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.     

Effects of Neem EC on gas exchange, tracheal ventilation, and water loss in diapausing pupae of Pieris brassicae

Effects of Neem EC (The Indian Neem Tree Company^TM, 1% azadirachtin) on gas exchange cycles, tracheal ventilation, and water loss in diapausing pupae of the large white butterfly, Pieris brassicae L. (Lepidoptera: Pieridae), were studied using a constant volume respirometer combined with an infrared probe actograph. The non‐treated pupae displayed discontinuous gas exchange cycles (DGC) with a trend coinciding with the bursts of carbon dioxide (CO₂) release, active tracheal ventilation, and the heartbeat periods. Two independent forms of tracheal ventilation were observed, relatively vigorous abdominal shaking movements and weak abdominal pulsations. The ability to respond to mechanical excitation with abdominal movements was entirely lost on the 2nd day after treatments with Neem EC, and also a reduced tendency to use a DGC was observed. During 2–3 days after treatments, the DGCs and gas exchange microcycles were entirely lost, as was active ventilation. Before treatments, body mass loss, that is, water loss, was 0.6–0.9 mg g^?1 day^?1. After the treatments, water loss increased to 3–5 mg g^?1 day^?1. The pupae remained alive for 10–15 days after the treatments and died after having lost about 50% of their initial body mass. The absence of heartbeats measured during at least 4–5 h was the main criterion for ascertaining death of pupae. The results suggested that respiratory failures, that is, the loss of cyclic gas exchange, evoked by Neem EC were the primary cause of lethal desiccation. Thus, the hypothesis that the cyclic gas exchange is an adaptation for restricting water losses in insects was supported.     

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.     

Detailed mtDNA genotypes permit a reassessment of the settlement and population structure of the Andaman Islands

The population genetics of the Indian subcontinent is central to understanding early human prehistory due to its strategic location on the proposed corridor of human movement from Africa to Australia during the late Pleistocene. Previous genetic research using mtDNA has emphasized the relative isolation of the late Pleistocene colonizers, and the physically isolated Andaman Island populations of Island South-East Asia remain the source of claims supporting an early split between the populations that formed the patchy settlement pattern along the coast of the Indian Ocean. Using whole-genome sequencing, combined with multiplexed SNP typing, this study investigates the deep structure of mtDNA haplogroups M31 and M32 in India and the Andaman Islands. The identification of a so far unnoticed rare polymorphism shared between these two lineages suggests that they are actually sister groups within a single haplogroup, M31'32. The enhanced resolution of M31 allows for the inference of a more recent colonization of the Andaman Islands than previously suggested, but cannot reject the very early peopling scenario. We further demonstrate a widespread overlap of mtDNA and cultural markers between the two major language groups of the Andaman archipelago. Given the "completeness" of the genealogy based on whole genome sequences, and the multiple scenarios for the peopling of the Andaman Islands sustained by this inferred genealogy, our study hints that further mtDNA based phylogeographic studies are unlikely to unequivocally support any one of these possibilities.     

Abdominal movements, heartbeats and gas exchange in pupae of the Colorado potato beetle, Leptinotarsa decemlineata

The rhythms of abdominal movements, heartbeats and gas exchange in the pupae of Leptiontarsa decemlineata (Say) were recorded simultaneously using an electrolytic respirometer and infrared gas analyser, both combined with contact thermography. Abdominal pulsations and heartbeat occurred periodically with little variance among individuals. The abdominal pulsations and heartbeat pauses varied individually within large limits, with the frequency of abdominal pulsations being six to seven times lower than that of the heart pulses. A proportion of the pupae (20%) showed discontinuous gas exchange with large, actively ventilated CO₂ bursts, whereas others (≈ 25%) exhibited continuous regular microcycles (flutter) with abrupt intake of air into the tracheae before discrete microbursts of carbon dioxide. The abdominal pulsations exerted only a minor influence on ventilation during the microcycles. More than 90% of the bursts of abdominal movement coincided with a series of forward directed heartbeats, but interspersed between the bouts of abdominal movement commonly two to three heartbeat pulses were observed that were not associated with abdominal movements. A period of abdominal movement associated with a heartbeat pulse was commonly initiated by one or two vigorous strokes of abdominal rotation.     

A novel snoRNA (U73) is encoded within the introns of the human and mouse ribosomal protein S3a genes

The mouse ribosomal protein S3a-encoding gene (mRPS3a) was cloned and sequenced in this study. mRPS3a shares identical exon/intron structure with its human counterpart. Both genes are split to six exons and exhibit remarkable conservation of the promoter region (68.8% identity in the 250 bp upstream of cap site) and coding region (the proteins differ in two amino acids). mRPS3a displays many features common to other r-protein genes, including the CpG-island at 5′-end of the gene, cap site within an oligopyrimidine tract and no consensus TATA or CAAT boxes. However, mRPS3a represents a rare subclass of r-protein genes that possess a long coding sequence in the first exon. Comparison of human and mouse S3a genes revealed sequence fragments with striking similarity within introns 3 and 4. Here we demonstrate that these sequences encode for a novel small nucleolar RNA (snoRNA) designated U73. U73 contains C, D and D′ boxes and a 12-nucleotide antisense complementarity to the 28S ribosomal RNA. These features place U73 into the family of intron-encoded antisense snoRNAs that guide site-specific 2′-O-ribose methylation of pre-rRNA. We propose that U73 is involved in methylation of the G1739 residue of the human 28S rRNA. In addition, we present the mapping of human ribosomal protein S3a gene (hRPS3a) and internally nested U73 gene to the human chromosome 4q31.2–3.     

Sequence variation in nuclear ribosomal small subunit,internal transcribed spacer and large subunit regions of Rhizophagus irregularis and Gigaspora margarita is high and isolate‐dependent

Arbuscular mycorrhizal (AM) fungi are known to exhibit high intra‐organism genetic variation. However, information about intra‐ vs. interspecific variation among the genes commonly used in diversity surveys is limited. Here, the nuclear small subunit (SSU) rRNA gene, internal transcribed spacer (ITS) region and large subunit (LSU) rRNA gene portions were sequenced from 3 to 5 individual spores from each of two isolates of Rhizophagus irregularis and Gigaspora margarita. A total of 1482 Sanger sequences (0.5 Mb) from 239 clones were obtained, spanning ~4370 bp of the ribosomal operon when concatenated. Intrasporal and intra‐isolate sequence variation was high for all three regions even though variant numbers were not exhausted by sequencing 12–40 clones per isolate. Intra‐isolate nucleotide variation levels followed the expected order of ITS > LSU > SSU, but the values were strongly dependent on isolate identity. Single nucleotide polymorphism (SNP) densities over 4 SNP/kb in the ribosomal operon were detected in all four isolates. Automated operational taxonomic unit picking within the sequence set of known identity overestimated species richness with almost all cut‐off levels, markers and isolates. Average intraspecific sequence similarity values were 99%, 96% and 94% for amplicons in SSU, LSU and ITS, respectively. The suitability of the central part of the SSU as a marker for AM fungal community surveys was further supported by its level of nucleotide variation, which is similar to that of the ITS region; its alignability across the entire phylum; its appropriate length for next‐generation sequencing; and its ease of amplification in single‐step PCR.     

In search of secondary plants to enhance the efficiency of cabbage seed weevil management

The infestation rate and parasitoid communities of Ceutorhynchus obstrictus (Marsham) (Coleoptera: Curculionidae) were assessed on seven spring sown brassicaceous plant species to find potential secondary plants that might help increase the parasitism rates of this serious oilseed pest. Over the three-year study, the average infestation rate of pods by C. obstrictus remained below 10 % for each plant species. Despite the low pest abundance, C. obstrictus was parasitized by hymenopteran parasitoids on all plant species, except on Eruca vesicaria subsp. sativa ((Mill.) Thell.). Parasitism rates were remarkably high: between 33.7 and 70.8 % on average and peaked at 94.7 % on Raphanus sativus (L.) var. oleiformis (Pers.). Not only was the parasitism rate high on R. sativus, but it also had a different parasitoid species composition consisting mainly of egg parasitoids (Mymaridae), while on the other plant species larval parasitoids (Pteromalidae) dominated. These findings are important for planning new sustainable pest management approaches.