Genetic structure of four socio-culturally diversified caste populations of southwest India and their affinity with related Indian and global groups

Background  

A large number of microsatellites have been extensively used to comprehend the genetic diversity of different global groups. This paper entails polymorphism at 15 STR in four predominant and endogamous populations representing Karnataka, located on the southwest coast of India. The populations residing in this region are believed to have received gene flow from south Indian populations and world migrants, hence, we carried out a detailed study on populations inhabiting this region to understand their genetic structure, diversity related to geography and linguistic affiliation and relatedness to other Indian and global migrant populations.     

Rapid evolution in response to introduced predators I: rates and patterns of morphological and life-history trait divergence

Background  

Introduced species can have profound effects on native species, communities, and ecosystems, and have caused extinctions or declines in native species globally. We examined the evolutionary response of native zooplankton populations to the introduction of non-native salmonids in alpine lakes in the Sierra Nevada of California, USA. We compared morphological and life-history traits in populations of Daphnia with a known history of introduced salmonids and populations that have no history of salmonid introductions.     

A theoretical approach to predicting the success of genetic manipulation of malaria mosquitoes in malaria control

Background  

Mosquitoes that have been genetically modified to better encapsulate the malaria parasite Plasmodium falciparum are being considered as a possible tool in the control of malaria. Hopes for this have been raised with the identification of genes involved in the encapsulation response and with advances in the tools required to transform mosquitoes. However, we have only very little understanding of the conditions that would allow such genes to spread in natural populations.     

Similar Levels of X-linked and Autosomal Nucleotide Variation in African and non-African populations of <Emphasis Type="Italic">Drosophila melanogaster</Emphasis>

Background  

Levels of molecular diversity in Drosophila have repeatedly been shown to be higher in ancestral, African populations than in derived, non-African populations. This pattern holds for both coding and noncoding regions for a variety of molecular markers including single nucleotide polymorphisms and microsatellites. Comparisons of X-linked and autosomal diversity have yielded results largely dependent on population of origin.     

iHAP – integrated haplotype analysis pipeline for characterizing the haplotype structure of genes

Background  

The advent of genotype data from large-scale efforts that catalog the genetic variants of different populations have given rise to new avenues for multifactorial disease association studies. Recent work shows that genotype data from the International HapMap Project have a high degree of transferability to the wider population. This implies that the design of genotyping studies on local populations may be facilitated through inferences drawn from information contained in HapMap populations.     

Widespread latitudinal asymmetry in the performance of marginal populations: A meta-analysis

Aim

Range shifts are expected to occur when populations at one range margin perform better than those at the other margin, yet no global trend in population performances at range margins has been demonstrated empirically across a wide range of taxa and biomes. Here we test the prediction that, if impacts of ongoing climate change on performance in marginal populations are widespread, then populations from the high-latitude margin (HLM) should perform as well as or better than central populations, whereas low-latitude margin (LLM) populations should perform worse.

Location

Global.

Time period

1995–2019.

Major taxa studied

Plants and animals.

Methods

To test our prediction, we used a meta-analysis to quantify empirical support for asymmetry in the performance of high- and low-latitude margin populations compared to central populations. Performance estimates (survival, reproduction, or lifetime fitness) for populations occurring in their natural environment were derived from 51 papers involving 113 margin-centre comparisons from 54 species and 705 populations from the Americas, Europe, Africa and Australia. We then related these performance differences to climatic differences among populations. We also tested whether patterns are consistent across taxonomic kingdoms (plants vs animals) and across realms (marine vs terrestrial).

Results

Populations at margins performed significantly worse than central populations, and this trend was primarily driven by the low-latitude margin. Although the difference was of small magnitude, it was largely consistent across biological kingdoms and realms. Differences in performance were weakly (p = .08) related to the difference in average temperatures between central and marginal populations.

Main conclusions

The observed asymmetry in performance in marginal populations is consistent with predictions about the effects of global climate change, though further research is needed to confirm the effect of climate. It indicates that changes in demographic rates in marginal populations can serve as early-warning signals of impending range shifts.     

Island selection on mammalian life-histories: genetic differentiation in offspring size

Background  

Since Darwin's pioneering work, evolutionary changes in isolated island populations of vertebrates have continued to provide the strongest evidence for the theory of natural selection. Besides macro-evolutionary changes, micro-evolutionary changes and the relative importance of natural selection vs. genetic drift are under intense investigation. Our study focuses on the genetic differentiation in morphological and life-history traits in insular populations of a small mammal the bank vole Myodes glareolus.     

Flow cytometric characterization of freshly isolated and culture expanded human synovial cell populations in patients with chronic arthritis

Introduction  

The synovium is a major target tissue in chronic arthritis and is intensively studied at the cellular and molecular level. The aim of this study was to develop flow cytometry for the quantitative analysis of synovial cell populations pre and post culture and to characterize mesenchymal cell populations residing in the inflammatory synovium.     

SNP frequency, haplotype structure and linkage disequilibrium in elite maize inbred lines

Background  

Recent studies of ancestral maize populations indicate that linkage disequilibrium tends to dissipate rapidly, sometimes within 100 bp. We set out to examine the linkage disequilibrium and diversity in maize elite inbred lines, which have been subject to population bottlenecks and intense selection by breeders. Such population events are expected to increase the amount of linkage disequilibrium, but reduce diversity. The results of this study will inform the design of genetic association studies.     

A high-throughput chemically induced inflammation assay in zebrafish

Background  

Studies on innate immunity have benefited from the introduction of zebrafish as a model system. Transgenic fish expressing fluorescent proteins in leukocyte populations allow direct, quantitative visualization of an inflammatory response in vivo. It has been proposed that this animal model can be used for high-throughput screens aimed at the identification of novel immunomodulatory lead compounds. However, current assays require invasive manipulation of fish individually, thus preventing high-content screening.     

Genomic signatures of local directional selection in a high gene flow marine organism; the Atlantic cod (Gadus morhua)

Background  

Marine fishes have been shown to display low levels of genetic structuring and associated high levels of gene flow, suggesting shallow evolutionary trajectories and, possibly, limited or lacking adaptive divergence among local populations. We investigated variation in 98 gene-associated single nucleotide polymorphisms (SNPs) for evidence of selection in local populations of Atlantic cod (Gadus morhua L.) across the species distribution.     

Forward-time simulation of realistic samples for genome-wide association studies

Background  

Forward-time simulations have unique advantages in power and flexibility for the simulation of genetic samples of complex human diseases because they can closely mimic the evolution of human populations carrying these diseases. However, a number of methodological and computational constraints have prevented the power of this simulation method from being fully explored in existing forward-time simulation methods.     

Multiple endosymbionts in populations of the ant <Emphasis Type="Italic">Formica cinerea</Emphasis>

Background  

Many insects, including ants, are infected by maternally inherited Wolbachia endosymbiotic bacteria though other secondary endosymbionts have not been reported in ants. It has been suggested that the ability of Wolbachia to invade and remain in an ant population depends on the number of coexisting queens in a colony. We study the genetic and social structure of populations in the ant Formica cinerea which is known to have populations with either monogynous or polygynous colonies. We screen populations for several endosymbiotic bacteria to evaluate the presence of different endosymbionts, possible association between their prevalence and the social structure, and the association between endosymbiont prevalence and genetic differentiation of ant populations.     

The identity,distribution, and impacts of non-native apple snails in the continental United States

Background  

Since the mid 1990s populations of non-native apple snails (Ampullariidae) have been discovered with increasing frequency in the continental United States. Given the dramatic effects that introduced apple snails have had on both natural habitats and agricultural areas in Southeast Asia, their introduction to the mainland U.S. is cause for concern. We combine phylogenetic analyses of mtDNA sequences with examination of introduced populations and museum collections to clarify the identities, introduced distributions, geographical origins, and introduction histories of apple snails.     

Selecting additional tag SNPs for tolerating missing data in genotyping

Background  

Recent studies have shown that the patterns of linkage disequilibrium observed in human populations have a block-like structure, and a small subset of SNPs (called tag SNPs) is sufficient to distinguish each pair of haplotype patterns in the block. In reality, some tag SNPs may be missing, and we may fail to distinguish two distinct haplotypes due to the ambiguity caused by missing data.     

Expression profiling of human glial precursors

Background  

We have generated gene expression databases for human glial precursors, neuronal precursors, astrocyte precursors and neural stem cells and focused on comparing the profile of glial precursors with that of other populations.     

The mechanisms responsible for 2-dimensional pattern formation in bacterial macrofiber populations grown on solid surfaces: fiber joining and the creation of exclusion zones

Background  

When Bacillus subtilis is cultured in a complex fluid medium under conditions where cell separation is suppressed, populations of multicellular macrofibers arise that mature into ball-like structures. The final sedentary forms are found distributed in patterns on the floor of the growth chamber although individual cells have no flagellar-driven motility. The nature of the patterns and their mode of formation are described in this communication.     

Regionally and climatically restricted patterns of distribution of genetic diversity in a migratory bat species, <Emphasis Type="Italic">Miniopterus schreibersii</Emphasis>(Chiroptera: Vespertilionidae)

Background  

Various mechanisms such as geographic barriers and glacial episodes have been proposed as determinants of intra-specific and inter-specific differentiation of populations, and the distribution of their genetic diversity. More recently, habitat and climate differences, and corresponding adaptations have been shown to be forces influencing the phylogeographic evolution of some vertebrates. In this study, we examined the contribution of these various factors on the genetic differentiation of the bent-winged bat, Miniopterus schreibersii, in southeastern Europe and Anatolia.     

Long-term experimental evolution in Escherichia coli. XI. Rejection of non-transitive interactions as cause of declining rate of adaptation

Background  

Experimental populations of Escherichia coli have evolved for 20,000 generations in a uniform environment. Their rate of improvement, as measured in competitions with the ancestor in that environment, has declined substantially over this period. This deceleration has been interpreted as the bacteria approaching a peak or plateau in a fitness landscape. Alternatively, this deceleration might be caused by non-transitive competitive interactions, in particular such that the measured advantage of later genotypes relative to earlier ones would be greater if they competed directly.     

Construction of a consensus linkage map for red clover (Trifolium pratense L.)

Background  

Red clover (Trifolium pratense L.) is a major forage legume that has a strong self-incompatibility system and exhibits high genetic diversity within populations. For several crop species, integrated consensus linkage maps that combine information from multiple mapping populations have been developed. For red clover, three genetic linkage maps have been published, but the information in these existing maps has not been integrated.