Genetic variation in South Indian castes: evidence from Y-chromosome, mitochondrial, and autosomal polymorphisms

Background

Major population movements, social structure, and caste endogamy have influenced the genetic structure of Indian populations. An understanding of these influences is increasingly important as gene mapping and case-control studies are initiated in South Indian populations.

Results

We report new data on 155 individuals from four Tamil caste populations of South India and perform comparative analyses with caste populations from the neighboring state of Andhra Pradesh. Genetic differentiation among Tamil castes is low (R_ST = 0.96% for 45 autosomal short tandem repeat (STR) markers), reflecting a largely common origin. Nonetheless, caste- and continent-specific patterns are evident. For 32 lineage-defining Y-chromosome SNPs, Tamil castes show higher affinity to Europeans than to eastern Asians, and genetic distance estimates to the Europeans are ordered by caste rank. For 32 lineage-defining mitochondrial SNPs and hypervariable sequence (HVS) 1, Tamil castes have higher affinity to eastern Asians than to Europeans. For 45 autosomal STRs, upper and middle rank castes show higher affinity to Europeans than do lower rank castes from either Tamil Nadu or Andhra Pradesh. Local between-caste variation (Tamil Nadu R_ST = 0.96%, Andhra Pradesh R_ST = 0.77%) exceeds the estimate of variation between these geographically separated groups (R_ST = 0.12%). Low, but statistically significant, correlations between caste rank distance and genetic distance are demonstrated for Tamil castes using Y-chromosome, mtDNA, and autosomal data.

Conclusion

Genetic data from Y-chromosome, mtDNA, and autosomal STRs are in accord with historical accounts of northwest to southeast population movements in India. The influence of ancient and historical population movements and caste social structure can be detected and replicated in South Indian caste populations from two different geographic regions.     

Brief communication: evidence of Bartonella quintana infections in skeletons of a historical mass grave in Kassel, Germany

In 2008, a mass grave was found on the grounds of the University of Kassel, Germany. Historians hypothesized that the individuals died in a typhoid fever epidemic in winter 1813/14. To test this hypothesis, the bones were investigated on the presence of specific DNA of pathogens linked to the historical diagnosis oftyphoid fever. It was possible to prove the specific DNA of Bartonella quintana in three individuals, suggesting that their cause of death is linked to an epidemic background.     

Termite cohabitation: the relative effect of biotic and abiotic factors on mound biodiversity

1. Termites are important ecosystem engineers that improve primary productivity in trees and animal diversity outside their mounds. However, their ecological relationship with the species nesting inside their mounds is poorly understood. 2. The presence of termite cohabitant colonies inside 145 Cornitermes cumulans mounds of known size and location was recorded. Using network‐theoretical methods in conjunction with a suite of statistical analyses, the relative influence of biotic and abiotic drivers of termite within‐mound diversity on the composition and species richness of the termite community was investigated, specifically builder presence and physical aspects of the mound. 3. We found that richness inside the mound increases with mound size, and the species similarity between mounds decreases with distance. The physical attributes (abiotic drivers) of termite mounds (size and relative distance to other mounds) are the strongest predictors of termite species richness and composition. The biotic driver (presence of a builder colony) has an important, though smaller, negative effect on within‐mound termite species richness. 4. The findings suggest that the termites' physical manipulation of their environment is an important driver of within‐mound community diversity. More generally, the approach taken here, using a combination of statistical and network‐theoretical methods, can be used to determine the relative importance of abiotic and biotic drivers of diversity in a wide range of communities of interacting species.     

Analyses to help identify individuals from a historical mass grave in Kassel, Germany

In 2008, the skeletal remains of more than 60 human individuals were found in a mass grave on the grounds of the University of Kassel, Germany. There was no evidence helping to identify them or throwing light on the cause of their death. Mainly due to 14C age determination and initial hints on age and sex distribution, historians hypothesized that they had been soldiers of Napoleon's army who died in an epidemic in the winter of 1813/14. To test this assumption, morphological and molecular analyses were carried out on a sample. The morphological analyses comprised an age and sex determination as well as a macro- and micro-morphological inspection for pathological deviations after the commingled bones had been assembled as individuals. The molecular investigations aimed to identify the geographic origin of the remains. For this, mitochondrial and Y-chromosomal haplotypings were carried out. The results point to a group of mainly young men, some of them suffering from systemic inflammation of the periosteum. Others revealed severe aberrations in bone microstructure. The greatest similarities revealed by Y-haplogroup and -haplotype distribution were to populations that live in what are now the Benelux countries. All aspects support the thesis that these were soldiers of the Napoleonic army.     

Molecular evolution modeled as a fractal Poisson process in agreement with mammalian sequence comparisons

The fractal doubly stochastic Poisson process (FDSPP) model of molecular evolution, like other doubly stochastic Poisson models, agrees with the high estimates for the index of dispersion found from sequence comparisons. Unlike certain previous models, the FDSPP also predicts a positive geometric correlation between the index of dispersion and the mean number of substitutions. Such a relationship is statistically proven herein using comparisons between 49 mammalian genes. There is no characteristic rate associated with molecular evolution according to this model, but there is a scaling relationship in rates according to a fractal dimension of evolution. The FDSPP is a suitable replacement for the homogeneous Poisson process in tests of the lineage dependence of rates and in estimating confidence intervals for divergence times. As opposed to other fractal models, this model can be interpreted in terms of Darwinian selection and drift.      

Parallelized TCSPC for Dynamic Intravital Fluorescence Lifetime Imaging: Quantifying Neuronal Dysfunction in Neuroinflammation

Two-photon laser-scanning microscopy has revolutionized our view on vital processes by revealing motility and interaction patterns of various cell subsets in hardly accessible organs (e.g. brain) in living animals. However, current technology is still insufficient to elucidate the mechanisms of organ dysfunction as a prerequisite for developing new therapeutic strategies, since it renders only sparse information about the molecular basis of cellular response within tissues in health and disease. In the context of imaging, Förster resonant energy transfer (FRET) is one of the most adequate tools to probe molecular mechanisms of cell function. As a calibration-free technique, fluorescence lifetime imaging (FLIM) is superior for quantifying FRET in vivo. Currently, its main limitation is the acquisition speed in the context of deep-tissue 3D and 4D imaging. Here we present a parallelized time-correlated single-photon counting point detector (p-TCSPC) (i) for dynamic single-beam scanning FLIM of large 3D areas on the range of hundreds of milliseconds relevant in the context of immune-induced pathologies as well as (ii) for ultrafast 2D FLIM in the range of tens of milliseconds, a scale relevant for cell physiology. We demonstrate its power in dynamic deep-tissue intravital imaging, as compared to multi-beam scanning time-gated FLIM suitable for fast data acquisition and compared to highly sensitive single-channel TCSPC adequate to detect low fluorescence signals. Using p-TCSPC, 256×256 pixel FLIM maps (300×300 µm²) are acquired within 468 ms while 131×131 pixel FLIM maps (75×75 µm²) can be acquired every 82 ms in 115 µm depth in the spinal cord of CerTN L15 mice. The CerTN L15 mice express a FRET-based Ca-biosensor in certain neuronal subsets. Our new technology allows us to perform time-lapse 3D intravital FLIM (4D FLIM) in the brain stem of CerTN L15 mice affected by experimental autoimmune encephalomyelitis and, thereby, to truly quantify neuronal dysfunction in neuroinflammation.     

Screening Global Positioning System Location Data for Errors Using Animal Movement Characteristics

Abstract: Animal locations estimated by Global Positioning System (GPS) inherently contain errors. Screening procedures used to remove large positional errors often trade data accuracy for data loss. We developed a simple screening method that identifies locations arising from unrealistic movement patterns. When applied to a large data set of moose (Alces alces) locations, our method identified virtually all known errors with minimal loss of data. Thus, our method for screening GPS data improves the quality of data sets and increases the value of such data for research and management.     

Effects of Hunting on Response Behaviors of Wild Reindeer

ABSTRACT Because wild reindeer (Rangifer tarandus) are hunted in southern Norway, reindeer may perceive all recreationists as threats. Potential adverse effects of hunting on reindeer behavior may be exacerbated by other forms of recreation because the number of skiers and hikers in areas inhabited by reindeer has also increased. The Norefjell-Reinsjøfjell wild reindeer area is used extensively for recreation and tourism. Reindeer hunting was introduced in the area in 1992, and harvest rate has been stable at about 38% of winter herd size. We recorded behavioral responses of reindeer to a person approaching directly on foot or skis during 1992 and again in 2002–2006. Compared to 1992, flight-initiation distance increased and fewer groups assessed the observer before taking flight during 2002–2006. In winter, when reindeer are usually comparably more vigilant than in other seasons, flight-initiation distance increased from only 60 m to 115 m and escape distance decreased from 400 m to 210 m. Neither alert distance, calf carcass weights (23.6 ± 0.7 [SE] kg to 22.4 ± 0.2 kg), nor reindeer herd size (661 ± 73 to 579 ± 15) changed during the 15 years of our study. Reindeer appeared to habituate to the observer because they initiated flight at shorter distances as the number of approaches on the same day increased. In Norefjell-Reinsjøfjell, encounters with a person on foot or skis did not result in behavioral responses likely to entail substantial energy costs for reindeer; therefore, hunting at current levels appears compatible with other recreational activities.     

Temperature,predator–prey interaction strength and population stability

Warming could strongly stabilize or destabilize populations and food webs by changing the interaction strengths between predators and their prey. Predicting the consequences of warming requires understanding how temperature affects ingestion (energy gain) and metabolism (energy loss). Here, we studied the temperature dependence of metabolism and ingestion in laboratory experiments with terrestrial arthropods (beetles and spiders). From this data, we calculated ingestion efficiencies (ingestion/metabolism) and per capita interaction strengths in the short and long term. Additionally, we investigated if and how body mass changes these temperature dependencies. For both predator groups, warming increased metabolic rates substantially, whereas temperature effects on ingestion rates were weak. Accordingly, the ingestion efficiency (the ratio of ingestion to metabolism) decreased in all treatments. This result has two possible consequences: on the one hand, it suggests that warming of natural ecosystems could increase intrinsic population stability, meaning less fluctuations in population density; on the other hand, decreasing ingestion efficiencies may also lead to higher extinction risks because of starvation. Additionally, predicted long‐term per capita interaction strengths decreased with warming, which suggests an increase in perturbation stability of populations, i.e., a higher probability of returning to the same equilibrium density after a small perturbation. Together, these results suggest that warming has complex and potentially profound effects on predator–prey interactions and food‐web stability.