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.     

The rarity concept and the commonness of rarity in freshwater zooplankton

1. Regional distribution, frequency of occurrence and relative abundance were scored in 2467 Norwegian lakes for all the recorded 130 species of crustacean zooplankton. The majority of species were rare in the sense that 65% of species were recorded in fewer than 10% of localities. Only six species were recorded in more than 50% of localities, and the median number of species in a given locality was 14 (i.e. 10% of the total species pool). 2. Abundances of all species were scored according to the fraction of lakes in which they were recorded, their geographical range of distribution, and their numerical abundance. Typically the most rare species were rare by all three criteria, and vice versa for the common species, pointing to rarity as an inherent property of some species. For some species this rarity reflects being on the edge of their distributional range, while for others rarity seems to be a consequence of their life cycle strategies. 3. Some of the truly rare species have high dispersal rates and high colonization abilities, but are rapidly replaced by other species. Others are confined to specific habitats, often highly eutrophic, pointing to highly specialized niche adaptations. 4. A major cause for the few truly common species seems to be the limited number of species that are able to coexist within a given locality, reflecting ‘the ghost of competition past’ and predation pressure. 5. While species composition and species richness may reflect colonization abilities and stochastic events, the presence or absence of species is not only a random lottery but also a consequence of species‐specific attributes.     

The extensor digitorum brevis muscle island flap for soft-tissue loss around the ankle

The extensor digitorum brevis muscle flap, which has already been suggested as a local flap for the foot, has been applied by us in 2 cases with excellent results. This flap, as with other muscle flaps, provides an excellent bed for the skin graft. Furthermore, because of its width, it allows for covering an area of skin loss 5 X 7 cm in size in areas that are difficult to cover by other reconstructive means. The arch of rotation of this flap allows for coverage of the lateromedial and posterior surfaces of the ankle with no functional loss at the donor site. The relative ease of elevating this flap presents a reasonable justification for its wider application as a single local procedure for skin problems around the ankle.     

Bill morphology reflects adaptation to a fibrous diet in the kākāpō (Strigops: Psittaciformes)

We describe the upper portion of the bill sheath (rhinotheca) of the kākāpō (Strigops habroptilus) from three adult female specimens. The external buccal surface of the rhinotheca is deeply concave with a prominent palatal stop and hardened chevrons creating a ‘milling apparatus’ that the kākāpō uses to grind food. The palatal stop presents a working face of 40–50?mm². The internal surface of the rhinotheca mirrors the overlying premaxilla and provides a distinct thickened abutment consistent with resistance against the increased workload of the mandibles (gnathotheca) due to the kākāpō’s fibrous diet and chewing style. Along the midline, the rhinotheca at the abutment is up to 5.6?mm thick, compared with as thin as 2.1?mm elsewhere on the midline. The closely related Nestor parrots have less developed palatal stops, chevrons and abutments on their rhinothecas consistent with their lower preference for fibrous plant material. The form of the rhinotheca agrees with the kākāpō’s feeding ecology as a generalist herbivore that grinds locally available fibrous material to assist digestion.     

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.      

Two-dimensional, computer-controlled film scanner: quantitation of fluorescence from ethidium bromide-stained DNA gels

A two-dimensional scanner based on a digital plotter is described. The device is used to analyze photographic negatives of ethidium bromide-stained DNA-agarose gels. Scanning is controlled by and photometric data transferred to a computer for processing, storage, display, and analysis such as integration of the areas under bands and determination of the mean distances of migration of polydisperse samples. An integral light source and detector module designed for reading optical "bar-codes" is mounted in place of the pen of the plotter. Spatial resolution and reproducibility are about 0.2 and 0.005 mm, respectively. Photometric precision as good as one part per thousand is achieved by sinusoidal modulation of the intensity of the light source and synchronous, phase-sensitive detection of the signal from the detector by a lock-in amplifier. No part of the sensor assembly touches the surface of the negative. In contrast to a densitometer, the computer transforms photometric data to values directly proportional to the amount of DNA at given points on the original gel. The ability to move the sensor in two dimensions over the negative allows for the integration across the width of a lane correctly allowing for the nonuniform distribution of the DNA.     

Excitation–Contraction Coupling: Calcium current modulation by the γ1 subunit depends on alternative splicing of CaV1.1

The skeletal muscle voltage-gated calcium channel (Ca_V1.1) primarily functions as a voltage sensor for excitation–contraction coupling. Conversely, its ion-conducting function is modulated by multiple mechanisms within the pore-forming α_1S subunit and the auxiliary α₂δ-1 and γ₁ subunits. In particular, developmentally regulated alternative splicing of exon 29, which inserts 19 amino acids in the extracellular IVS3-S4 loop of Ca_V1.1a, greatly reduces the current density and shifts the voltage dependence of activation to positive potentials outside the physiological range. We generated new HEK293 cell lines stably expressing α₂δ-1, β₃, and STAC3. When the adult (Ca_V1.1a) and embryonic (Ca_V1.1e) splice variants were expressed in these cells, the difference in the voltage dependence of activation observed in muscle cells was reproduced, but not the reduced current density of Ca_V1.1a. Only when we further coexpressed the γ₁ subunit was the current density of Ca_V1.1a, but not that of Ca_V1.1e, reduced by >50%. In addition, γ₁ caused a shift of the voltage dependence of inactivation to negative voltages in both variants. Thus, the current-reducing effect of γ₁, unlike its effect on inactivation, is specifically dependent on the inclusion of exon 29 in Ca_V1.1a. Molecular structure modeling revealed several direct ionic interactions between residues in the IVS3-S4 loop and the γ₁ subunit. However, substitution of these residues by alanine, individually or in combination, did not abolish the γ₁-dependent reduction of current density, suggesting that structural rearrangements in Ca_V1.1a induced by inclusion of exon 29 may allosterically empower the γ₁ subunit to exert its inhibitory action on Ca_V1.1 calcium currents.