Mapping Post-Glacial expansions: The Peopling of Southwest Asia

Saturated fat in an evolutionary context

Evolutionary perspectives have yielded profound insights in health and medical sciences. A fundamental recognition is that modern diet and lifestyle practices are mismatched with the human physiological constitution, shaped over eons in response to environmental selective pressures. This Darwinian angle can help illuminate and resolve issues in nutrition, including the contentious issue of fat consumption. In the present paper, the intake of saturated fat in ancestral and contemporary dietary settings is discussed. It is shown that while saturated fatty acids have been consumed by human ancestors across time and space, they do not feature dominantly in the diets of hunter-gatherers or projected nutritional inputs of genetic accommodation. A higher intake of high-fat dairy and meat products produces a divergent fatty acid profile that can increase the risk of cardiovascular and inflammatory disease and decrease the overall satiating-, antioxidant-, and nutrient capacity of the diet. By prioritizing fiber-rich and micronutrient-dense foods, as well as items with a higher proportion of unsaturated fatty acids, and in particular the long-chain polyunsaturated omega-3 fatty acids, a nutritional profile that is better aligned with that of wild and natural diets is achieved. This would help prevent the burdening diseases of civilization, including heart disease, cancer, and neurodegenerative conditions. Saturated fat is a natural part of a balanced diet; however, caution is warranted in a food environment that differs markedly from the one to which we are adapted.

Human migration from the Levant and Arabia into Yemen since Last Glacial Maximum

While a broad consensus about the first successful migration modern humans out of Africa seems established, the peopling of Arabia remains somewhat enigmatic. Identifying the ancestral populations that contributed to the gene pool of the current populations inhabiting Arabia and the impact of their contributions remains a challenging task. We investigate the genetic makeup of the current Yemeni population using 46 whole genomes and 169 genotype arrays derived from Yemeni individuals from all geographic regions across Yemen and 351 genotype arrays derived from neighboring populations providing regional context. Principal Component Analysis shows stratification between Yemen districts but also with respect to nearby populations: Yemeni, other Arabian and Bedouin samples form a continuum towards the populations of the Levant, whereas East Africa and India appear strongly differentiated. This finding is further supported by higher Principal Components, admixture and haplogroup analyses, and F-statistics. Moreover, two-reference linkage disequilibrium decay estimates are most significant for Yemeni admixture from an ancient northern influx (up to 5220BP from Palestine) and East Africa (750BP). We show that the initial gene flow into the Yemeni populations of today came from the rest of Arabia and the Levant, and a less substantial and more recent genetic impact into coastal Yemen from East Africa, particularly.

An economic model and evidence of the evolution of human intelligence in the Middle Pleistocene: Climate change and assortative mating

A main objective of this paper is to provide the first model of how climate change, working through sexual selection, could have led to dramatic increases in hominin brain size, and presumably intelligence, in the Middle Pleistocene. The model is built using core elements from the field of family economics, including assortative mating and specialization and complementarities between mates. The main assumptions are that family public goods (e.g., conversation, shelter, fire) were particularly cognitively intensive to produce and became increasingly important for child survival during glacial phases. Intermediate climates (e.g., not the depths of severe glacial phases) create the largest gains from specialization, encouraging negative assortative mating. In contrast, severe glacial phases encourage positive assortative mating because of the rising importance of family public goods. One testable hypothesis is that absence of severe glacial phases should have led to stasis in brain size. Two other testable hypotheses are that severe glacial phases should have led to speciation events, as well as increases in brain size. The evidence shows that there was a million-year stasis in cranial size prior to the start of the severe glacial phases. This stasis is broken by a speciation event (Homo heidelbergensis), with the oldest fossil evidence dated near the close of the first severe glacial phase. In the next 300 kyr, there are two additional severe glacial phases, accompanied by considerable increases in cranial capacity. The last speciation event is Homo sapiens, with the earliest fossils dated near the end of the last of these two glacial phases.

Challenges in the recovery of the genetic data from human remains found on the Western Balkan migration route

Traditional DNA-based identification of human remains relies on the system of matching STR profile of the deceased with the family references or antemortem samples. In forensic cases without any available samples for the comparison, the body remains unidentified. The aim of this study was to assess the applicability of massively parallel sequencing (MPS) approach in the forensic cases of five drowned individuals recovered on the Western Balkan migration route. Besides capillary electrophoresis (CE)-based genetic profiling (aSTR, Y STR, and mitochondrial control region sequencing) of postmortem samples, we applied ForenSeq DNA Signature Prep Kit/Primer Mix B on MiSeqFGx platform and concomitant ForenSeq Universal Analysis (UAS) software. The assay showed high reproducibility and complete concordance with CE-based data except in locus DYF387S1. Allele and locus drop was evident in 2.9% of total SNPs that slightly reduced the completeness of the data. We endeavored to predict the phenotype of the tested samples and accurate biogeographical ancestry of European individual. UAS was less informative for the remaining samples assigned to Admixed American cluster. Nevertheless, the application of FROG-kb and Snipper tools along with admixture analysis in STRUCTURE and lineage markers revealed likely Middle Eastern and North African ancestry. We conclude that the combination of the phenotype and biogeographical ancestry predictions, including paternal and maternal genetic ancestry, represent a promising tool for humanitarian identification of dead migrants. Nevertheless, the data interpretation remains a challenging task.

Comparative embryogenesis in ungulate domesticated species

We compared embryogenesis of five species of domesticated even-toed and one odd-toed ungulate and used a phylogenetic framework to contextualize such comparison. Organ systems that occur relatively earlier in embryogenesis generally have more time to develop and therefore are found to be more mature at birth when compared to structures that appear later in development. We hypothesized that the less mature the animals' organs are at birth, the more they are susceptible to artificial selection. The horse had the most mature organs at birth, followed by cattle, reindeer, sheep/goat, and pig. This pattern of maturity could be observed almost during the entire development. Heterochronic shifts among species were observed only after fur starts to develop. Changes in the fur coloration are one of the first observable signs of domestication and the heterochrony of this trait may be related to the effects on neural crest-derived pigment cells by artificial selection. The six ungulate species also differ in the relative duration of their weaning period and the potential extent of its artificial shortening. We put all these traits in the context of their inherited evolutionary characteristics and artificial domestication process. Related to their altriciality, carnivoran domesticates, which also belong to Scrotifera, are less mature at birth than all domesticated ungulates. Although we detected clear character correlations to life history traits, it is impossible based on the present data, to trace specific exaptations to the domestication process. We hypothesize a deep time developmental penetration of adult characters into embryogenesis.

Climate Warming Since the Holocene Accelerates West-East Communication for the Eurasian Temperate Water Strider Species Aquarius paludum

Holocene climate warming has dramatically altered biological diversity and distributions. Recent human-induced emissions of greenhouse gases will exacerbate global warming and thus induce threats to cold-adapted taxa. However, the impacts of this major climate change on transcontinental temperate species are still poorly understood. Here, we generated extensive genomic datasets for a water strider, Aquarius paludum, which was sampled across its entire distribution in Eurasia and used these datasets in combination with ecological niche modeling (ENM) to elucidate the influence of the Holocene and future climate warming on its population structure and demographic history. We found that A. paludum consisted of two phylogeographic lineages that diverged in the middle Pleistocene, which resulted in a “west–east component” genetic pattern that was probably triggered by Central Asia-Mongoxin aridification and Pleistocene glaciations. The diverged western and eastern lineages had a second contact in the Holocene, which shaped a temporary hybrid zone located at the boundary of the arid–semiarid regions of China. Future predictions detected a potentially novel northern corridor to connect the western and eastern populations, indicating west–east gene flow would possibly continue to intensify under future warming climate conditions. Further integrating phylogeographic and ENM analyses of multiple Eurasian temperate taxa based on published studies reinforced our findings on the “west–east component” genetic pattern and the predicted future northern corridor for A. paludum. Our study provided a detailed paradigm from a phylogeographic perspective of how transcontinental temperate species differ from cold-adapted taxa in their response to climate warming.

Y-chromosome variability and genetic history of Commons from Northern Italy

Objectives

Genetic drift and admixture are driving forces in human evolution, but their concerted impact to population evolution in historical times and at a micro‐geographic scale is poorly assessed. In this study we test a demographic model encompassing both admixture and drift to the case of social‐cultural isolates such as the so‐called “Commons.”

Materials and methods

Commons are peculiar institutions of medieval origins whose key feature is the tight relationship between population and territory, mediated by the collective property of shared resources. Here, we analyze the Y‐chromosomal genetic structure of four Commons (for a total of 366 samples) from the Central and Eastern Padana plain in Northern Italy.

Results

Our results reveal that all these groups exhibit patterns of significant diversity reduction, peripheral/outlier position within the Italian/European genetic space and high frequency of Common‐specific haplogroups. By explicitly testing different drift‐admixture models, we show that a drift‐only model is more probable for Central Padana Commons, while additional admixture (~20%) from external population around the same time of their foundation cannot be excluded for the Eastern ones.

Discussion

Building on these results, we suggest central Middle Ages as the most probable age of foundation for three of the considered Commons, the remaining one pointing to late antiquity. We conclude that an admixture‐drift model is particularly useful for interpreting the genetic structure and recent demographic history of small‐scale populations in which social‐cultural features play a significant role.

Origin and diffusion of human Y chromosome haplogroup J1-M267

Human Y chromosome haplogroup J1-M267 is a common male lineage in West Asia. One high-frequency region-encompassing the Arabian Peninsula, southern Mesopotamia, and the southern Levant-resides ~ 2000 km away from the other one found in the Caucasus. The region between them, although has a lower frequency, nevertheless demonstrates high genetic diversity. Studies associate this haplogroup with the spread of farming from the Fertile Crescent to Europe, the spread of mobile pastoralism in the desert regions of the Arabian Peninsula, the history of the Jews, and the spread of Islam. Here, we study past human male demography in West Asia with 172 high-coverage whole Y chromosome sequences and 889 genotyped samples of haplogroup J1-M267. We show that this haplogroup evolved ~ 20,000 years ago somewhere in northwestern Iran, the Caucasus, the Armenian Highland, and northern Mesopotamia. The major branch-J1a1a1-P58-evolved during the early Holocene ~ 9500 years ago somewhere in the Arabian Peninsula, the Levant, and southern Mesopotamia. Haplogroup J1-M267 expanded during the Chalcolithic, the Bronze Age, and the Iron Age. Most probably, the spread of Afro-Asiatic languages, the spread of mobile pastoralism in the arid zones, or both of these events together explain the distribution of haplogroup J1-M267 we see today in the southern regions of West Asia.

Cattle mitogenome variation reveals a post-glacial expansion of haplogroup P and an early incorporation into northeast Asian domestic herds

Surveys of mitochondrial DNA (mtDNA) variation have shown that worldwide domestic cattle are characterized by just a few major haplogroups. Two, T and I, are common and characterize Bos taurus and Bos indicus, respectively, while the other three, P, Q and R, are rare and are found only in taurine breeds. Haplogroup P is typical of extinct European aurochs, while intriguingly modern P mtDNAs have only been found in northeast Asian cattle. These Asian P mtDNAs are extremely rare with the exception of the Japanese Shorthorn breed, where they reach a frequency of 45.9%. To shed light on the origin of this haplogroup in northeast Asian cattle, we completely sequenced 14 Japanese Shorthorn mitogenomes belonging to haplogroup P. Phylogenetic and Bayesian analyses revealed: (1) a post-glacial expansion of aurochs carrying haplogroup P from Europe to Asia; (2) that all Asian P mtDNAs belong to a single sub-haplogroup (P1a), so far never detected in either European or Asian aurochs remains, which was incorporated into domestic cattle of continental northeastern Asia possibly ~ 3700 years ago; and (3) that haplogroup P1a mtDNAs found in the Japanese Shorthorn breed probably reached Japan about 650 years ago from Mongolia/Russia, in agreement with historical evidence.

Distinct genetic variation and heterogeneity of the Iranian population

Iran, despite its size, geographic location and past cultural influence, has largely been a blind spot for human population genetic studies. With only sparse genetic information on the Iranian population available, we pursued its genome-wide and geographic characterization based on 1021 samples from eleven ethnic groups. We show that Iranians, while close to neighboring populations, present distinct genetic variation consistent with long-standing genetic continuity, harbor high heterogeneity and different levels of consanguinity, fall apart into a cluster of similar groups and several admixed ones and have experienced numerous language adoption events in the past. Our findings render Iran an important source for human genetic variation in Western and Central Asia, will guide adequate study sampling and assist the interpretation of putative disease-implicated genetic variation. Given Iran's internal genetic heterogeneity, future studies will have to consider ethnic affiliations and possible admixture.

Extensive geographical and social structure in the paternal lineages of Saudi Arabia revealed by analysis of 27 Y-STRs

Saudi Arabia's indigenous population is organized into patrilineal descent groups, but to date, little has been done to characterize its population structure, in particular with respect to the male-specific region of the Y chromosome. We have used the 27-STR Yfiler^® Plus kit to generate haplotypes in 597 unrelated Saudi males, classified into five geographical regions (North, South, Central, East and West). Overall, Yfiler^® Plus provides a good discrimination capacity of 95.3%, but this is greatly reduced (74.7%) when considering the reduced Yfiler^® set of 17 Y-STRs, justifying the use of the expanded set of markers in this population. Comparison of the five geographical divisions reveals striking differences, with low diversity and similar haplotype spectra in the Central and Northern regions, and high diversity and similar haplotype spectra in the East and West. These patterns likely reflect the geographical isolation of the desert heartland of the peninsula, and the proximity to the sea of the Eastern and Western areas, and consequent historical immigration. We predicted haplogroups from Y-STR haplotypes, testing the performance of prediction by using a large independent set of Saudi Arabian Y-STR + Y-SNP data. Prediction indicated predominance (71%) of haplogroup J1, which was significantly more common in Central, Northern and Southern groups than in East and West, and formed a star-like expansion cluster in a median-joining network with an estimated age of ∼2800 years. Most of our 597 participants were sampled within Saudi Arabia itself, but ∼16% were sampled in the UK. Despite matching these two groups by home sub-region, we observed significant differences in haplotype and predicted haplogroup constitutions overall, and for most sub-regions individually. This suggests social structure influencing the probability of leaving Saudi Arabia, correlated with different Y-chromosome compositions. The UK-recruited sample is an inappropriate proxy for Saudi Arabia generally, and caution is needed when considering expatriate groups as representative of country of origin. Our study shows the importance of geographical and social structuring that may affect the utility of forensic databases and the interpretation of Y-STR profiles.

Continuity and Admixture in the Last Five Millennia of Levantine History from Ancient Canaanite and Present-Day Lebanese Genome Sequences

The Canaanites inhabited the Levant region during the Bronze Age and established a culture that became influential in the Near East and beyond. However, the Canaanites, unlike most other ancient Near Easterners of this period, left few surviving textual records and thus their origin and relationship to ancient and present-day populations remain unclear. In this study, we sequenced five whole genomes from ∼3,700-year-old individuals from the city of Sidon, a major Canaanite city-state on the Eastern Mediterranean coast. We also sequenced the genomes of 99 individuals from present-day Lebanon to catalog modern Levantine genetic diversity. We find that a Bronze Age Canaanite-related ancestry was widespread in the region, shared among urban populations inhabiting the coast (Sidon) and inland populations (Jordan) who likely lived in farming societies or were pastoral nomads. This Canaanite-related ancestry derived from mixture between local Neolithic populations and eastern migrants genetically related to Chalcolithic Iranians. We estimate, using linkage-disequilibrium decay patterns, that admixture occurred 6,600–3,550 years ago, coinciding with recorded massive population movements in Mesopotamia during the mid-Holocene. We show that present-day Lebanese derive most of their ancestry from a Canaanite-related population, which therefore implies substantial genetic continuity in the Levant since at least the Bronze Age. In addition, we find Eurasian ancestry in the Lebanese not present in Bronze Age or earlier Levantines. We estimate that this Eurasian ancestry arrived in the Levant around 3,750–2,170 years ago during a period of successive conquests by distant populations.