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.     

Multiple factors determine the effect of anthropogenic barriers to connectivity on riverine fish

Habitat fragmentation is a key anthropogenic factor in biodiversity decline, particularly in aquatic ecosystems. We predicted that differences in fish assemblage composition due to the impact of fragmentation would most strongly affect migratory species, and these effects would be dependent on the interaction between the characteristics of each barrier and the antecedent flow conditions that determine temporal variation in connectivity. These hypotheses were applied to a coastal river network in eastern Australia that is fragmented by multiple weirs and dams, including some with passage facilities. How these facilities interact with flow to mediate hydrological connectivity and hence patterns of community structure is unknown. Five distinct assemblages were identified that were associated with different combinations of environmental factors and barrier characteristics (spatial arrangement, passability), and key differences were due to variation in migration traits. Two spatially distinct assemblages were associated with fragmentation by two impassable barriers. However, the migration traits that accompanied these community changes were inconsistent between these groups, and likely reflected effects of barriers near the estuary and in the middle of the stream network on diadromous and freshwater-migratory species, respectively. Two assemblage groups in the vicinity of passable weirs varied temporally as a function of hydrology and the seasonal upstream movement of juvenile diadromous species. The effect of habitat loss in conjunction with fragmentation was evident, with a further assemblage group occurring in reaches where riparian vegetation and instream habitat have been altered by poor management of agriculture. This study indicates that the impact of habitat fragmentation in rivers depends on the interaction of the migration characteristics of biota, temporal variation in hydrology which mediates connectivity, and the location of anthropogenic barriers. Conservation policies aimed at minimizing human impacts on aquatic biodiversity need to jointly account for the separate impacts of habitat fragmentation and habitat loss.     

Attention-Dependent Modulation of Cortical Taste Circuits Revealed by Granger Causality with Signal-Dependent Noise

We show, for the first time, that in cortical areas, for example the insular, orbitofrontal, and lateral prefrontal cortex, there is signal-dependent noise in the fMRI blood-oxygen level dependent (BOLD) time series, with the variance of the noise increasing approximately linearly with the square of the signal. Classical Granger causal models are based on autoregressive models with time invariant covariance structure, and thus do not take this signal-dependent noise into account. To address this limitation, here we describe a Granger causal model with signal-dependent noise, and a novel, likelihood ratio test for causal inferences. We apply this approach to the data from an fMRI study to investigate the source of the top-down attentional control of taste intensity and taste pleasantness processing. The Granger causality with signal-dependent noise analysis reveals effects not identified by classical Granger causal analysis. In particular, there is a top-down effect from the posterior lateral prefrontal cortex to the insular taste cortex during attention to intensity but not to pleasantness, and there is a top-down effect from the anterior and posterior lateral prefrontal cortex to the orbitofrontal cortex during attention to pleasantness but not to intensity. In addition, there is stronger forward effective connectivity from the insular taste cortex to the orbitofrontal cortex during attention to pleasantness than during attention to intensity. These findings indicate the importance of explicitly modeling signal-dependent noise in functional neuroimaging, and reveal some of the processes involved in a biased activation theory of selective attention.     

Biotic homogenisation and differentiation as directional change in beta diversity: synthesising driver–response relationships to develop conceptual models across ecosystems

Biotic homogenisation is defined as decreasing dissimilarity among ecological assemblages sampled within a given spatial area over time. Biotic differentiation, in turn, is defined as increasing dissimilarity over time. Overall, changes in the spatial dissimilarities among assemblages (termed ‘beta diversity’) is an increasingly recognised feature of broader biodiversity change in the Anthropocene. Empirical evidence of biotic homogenisation and biotic differentiation remains scattered across different ecosystems. Most meta-analyses quantify the prevalence and direction of change in beta diversity, rather than attempting to identify underlying ecological drivers of such changes. By conceptualising the mechanisms that contribute to decreasing or increasing dissimilarity in the composition of ecological assemblages across space, environmental managers and conservation practitioners can make informed decisions about what interventions may be required to sustain biodiversity and can predict potential biodiversity outcomes of future disturbances. We systematically reviewed and synthesised published empirical evidence for ecological drivers of biotic homogenisation and differentiation across terrestrial, marine, and freshwater realms to derive conceptual models that explain changes in spatial beta diversity. We pursued five key themes in our review: (i) temporal environmental change; (ii) disturbance regime; (iii) connectivity alteration and species redistribution; (iv) habitat change; and (v) biotic and trophic interactions. Our first conceptual model highlights how biotic homogenisation and differentiation can occur as a function of changes in local (alpha) diversity or regional (gamma) diversity, independently of species invasions and losses due to changes in species occurrence among assemblages. Second, the direction and magnitude of change in beta diversity depends on the interaction between spatial variation (patchiness) and temporal variation (synchronicity) of disturbance events. Third, in the context of connectivity and species redistribution, divergent beta diversity outcomes occur as different species have different dispersal characteristics, and the magnitude of beta diversity change associated with species invasions also depends strongly on alpha and gamma diversity prior to species invasion. Fourth, beta diversity is positively linked with spatial environmental variability, such that biotic homogenisation and differentiation occur when environmental heterogeneity decreases or increases, respectively. Fifth, species interactions can influence beta diversity via habitat modification, disease, consumption (trophic dynamics), competition, and by altering ecosystem productivity. Our synthesis highlights the multitude of mechanisms that cause assemblages to be more or less spatially similar in composition (taxonomically, functionally, phylogenetically) through time. We consider that future studies should aim to enhance our collective understanding of ecological systems by clarifying the underlying mechanisms driving homogenisation or differentiation, rather than focusing only on reporting the prevalence and direction of change in beta diversity, per se.     

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.     

Activities of some metabolic enzymes in the small intestinal mucosa during pregnancy and lactation in the rat

The food intake, gut weight, gut length, mucosal protein and mucosal activities of alkaline phosphate (EC 3.1.3.1), acid phosphate (EC 3.1.3.2), isocitric dehydrogenase (EC 1.1.1.42) and glucose-6-phosphate (EC 3.1.3.9) were measured in rats during pregnancy, lactation and after the young were weaned. In general, the quantities measured increased slightly during pregnancy and considerably during lactation, reaching maximum values during the 3rd weeks of lacation and falling more or less rapidly after the young were weaned to the same levels as those in unmated animals. However, the gut length and mucosal protein remained higher even 3 weeks after weaning, so that weight per unit length and specific enzyme activities (per mg protein) tended to be lower in mated than in unmated rats. Changes in the specific activities of enzymes indicate alterations of the metabolic function of the enterocytes during breeding similar to changes reported for digestive enzymes. It is suggested that the intestine may reflect changes that take place in the liver.     

Phosphorus-31 and cadmium-113 NMR studies of some cadmium(II) complexes containing tricyclohexylphosphine and tributylphosphine

Phosphorus-31 and cadmium-113 NMR spectroscopy has been used to study the interaction between tertiary phosphines (P(c-C₆H₁₁)₃ and PBu₃) and Cd(O₃SCF₃)₂, Cd(ClO₄)₂, Cd(CF₃COO)₂ and Cd(SCN)₂ salts in solution. the NMR data imply the formation in solution of novel 1:1 adducts CdX₂(phos) (X = O₃SCF₃, ClO₄, CF₃COO, phos = P(c-C₆H₁₁)₃, PBu₃) in which there is substantial interaction between the anions and cadmium. Data are also presented for mixed phosphine complexes CdX₂[P(c-C₆H₁₁)₃][PBu₃] (X = O₃SCF₃, ClO₄, NO₃, CF₃COO, CH₃COO, Cl, Br, I, SCN). The two bond coupling constants ²J(P′P) of these mixed phosphine complexes decrease as the coordination ability of the anion increases and cover the narrow range from 95 Hz to 66 Hz.     

The Simulium vernum group (Diptera: Simuliidae) in Europe: multiple character sets for assessing species status

The value of using characters from multiple sources – chromosomes, ecology, gene sequences, and morphology – to evaluate the species status of closely related black flies is demonstrated for three European members of the Simulium vernum group: Simulium crenobium (Knoz, 1961), Simulium juxtacrenobium Bass & Brockhouse, 1990, and Simulium vernum s.s. Macquart, 1826. Simulium juxtacrenobium is a chromosomally, molecularly, and morphologically distinct species that diverged from S. crenobium and S. vernum s.s. about 2 Mya. It is specialized for intermittent streams, is univoltine, and is recorded for the first time from northern Europe, based on collections from Finland and Sweden, representing a range extension of about 1800 km. In contrast, S. crenobium, although confirmed as a distinct species, differs from S. vernum s.s. by only a few larval and chromosomal characters, and by a breeding habitat restricted to mountain spring brooks. Whereas all four character sets independently support the specific distinctness of S. juxtacrenobium and S. vernum s.s., multiple character sets are required to establish the specific validity of S. crenobium.