Demographic and genetic interrelationships among the Gavlis of Dharwad

Lot of work has been done in recent years on the genetics of isolated and small population groups. But J. Sutter (1963) notes that these studies have not yielded satisfactory results, because these investigators have applied the formulae and models constructed by the mathematicians which are based on the assumption of panmixia, whereas panmixia cannot occur in human populations especially if the population is very small. Sometimes we speak of genetic drift and selection without taking into account the fact that the population at the same time is controlled by two most important demographic parameters of fertility and mortality which can alter genetic drift and selection. The geneticists are primarily interested in fertility. They want to determine, for any given couple, the number of offspring reaching the age of reproduction. One might therefore assume that the measurement of fertility should play a major role in population genetics. Thus, there is an urgent need for the establishment of meaningful relationship between demography and population genetics. In view of the above facts, an attempt is made in the present study to analyse the “Demographic and Genetic Interrelationships among the Gavlis of Dharwad” so as to throw light on some of the complex genetic issues like endogamy, inbreeding and selection potential.     

Ecological opportunities and specializations shaped genetic divergence in a highly mobile marine top predator

Environmental conditions can shape genetic and morphological divergence. Release of new habitats during historical environmental changes was a major driver of evolutionary diversification. Here, forces shaping population structure and ecotype differentiation (‘pelagic’ and ‘coastal’) of bottlenose dolphins in the North-east Atlantic were investigated using complementary evolutionary and ecological approaches. Inference of population demographic history using approximate Bayesian computation indicated that coastal populations were likely founded by the Atlantic pelagic population after the Last Glacial Maxima probably as a result of newly available coastal ecological niches. Pelagic dolphins from the Atlantic and the Mediterranean Sea likely diverged during a period of high productivity in the Mediterranean Sea. Genetic differentiation between coastal and pelagic ecotypes may be maintained by niche specializations, as indicated by stable isotope and stomach content analyses, and social behaviour. The two ecotypes were only weakly morphologically segregated in contrast to other parts of the World Ocean. This may be linked to weak contrasts between coastal and pelagic habitats and/or a relatively recent divergence. We suggest that ecological opportunity to specialize is a major driver of genetic and morphological divergence. Combining genetic, ecological and morphological approaches is essential to understanding the population structure of mobile and cryptic species.     

Inference of Super-exponential Human Population Growth via Efficient Computation of the Site Frequency Spectrum for Generalized Models

The site frequency spectrum (SFS) and other genetic summary statistics are at the heart of many population genetic studies. Previous studies have shown that human populations have undergone a recent epoch of fast growth in effective population size. These studies assumed that growth is exponential, and the ensuing models leave an excess amount of extremely rare variants. This suggests that human populations might have experienced a recent growth with speed faster than exponential. Recent studies have introduced a generalized growth model where the growth speed can be faster or slower than exponential. However, only simulation approaches were available for obtaining summary statistics under such generalized models. In this study, we provide expressions to accurately and efficiently evaluate the SFS and other summary statistics under generalized models, which we further implement in a publicly available software. Investigating the power to infer deviation of growth from being exponential, we observed that adequate sample sizes facilitate accurate inference; e.g., a sample of 3000 individuals with the amount of data expected from exome sequencing allows observing and accurately estimating growth with speed deviating by ≥10% from that of exponential. Applying our inference framework to data from the NHLBI Exome Sequencing Project, we found that a model with a generalized growth epoch fits the observed SFS significantly better than the equivalent model with exponential growth (P-value = 3.85 × 10^?6). The estimated growth speed significantly deviates from exponential (P-value  ? 10^?12), with the best-fit estimate being of growth speed 12% faster than exponential.     

SPAms: A user-friendly software to simulate population genetics data under complex demographic models

Patterns of genetic diversity can be used to reconstruct populations demographic history. Thus, it is crucial to understand the statistical properties of data sets generated under different scenarios. SPAms is a graphical application that allows the simulation of data under a set of demographic models of increasing complexity: (i) population size change (ii) admixture and (iii) population structure (n-island or stepping stone model). SPAms generates data under the infinite site and the stepwise mutation models and computes a set of commonly used statistics. It should thus be a useful tool for both research and teaching purposes.