A different view on fine-scale population structure in Western African populations

Hunter-gatherer genetics research: Importance and avenues

Major developments in the field of genetics in the past few decades have revolutionised notions of what it means to be human. Although currently only a few populations around the world practise a hunting and gathering lifestyle, this mode of subsistence has characterised members of our species since its very origins and allowed us to migrate across the planet. Therefore, the geographical distribution of hunter-gatherer populations, dependence on local ecosystems and connections to past populations and neighbouring groups have provided unique insights into our evolutionary origins. However, given the vulnerable status of hunter-gatherers worldwide, the development of the field of anthropological genetics requires that we reevaluate how we conduct research with these communities. Here, we review how the inclusion of hunter-gatherer populations in genetics studies has advanced our understanding of human origins, ancient population migrations and interactions as well as phenotypic adaptations and adaptability to different environments, and the important scientific and medical applications of these advancements. At the same time, we highlight the necessity to address yet unresolved questions and identify areas in which the field may benefit from improvements.

Harmine and 7,8-dihydroxyflavone synergistically suitable for amyotrophic lateral sclerosis management: An in silico study

Introduction: Amyotrophic lateral sclerosis (ALS) is a fatal neurological disease characterized by progressive degeneration of both upper and lower motor neurons, resulting in paralysis and eventually leads to death from respiratory failure typically within 3 to 5 years of symptom onset. The aim of this work was to predict the pharmacokinetics and identify unique protein targets that are associated with potential anti-ALS phytochemicals and FDA-approved drugs, by in silico approaches.

Materials and methods: Standard computational tools (webserver and software) were used, and the methods used are clustering analysis, pharmacokinetics and molecular target predictions, and molecular docking simulation.

Results and discussion: The results show that riluzole, β-asarone, cryptotanshinone, harmine and 7,8-dihydroxyflavone have similar pharmacokinetics properties. Riluzole and harmine show 95% probability of target on norepinephrine transporter. Huperzine-A and cryptotanshinone show 100% probability of target on acetylcholinesterase. 7,8-dihydroxyflavone shows 35% probability of target on several carbonic anhydrases, 40% probability of target on CYP19A1, and 100% probability of target on inhibitor of nuclear factor kappa B kinase beta subunit and neurotrophic tyrosine kinase receptor type 2, respectively. Harmine also shows 95% probability of target on dual specificity tyrosine-phosphorylation-regulated kinases, threonine-protein kinases (haspin and PIM3), adrenergic receptors, cyclin-dependent kinases (CDK5 and CDK9), monoamine oxidase A, casein kinase I delta, serotonin receptors, dual specificity protein kinases (CLK1, CLK2, and CLK4), and nischarin, respectively. Also, the results of gene expression network show possible involvement of CDK1, CDK2, CDK4, ERK1, ERK2 and MAPK14 signaling pathways. This study shows that riluzole and harmine have closely similar physicochemical and pharmacokinetics properties as well as molecular targets, such as norepinephrine transporter (SLC6A2). Harmine, huperzine-A and cryptotanshinone could modulate acetylcholinesterase (AChE), which is involved in ALS-pathogenesis. The impact of 7,8-dihydroxyflavone on several carbonic anhydrases (CA) I, II, VII, IX, XII, and XIV, as well as CYP19A1, could help in remediating the respiratory failure associated with ALS.

Conclusion: Overall, harmine is found to be superior to riluzole, and the combination of harmine with 7,8-dihydroxyflavone can provide more effective treatment for ALS than the current regime. Further work is needed to validate the predicted therapeutic targets of harmine identified in this study on ALS model or clinical trials, using in silico, in vitro and in vivo techniques.

Graphical abstract:

ddRAD-Seq reveals evolutionary insights into population differentiation and the cryptic phylogeography of Hyporhamphus intermedius in Mainland China

Species differentiation and local adaptation in heterogeneous environments have attracted much attention, although little is known about the mechanisms involved. Hyporhamphus intermedius is an anadromous, brackish-water halfbeak that is widely distributed in coastal areas and hyperdiverse freshwater systems in China, making it an interesting model for research on phylogeography and local adaptation. Here, 156 individuals were sampled at eight sites from heterogeneous aquatic habitats to examine environmental and genetic contributions to phenotypic divergence. Using double-digest restriction-site-associated DNA sequencing (ddRAD-Seq) in the specimens from the different watersheds, 5498 single nucleotide polymorphisms (SNPs) were found among populations, with obvious population differentiation. We find that present-day Mainland China populations are structured into distinct genetic clusters stretching from southern and northern ancestries, mirroring geography. Following a transplant event in Plateau Lakes, there were virtually no variations of genetic diversity occurred in two populations, despite the fact two main splits were unveiled in the demographic history. Additionally, dorsal, and anal fin traits varied widely between the southern group and the others, which highlighted previously unrecognized lineages. We then explore genotype-phenotype-environment associations and predict candidate loci. Subgroup ranges appeared to correspond to geographic regions with heterogeneous hydrological factors, indicating that these features are likely important drivers of diversification. Accordingly, we conclude that genetic and phenotypic polymorphism and a moderate amount of genetic differentiation occurred, which might be ascribed to population subdivision, and the impact of abiotic factors.

Fully exploiting SNP arrays: a systematic review on the tools to extract underlying genomic structure

Single nucleotide polymorphisms (SNPs) are the most abundant type of genomic variation and the most accessible to genotype in large cohorts. However, they individually explain a small proportion of phenotypic differences between individuals. Ancestry, collective SNP effects, structural variants, somatic mutations or even differences in historic recombination can potentially explain a high percentage of genomic divergence. These genetic differences can be infrequent or laborious to characterize; however, many of them leave distinctive marks on the SNPs across the genome allowing their study in large population samples. Consequently, several methods have been developed over the last decade to detect and analyze different genomic structures using SNP arrays, to complement genome-wide association studies and determine the contribution of these structures to explain the phenotypic differences between individuals. We present an up-to-date collection of available bioinformatics tools that can be used to extract relevant genomic information from SNP array data including population structure and ancestry; polygenic risk scores; identity-by-descent fragments; linkage disequilibrium; heritability and structural variants such as inversions, copy number variants, genetic mosaicisms and recombination histories. From a systematic review of recently published applications of the methods, we describe the main characteristics of R packages, command-line tools and desktop applications, both free and commercial, to help make the most of a large amount of publicly available SNP data.

Evolutionary history of sickle-cell mutation: implications for global genetic medicine

Resistance afforded by the sickle-cell trait against severe malaria has led to high frequencies of the sickle-cell mutation [HBB; c.20T>A, p.Glu6Val; OMIM: 141900 (HBB-βS)] in most parts of Africa. High-coverage sequencing and genotype data have now confirmed the single African origin of the sickle-cell gene variant [HBB; c.20T>A, p.Glu6Val; OMIM: 141900 (HBB-βS)]. Nevertheless, the classical HBB-like genes cluster haplotypes remain a rich source of HBB-βS evolutionary information. The overlapping distribution of HBB-βS and other disease-associated variants means that their evolutionary genetics must be investigated concurrently. In this review: (1) we explore the evolutionary history of HBB-βS and its implications in understanding human migration within and out of Africa: e.g. HBB haplotypes and recent migration paths of the Bantu expansion, occurrence of ~7% of the Senegal haplotype in Angola reflecting changes in population/SCD dynamics, and existence of all five classical HBB haplotype in Cameroon and Egypt suggesting a much longer presence of HBB-βS in these regions; (2) we discuss the time estimates of the emergence of HBB-βS in Africa and finally, (3) we discuss implications for genetic medicine in understanding complex epistatic interactions between HBB-βS and other gene variants selected under environmental pressure in Africa e.g. variants in HBB, HBA, G6PD, APOL1, APOE, OSBPL10 and RXRA.

Changes in the fine-scale genetic structure of Finland through the 20th century

Information about individual-level genetic ancestry is central to population genetics, forensics and genomic medicine. So far, studies have typically considered genetic ancestry on a broad continental level, and there is much less understanding of how more detailed genetic ancestry profiles can be generated and how accurate and reliable they are. Here, we assess these questions by developing a framework for individual-level ancestry estimation within a single European country, Finland, and we apply the framework to track changes in the fine-scale genetic structure throughout the 20^th century. We estimate the genetic ancestry for 18,463 individuals from the National FINRISK Study with respect to up to 10 genetically and geographically motivated Finnish reference groups and illustrate the annual changes in the fine-scale genetic structure over the decades from 1920s to 1980s for 12 geographic regions of Finland. We detected major changes after a sudden, internal migration related to World War II from the region of ceded Karelia to the other parts of the country as well as the effect of urbanization starting from the 1950s. We also show that while the level of genetic heterogeneity in general increases towards the present day, its rate of change has considerable differences between the regions. To our knowledge, this is the first study that estimates annual changes in the fine-scale ancestry profiles within a relatively homogeneous European country and demonstrates how such information captures a detailed spatial and temporal history of a population. We provide an interactive website for the general public to examine our results.

We have inherited our genomes from our parents, who, in turn, inherited their genomes from their parents, etc. Hence, a comparison between genomes of present day individuals reveals genetic population structure due to the varying levels of genetic relatedness among the individuals. We have utilized over 18,000 Finnish samples to characterize the fine-scale genetic population structure in Finland starting from a binary East-West division and ending up with 10 Finnish source populations. Furthermore, we have applied the resulting ancestry information to generate records of how the population structure has evolved each year between 1923 and 1987 in 12 geographical regions of Finland. For example, the war-related evacuation of Karelians from Southeast Finland to other parts of the country show up as a clear, sudden increase in the Evacuated ancestry elsewhere in Finland between 1939 and 1945. Additionally, different regions of Finland show very different levels of genetic mixing in 1900s, from little mixed regions like Ostrobothnia to highly mixed regions like Southwestern Finland. To distribute the results among general public, we provide an interactive website for browsing the municipality and region-level genetic ancestry profiles at https://geneviz.aalto.fi/genetic_ancestry_finland/

Alternative Applications of Genotyping Array Data Using Multivariant Methods

One of the forerunners that pioneered the revolution of high-throughput genomic technologies is the genotyping microarray technology, which can genotype millions of single-nucleotide variants simultaneously. Owing to apparent benefits, such as high speed, low cost, and high throughput, the genotyping array has gained lasting applications in genome-wide association studies (GWAS) and thus accumulated an enormous amount of data. Empowered by continuous manufactural upgrades and analytical innovation, unconventional applications of genotyping array data have emerged to address more diverse genetic problems, holding promise of boosting genetic research into human diseases through the re-mining of the rich accumulated data. Here, we review several unconventional genotyping array analysis techniques that have been built on the idea of large-scale multivariant analysis and provide empirical application examples. These unconventional outcomes of genotyping arrays include polygenic score, runs of homozygosity (ROH)/heterozygosity ratio, distant pedigree computation, and mitochondrial DNA (mtDNA) copy number inference.