Inferring Signatures of Positive Selection in Whole-Genome Sequencing Data: An Overview of Haplotype-Based Methods

Signatures of positive selection in the genome are a characteristic mark of adaptation that can reveal an ongoing, recent, or ancient response to environmental change throughout the evolution of a population. New sources of food, climate conditions, and exposure to pathogens are only some of the possible sources of selective pressure, and the rise of advantageous genetic variants is a crucial determinant of survival and reproduction. In this context, the ability to detect these signatures of selection may pinpoint genetic variants that are responsible for a significant change in gene regulation, gene expression, or protein synthesis, structure, and function. This review focuses on statistical methods that take advantage of linkage disequilibrium and haplotype determination to reveal signatures of positive selection in whole-genome sequencing data, showing that they emerge from different descriptions of the same underlying event. Moreover, considerations are provided around the application of these statistics to different species, their suitability for ancient DNA, and the usefulness of discovering variants under selection for biomedicine and public health in an evolutionary medicine framework

Human pangenomics: promises and challenges of a distributed genomic reference

A pangenome is a collection of the common and unique genomes that are present in a given species. It combines the genetic information of all the genomes sampled, resulting in a large and diverse range of genetic material. Pangenomic analysis offers several advantages compared to traditional genomic research. For example, a pangenome is not bound by the physical constraints of a single genome, so it can capture more genetic variability. Thanks to the introduction of the concept of pangenome, it is possible to use exceedingly detailed sequence data to study the evolutionary history of two different species, or how populations within a species differ genetically. In the wake of the Human Pangenome Project, this review aims at discussing the advantages of the pangenome around human genetic variation, which are then framed around how pangenomic data can inform population genetics, phylogenetics, and public health policy by providing insights into the genetic basis of diseases or determining personalized treatments, targeting the specific genetic profile of an individual. Moreover, technical limitations, ethical concerns, and legal considerations are discussed

Methylmercury and polycyclic aromatic hydrocarbons in mediterranean seafood: A molecular anthropological perspective

Eating seafood has numerous health benefits; however, it constitutes one of the main sources of exposure to several harmful environmental pollutants, both of anthropogenic and natural origin. Among these, methylmercury and polycyclic aromatic hydrocarbons give rise to concerns related to their possible effects on human biology. In the present review, we summarize the results of epidemiological investigations on the genetic component of individual susceptibility to methylmercury and polycyclic aromatic hydrocarbons exposure in humans, and on the effects that these two pollutants have on human epigenetic profiles (DNA methylation). Then, we provide evidence that Mediterranean coastal communities represent an informative case study to investigate the potential impact of methylmercury and polycyclic aromatic hydrocarbons on the human genome and epigenome, since they are characterized by a traditionally high local seafood consumption, and given the characteristics that render the Mediterranean Sea particularly polluted. Finally, we discuss the challenges of a molecular anthropological approach to this topic

Ecological Sensing through Taste and Chemosensation Mediates Inflammation: A Biological Anthropological Approach

Ecological sensing and inflammation have evolved to ensure optima between organism survival and reproductive success in different and changing environments. At the molecular level, ecological sensing consists of many types of receptors located in different tissues that orchestrate integrated responses (immune, neuroendocrine systems) to external and internal stimuli. This review describes emerging data on taste and chemosensory receptors, proposing them as broad ecological sensors and providing evidence that taste perception is shaped not only according to sense epitopes from nutrients but also in response to highly diverse external and internal stimuli. We apply a biological anthropological approach to examine how ecological sensing has been shaped by these stimuli through human evolution for complex interkingdom communication between a host and pathological and symbiotic bacteria, focusing on population-specific genetic diversity. We then focus on how these sensory receptors play a major role in inflammatory processes that form the basis of many modern common metabolic diseases such as obesity, type 2 diabetes, and aging. The impacts of human niche construction and cultural evolution in shaping environments are described with emphasis on consequent biological responsiveness

Analysis of nucleotide diversity of NAT2 coding region reveals homogeneity across Native American populations and high intra-population diversity.

N-acetyltransferase 2 (NAT2), an important enzyme in clinical pharmacology, metabolizes antibiotics such as isoniazid and sulfamethoxazole, and catalyzes the transformation of aromatic and heterocyclic amines from the environment and diet into carcinogenic intermediates. Polymorphisms in NAT2 account for variability in the acetylator phenotype and the pharmacokinetics of metabolized drugs. Native Americans, settled in rural areas and large cities of Latin America, are under-represented in pharmacogenetics studies; therefore, we sequenced the coding region of NAT2 in 456 chromosomes from 13 populations from the Americas, and two from Siberia, detecting nine substitutions and 11 haplotypes. Variants *4 (37%), *5B (23%) and *7B (24%) showed high frequencies. Average frequencies of fast, intermediate and slow acetylators across Native Americans were 18, 56 and 25%, respectively. NAT2 intra-population genetic diversity for Native Americans is higher than East Asians and similar to the rest of the world, and NAT2 variants are homogeneously distributed across native populations of the continent

Life-history and diet of two populations of Natrix maura (Reptilia, Colubridae) from contrasted habitats in Sardinia

Aspects of general ecology and population biology of two populations of freeliving viperine snakes (Natrix maura) were studied in Mediterranean localities of the island of Sardinia (Thyrrenian Sea, Italy). The apparent adult sex-ratio was not significantly different from equality, but males were slightly more numerous than females. The diet consisted mainly of arnphibians, both adults and tadpoles (area A) or fish (area B). Females were significantly longer than males. Reproduction was yearly, and clutch size and female total length were positively correlated. A hundred and seven live offsprings were obtained from 135 eggs (79.2% of successful incubation rates). The proportion of unsuccessful incubation was not significantly correlated with either female total length or clutch size. There was no evidence of a trade-off between clutch size and offspring size, as hatchlings were no smaller in clutches that were unusually large in relation to maternal body size. Oviposition date was correlated with neither maternal length nor clutch size. lncubation period was significantly correlated with mean hatchling size, but not with either clutch size or maternal length. No female died after oviposition, thus suggesting a very low incidence of mortality rates dueto starvation and reproductive costs. A case of long-term sperm storage deriving from autumnal mating is described. Population size estimates are provided for both study areas. Key words: Natrix maura, Ecology, Mediterranean region, Sardinia.Aspects of general ecology and population biology of two populations of freeliving viperine snakes (Natrix maura) were studied in Mediterranean localities of the island of Sardinia (Thyrrenian Sea, Italy). The apparent adult sex-ratio was not significantly different from equality, but males were slightly more numerous than females. The diet consisted mainly of arnphibians, both adults and tadpoles (area A) or fish (area B). Females were significantly longer than males. Reproduction was yearly, and clutch size and female total length were positively correlated. A hundred and seven live offsprings were obtained from 135 eggs (79.2% of successful incubation rates). The proportion of unsuccessful incubation was not significantly correlated with either female total length or clutch size. There was no evidence of a trade-off between clutch size and offspring size, as hatchlings were no smaller in clutches that were unusually large in relation to maternal body size. Oviposition date was correlated with neither maternal length nor clutch size. lncubation period was significantly correlated with mean hatchling size, but not with either clutch size or maternal length. No female died after oviposition, thus suggesting a very low incidence of mortality rates dueto starvation and reproductive costs. A case of long-term sperm storage deriving from autumnal mating is described. Population size estimates are provided for both study areas. Key words: Natrix maura, Ecology, Mediterranean region, Sardinia.Aspects of general ecology and population biology of two populations of freeliving viperine snakes (Natrix maura) were studied in Mediterranean localities of the island of Sardinia (Thyrrenian Sea, Italy). The apparent adult sex-ratio was not significantly different from equality, but males were slightly more numerous than females. The diet consisted mainly of arnphibians, both adults and tadpoles (area A) or fish (area B). Females were significantly longer than males. Reproduction was yearly, and clutch size and female total length were positively correlated. A hundred and seven live offsprings were obtained from 135 eggs (79.2% of successful incubation rates). The proportion of unsuccessful incubation was not significantly correlated with either female total length or clutch size. There was no evidence of a trade-off between clutch size and offspring size, as hatchlings were no smaller in clutches that were unusually large in relation to maternal body size. Oviposition date was correlated with neither maternal length nor clutch size. lncubation period was significantly correlated with mean hatchling size, but not with either clutch size or maternal length. No female died after oviposition, thus suggesting a very low incidence of mortality rates dueto starvation and reproductive costs. A case of long-term sperm storage deriving from autumnal mating is described. Population size estimates are provided for both study areas. Key words: Natrix maura, Ecology, Mediterranean region, Sardinia

The genetic variability of APOE in different human populations and its implications for longevity

Human longevity is a complex phenotype resulting from the combinations of context-dependent gene-environment interactions that require analysis as a dynamic process in a cohesive ecological and evolutionary framework. Genome-wide association (GWAS) and whole-genome sequencing (WGS) studies on centenarians pointed toward the inclusion of the apolipoprotein E (APOE) polymorphisms \u3b52 and \u3b54, as implicated in the attainment of extreme longevity, which refers to their effect in age-related Alzheimer\u2019s disease (AD) and cardiovascular disease (CVD). In this case, the available literature on APOE and its involvement in longevity is described according to an anthropological and population genetics perspective. This aims to highlight the evolutionary history of this gene, how its participation in several biological pathways relates to human longevity, and which evolutionary dynamics may have shaped the distribution of APOE haplotypes across the globe. Its potential adaptive role will be described along with implications for the study of longevity in different human groups. This review also presents an updated overview of the worldwide distribution of APOE alleles based on modern day data from public databases and ancient DNA samples retrieved from literature in the attempt to understand the spatial and temporal frame in which present-day patterns of APOE variation evolved

Between Andes and Amazon: The genetic profile of the Arawak-speaking Yanesha

The Yanesha are a Peruvian population who inhabit an environment transitional between the Andes and Amazonia. They present cultural traits characteristic of both regions, including in the language they speak: Yanesha belongs to the Arawak language family (which very likely originated in the Amazon/Orinoco lowlands), but has been strongly influenced by Quechua, the most widespread language family of the Andes. Given their location and cultural make-up, the Yanesha make for an ideal case study for investigating language and population dynamics across the Andes-Amazonia divide. In this study, we analyze data from high and mid-altitude Yanesha villages, both Y chromosome (17 STRs and 16 SNPs diagnostic for assigning haplogroups) and mtDNA data (control region sequences and 3 SNPs and one INDEL diagnostic for assigning haplogroups). We uncover sex-biased genetic trends that probably arose in different stages: first, a male-biased gene flow from Andean regions, genetically consistent with highland Quechua-speakers and probably dating back to Inca expansion; and second, traces of European contact consistent with Y chromosome lineages from Italy and Tyrol, in line with historically documented migrations. Most research in the history, archaeology and linguistics of South America has long been characterized by perceptions of a sharp divide between the Andes and Amazonia; our results serve as a clear case-study confirming demographic flows across that \u2018divide\u2019

Attitudes and Perceptions of Local Communities towards Nile Crocodiles (Crocodylus niloticus) in the Sudd Wetlands, South Sudan

Conflicts between human populations and Nile crocodiles are widespread with crocodiles posing significant threats to fisherfolk and riverine communities across r-Saharan Africa. Hundreds of deadly attacks take place annually, and mortality rates may range from 50% to 100%. Attitudes and perceptions towards crocodiles were studied using structured questionnaires among fisherfolk along the River Nile and the Sudd wetlands in South Sudan. Local communities used crocodiles for their meat and skin/leather trades. The meat is regarded to enhance longevity, sexual potency, and protection against witchcraft. Crocodiles are perceived as a main threat to lives and livelihoods as they restrict people’s freedom of movement along water bodies, attack livestock and humans, and devastate fishing equipment. To assess whether responses were influenced by the intensity of crocodile threats, published data on fatal crocodile attacks on humans and livestock were analysed using Generalised Linear Models (GLMs). This analysis indicated a direct link between the number of crocodile attacks and human attitudes. Crocodiles were generally feared and hated, and there was the agreement of the need to destroy breeding habitats. However, some attitudes were complex and nuanced as highlighted by the agreement of local communities on the need to destroy Nile Crocodile breeding habitats on the one hand and the need to establish crocodile sanctuaries as the the preferred strategy to mitigate risks and conflict on the other hand. There is a need for the creation of a crocodile sanctuary in the Sudd wetlands to minimise the risks of illegal hunting and to buffer the increasing pressure on crocodiles due to human population growth and economic upturn after the civil war

Twenty-Seven Y-Chromosome Short Tandem Repeats Analysis of Italian Mummies of the 16th and 18th Centuries: An Interdisciplinary Research

Roccapelago (MO) is a small village located in the Northern Central Apennines, with a population of 31 inhabitants (2014). In 2010, more than 400 individuals dated between the end of the 16th and the 18th century, many of which partially mummified, were discovered in the crypt of the church. This small village, because of its geographical location and surrounding environment, seems to possess the characteristics of a genetic isolate, useful for population genetics and genealogical analyses. Thus, a diachronic study of DNA aimed at investigating the structure and dynamics of the population of Roccapelago over the about 4 centuries, was conducted by analyzing ancient and modern inhabitants of the village. The 14 modern samples were selected by considering both the founder surnames of the village, identified thanks to the study of parish registers, and the grandparent’s criterion. From 25 ancient mummies, morphologically assigned to male individuals, the petrous bone, that harbors high DNA amounts, was selected for the DNA extraction. The quantification and qualitative assessment of total human male DNA were evaluated by a real-time PCR assay using the Quantifiler Trio DNA Quantification Kit and multiplex PCR of 27 Y-chromosome short tandem repeat (Y-STR) markers included in the Yfiler Plus PCR Amplification Kit, with seven rapidly mutating Y-STR loci for improving discrimination of male lineages, was performed to genotype the samples. Y-STRs were analyzed according to the criteria of ancient DNA (aDNA) analysis to ensure that authentic DNA typing results were obtained from these ancient samples. The molecular analysis showed the usefulness of the Y chromosome to identify historically relevant remains and discover patterns of relatedness in communities moving from anthropology to genetic genealogy and forensics