandem repeats (STRs) have been widely used in population genetic and evolutionary studies. Compared to di-, tri-, and tetranucleotide repeats, STRs with longer repeat units occur more rarely and are far less commonly used.

Principal Findings

In order to study the evolutionary dynamics of STRs according to repeat unit size, we analysed variation at 24 Y chromosome repeat loci: 1 tri-, 14 tetra-, 7 penta-, and 2 hexanucleotide loci. According to our results, penta- and hexanucleotide repeats have approximately two times lower repeat variance and diversity than tri- and tetranucleotide repeats, indicating that their mutation rate is about half of that of tri- and tetranucleotide repeats. Thus, STR markers with longer repeat units are more robust in distinguishing Y chromosome haplogroups and, in some cases, phylogenetic splits within established haplogroups.

Conclusions

Our findings suggest that Y chromosome STRs of increased repeat unit size have a lower rate of evolution, which has significant relevance in population genetic and evolutionary studies.