Eurasian Populations Research Articles

Multiple-wave admixture and adaptive evolution of the Pamirian Wakhi people.

While whole-genome sequencing has been applied extensively to investigate the genetic diversity of global populations, ethnic minority groups in Pakistan are generally underrepresented. In particular, little is known about the genetic origin and highland adaptation of the Pamirian Wakhi people. According to Chinese historical records, the geographical location and language usage of Wakhi may be closely related to Xinjiang Tajiks (XJT). In this study, based on high-coverage (∼30×) whole-genome sequencing of eight Wakhi and 25 XJT individuals, we performed data analyses together with worldwide populations to gain insights into their genetic composition, demography, and adaptive evolution to the highland environment. The Wakhi derived more than 85% of their ancestry from West Eurasian populations (European ∼44.5%, South Asian ∼42.2%) and 10% from East Eurasian populations (Siberian ∼6.0%, East Asian ∼4.3%). Modeling the admixture history of the Wakhi indicated that the early West-East admixture occurred approximately 3,875-2,250 years ago and that the recent admixture occurred 750-375 years ago. We identified selection signatures across EGLN3, in particular, a distinctive evolutionary signature was observed, and a certain underlying selected haplotype showed higher frequency (87.5%) in the Wakhi than in nearby XJT and other highlanders. Interestingly, we found high-frequency archaic sequences in the Wakhi genome, which overlapped with several genes related to cellular signaling transduction, including MAGI2, previously associated with high-altitude adaptation. Our analysis indicates that the Wakhi are distinct from the XJTs and Tajikistan Tajiks, and shed light on the Wakhi's ancestral origin and genetic basis of high-altitude adaptation.

Local population dynamics of gray wolves Canis lupus and Eurasian lynx Lynx lynx exhibit consistency with intraspecific contest competition models

AbstractIn Europe, the gray wolf and Eurasian lynx populations are recovering after various levels of persecution. The two species differ in their social structure and spatial patterns of aggregation. Using model selection, we investigated the consistency of the available time series data on local wolf and lynx sub‐populations with a number of single‐species population growth models that pertain to two types of intraspecific competition, namely, scramble (SC) and contest competition (CC), and reflect random (R) or aggregated (A) distribution of individuals. The applied models of population growth—the Ricker (SCR), Skellam (CCR), Hassell (SCA), and Beverton–Holt (CCA) models—were all parameterized in terms of intrinsic growth rate and carrying capacity with unified definitions. The projected carrying capacity was allowed to show a temporal trend, which was justified by an observed increase in prey abundance in recent decades. For both species, the models pertaining to contest competition outperformed the scramble competition models, and the Beverton–Holt model had the greatest weight. However, for the lynx, the difference of performance between the scramble and contest competition models was considerably smaller than that for the wolves. In most of the models, when it was meaningful, an optional time lag operator was added to account for a delay in individual maturity and reproduction. However, the models with a time lag had a worse fit than the models without it. This study promotes the application of population models that reflect intraspecific competition for modeling population dynamics in a single‐ or multi‐species framework.

Was the steppe bison a grazing beast in Pleistocene landscapes?

The history and palaeoecology of the steppe bison (Bison priscus) remain incompletely understood despite its widespread distribution. Using dental microwear textural analysis (DMTA) and vegetation modelling, we reconstructed the diet and assessed the habitat of steppe bison inhabiting Eurasia and Alaska since the Middle Pleistocene. During the Late Pleistocene, steppe bison occupied a variety of biome types: from the mosaic of temperate summergreen forest and steppe/temperate grassland (Serbia) to the tundra biomes (Siberia and Alaska). Despite the differences in the identified biome types, the diet of steppe bison did not differ significantly among populations in Eurasia. DMTA classified it as a mixed forager in all populations studied. The DMTA of Bb1 bison-a recently identified genetically extinct sister-clade of Bison bonasus-was typical of a highly grazing bovid species and differed from all B. priscus populations. The results of the study temper the common perception that steppe bison were grazers in steppe habitats. The dietary plasticity of the steppe bison was lower when compared with modern European bison and may have played an important role in its extinction, even in the stable tundra biome of eastern Siberia, where it has survived the longest in all of Eurasia.

Modelling the demographic history of human North African genomes points to a recent soft split divergence between populations

BackgroundNorth African human populations present a complex demographic scenario due to the presence of an autochthonous genetic component and population substructure, plus extensive gene flow from the Middle East, Europe, and sub-Saharan Africa.ResultsWe conducted a comprehensive analysis of 364 genomes to construct detailed demographic models for the North African region, encompassing its two primary ethnic groups, the Arab and Amazigh populations. This was achieved through an Approximate Bayesian Computation with Deep Learning (ABC-DL) framework and a novel algorithm called Genetic Programming for Population Genetics (GP4PG). This innovative approach enabled us to effectively model intricate demographic scenarios, utilizing a subset of 16 whole genomes at > 30X coverage. The demographic model suggested by GP4PG exhibited a closer alignment with the observed data compared to the ABC-DL model. Both point to a back-to-Africa origin of North African individuals and a close relationship with Eurasian populations. Results support different origins for Amazigh and Arab populations, with Amazigh populations originating back in Epipaleolithic times, while GP4PG supports Arabization as the main source of Middle Eastern ancestry. The GP4PG model includes population substructure in surrounding populations (sub-Saharan Africa and Middle East) with continuous decaying gene flow after population split. Contrary to ABC-DL, the best GP4PG model does not require pulses of admixture from surrounding populations into North Africa pointing to soft splits as drivers of divergence in North Africa.ConclusionsWe have built a demographic model on North Africa that points to a back-to-Africa expansion and a differential origin between Arab and Amazigh populations.

Analysis of sex-biased gene expression in a Eurasian admixed population.

Sex-biased gene expression differs across human populations; however, the underlying genetic basis and molecular mechanisms remain largely unknown. Here, we explore the influence of ancestry on sex differences in the human transcriptome and its genetic effects on a Eurasian admixed population: Uyghurs living in Xinjiang (XJU), by analyzing whole-genome sequencing data and transcriptome data of 90 XJU and 40 unrelated Han Chinese individuals. We identified 302 sex-biased expressed genes and 174 sex-biased cis-expression quantitative loci (sb-cis-eQTLs) in XJU, which were enriched in innate immune-related functions, indicating sex differences in immunity. Notably, approximately one-quarter of the sb-cis-eQTLs showed a strong correlation with ancestry composition; i.e. populations of similar ancestry tended to show similar patterns of sex-biased gene expression. Our analysis further suggested that genetic admixture induced a moderate degree of sex-biased gene expression. Interestingly, analysis of chromosome interactions revealed that the X chromosome acted on autosomal immunity-associated genes, partially explaining the sex-biased phenotypic differences. Our work extends the knowledge of sex-biased gene expression from the perspective of genetic admixture and bridges the gap in the exploration of sex-biased phenotypes shaped by autosome and X-chromosome interactions. Notably, we demonstrated that sex chromosomes cannot fully explain sex differentiation in immune-related phenotypes.

Ancestral Origins and Admixture History of Kazakhs.

Kazakh people, like many other populations that settled in Central Asia, demonstrate an array of mixed anthropological features of East Eurasian (EEA) and West Eurasian (WEA) populations, indicating a possible scenario of biological admixture between already differentiated EEA and WEA populations. However, their complex biological origin, genomic makeup, and genetic interaction with surrounding populations are not well understood. To decipher their genetic structure and population history, we conducted, to our knowledge, the first whole-genome sequencing study of Kazakhs residing in Xinjiang (KZK). We demonstrated that KZK derived their ancestries from 4 ancestral source populations: East Asian (∼39.7%), West Asian (∼28.6%), Siberian (∼23.6%), and South Asian (∼8.1%). The recognizable interactions of EEA and WEA ancestries in Kazakhs were dated back to the 15th century BCE. Kazakhs were genetically distinctive from the Uyghurs in terms of their overall genomic makeup, although the 2 populations were closely related in genetics, and both showed a substantial admixture of western and eastern peoples. Notably, we identified a considerable sex-biased admixture, with an excess of western males and eastern females contributing to the KZK gene pool. We further identified a set of genes that showed remarkable differentiation in KZK from the surrounding populations, including those associated with skin color (SLC24A5, OCA2), essential hypertension (HLA-DQB1), hypertension (MTHFR, SLC35F3), and neuron development (CNTNAP2). These results advance our understanding of the complex history of contacts between Western and Eastern Eurasians, especially those living or along the old Silk Road.

Far away from home? Ancient DNA shows the presence of bicolored shrew (Crocidura leucodon) in Bronze Age Denmark.

An excavation of an Early Iron Age village near Aalborg in Denmark uncovered the jaws and skull fragments from a small mammal that were morphologically identified to the genus Crocidura (white-toothed shrews). Three Crocidura species are known from prehistoric continental Europe but none of them are distributed in Scandinavia, which is why this surprising finding warranted further analyses. The bone was radiocarbon-dated to 2840-2750 calibrated years before present (cal. BP), corresponding to the Late Bronze Age and hence earlier than the Iron Age archeological context in which it was found. Using highly optimized ancient DNA protocols, we extracted DNA from one tooth and shotgun-sequenced the sample to reconstruct a near-complete mitochondrial reference genome (17,317 bp, 32.6× coverage). Phylogenetic analyses determined this specimen as a bicolored shrew (Crocidura leucodon) but with a phylogenetic position basal to the clade of known sequences from this species. The confirmation of Crocidura presence in Denmark by the Late Bronze Age sheds new light on the prehistoric natural history of Scandinavia. We discuss the implications of this finding from both zoo-archeological and ecological perspectives. Furthermore, the mitochondrial genome reconstructed in this study offers a valuable resource for future research exploring the genetic makeup and evolutionary history of Eurasian shrew populations.

Genetic Differentiation of Reed Canarygrass (Phalaris arundinacea L.) within Eastern Europe and Eurasia.

Worldwide molecular research of economically important Phalaris arundinacea (Poaceae) is mainly focused on the invasions of this species from Europe to North America. Until the present study, the genetic diversity of the P. arundinacea had not been studied across the Baltic countries. The objective of this research is to evaluate the diversity of Lithuanian populations of P. arundinacea at simple sequence repeat (SSR) loci comparatively among populations of the Baltic countries, Luxembourg, and the Russian Far East (Eurasian), evaluating differentiation between Lithuanian populations and ornamental accessions, and relating these with environmental features. For six selected Lithuanian river basin populations, GBS low density SNPs were used to determine genetic diversity. Bayesian analysis showed that Eurasian populations of Phalaris arundinacea consist of two gene clusters. Statistically significant genetic differentiation among European and Eurasian populations was documented. Lithuanian genotypes growing naturally along rivers are genetically distinct from cultivated ornamentals. GBS-SNPs divided the six selected Nemunas river basins into three distinct groups with one, two, or three rivers in separate groupings for genetic diversity. Genetic diversity is primarily within, rather than among, Lithuanian, eastern European, and Eurasian populations of P. arundinacea across the continent. Thus, restoration efforts would benefit from local population seed origination.

Status assessment of a recently reintroduced eurasian lynx (Lynx lynx) population in the Palatinate Forest, South-West Germany

To reinforce Eurasian lynx populations in central Europe, 20 lynx from Slovakia and Switzerland were translocated to the Palatinate Forest between 2016 and 2020. Using a systematic camera trapping array consisting of 80 camera trapping sites in a 1,000 km² study area located in the centre of the approximately 1,800 km² Palatinate Forest, we aim to describe the status of the population in the final stages of the reintroduction project in winter and spring 2019/20 and 2020/21. We also use our data to provide a first estimate of population density of the newly established population. With an estimate of 0.52 independent individuals per 100 km², population density in the Palatinate Forest was still significantly lower than the densities of well-established reintroduced populations. The number of independent individuals detected in the study area decreased from 15 individuals in 2019/20 to 11 individuals in 2020/21, thus significantly below the number of lynx translocated. The low abundance in the Palatinate Forest can be explained by the dispersal of several individuals to the Vosges (France), which, together with the Palatinate Forest, form a continuous area of suitable lynx habitat of approximately 8,000 km². Our results may thus reflect the status of a young population that can expand over a potentially large area. Nevertheless, in light of the low population density, we strongly recommend a synchronized and harmonized transboundary monitoring program to keep track of the development of this important Franco-German lynx population. In case population density remains low, supportive measures need to be considered.

Competing forces: Subsistence strategies and human-carnivore interactions during the middle to Upper Palaeolithic transition in Northern Iberia

The comparative assessment of dietary choices as part of landscape use strategies deployed by Neanderthal and Anatomically Modern Human populations in Eurasia constitutes a fundamental avenue of Palaeolithic research. The increasing number of taphonomic assessments enables a better understanding of what remains were brought to sites by human hunters versus mammalian carnivores or raptors. A zooarchaeological approach can further elucidate the spatio-temporal dynamics of interaction between carnivores and human populations in terms of landscape use and prey choice during this transitional period. To achieve this objective, we conducted an examination of zooarchaeological and taphonomic data, carnivore indices, and other relevant variables across 36 Middle and Early Upper Palaeolithic sites in northern Iberia. These sites encompass 126 archaeological layers dating from 50,000 to 30,000 years ago. Our comprehensive bibliographic meta-analysis reveals that human occupations by both groups at sites across the region were punctuated by episodes influenced by carnivores. This observation implies that human occupations in northern Iberia during Marine Isotope Stage 3 were generally characterised by instability and limited to short periods, often seasonal in nature. From a zooarchaeological perspective, the combined assessment of taxonomic data, species richness and assemblage diversity highlights that the range and proportion of species acquired by these different human groups are similar, although Anatomically Modern Humans engaged in a sustained trend towards increasing dietary diversification even at sites with assemblages heavily dominated by one taxon.

Novel genetic association of the Furin gene polymorphism rs1981458 with COVID-19 severity among Indian populations

SARS CoV-2, the causative agent for the ongoing COVID-19 pandemic, it enters the host cell by activating the ACE2 receptor with the help of two proteasesi.e., Furin and TMPRSS2. Therefore, variations in these genes may account for differential susceptibility and severity between populations. Previous studies have shown that the role of ACE2 and TMPRSS2 gene variants in understanding COVID-19 susceptibility among Indian populations. Nevertheless, a knowledge gap exists concerning the COVID-19 susceptibility of Furin gene variants among diverse South Asian ethnic groups. Investigating the role of Furin gene variants and their global phylogeographic structure is essential to comprehensively understanding COVID-19 susceptibility in these populations. We have used 450 samples from diverse Indian states and performed linear regression to analyse the Furin gene variant's with COVID-19 Case Fatality Rate (CFR) that could be epidemiologically associated with disease severity outcomes. Associated genetic variants were further evaluated for their expression and regulatory potential through various Insilco analyses. Additionally, we examined the Furin gene using next-generation sequencing (NGS) data from 393 diverse global samples, with a particular emphasis on South Asia, to investigate its Phylogeographic structure among diverse world populations. We found a significant positive association for the SNP rs1981458 with COVID-19 CFR (p < 0.05) among diverse Indian populations at different timelines of the first and second waves. Further, QTL and other regulatory analyses showed various significant associations for positive regulatory roles of rs1981458 and Furin gene, mainly in Immune cells and virus infection process, highlighting their role in host immunity and viral assembly and processing. The Furin protein–protein interaction suggested that COVID-19 may contribute to Pulmonary arterial hypertension via a typical inflammation mechanism. The phylogeographic architecture of the Furin gene demonstrated a closer genetic affinity of South Asia with West Eurasian populations. Therefore, it is worth proposing that for the Furin gene, the COVID-19 susceptibility of South Asians will be more similar to the West Eurasian population. Our previous studies on the ACE2 and TMPRSS2 genes showed genetic affinity of South Asian with East Eurasians and West Eurasians, respectively. Therefore, with the collective information from these three important genes (ACE2, TMPRSS2 and Furin) we modelled COVID-19 susceptibilityof South Asia in between these two major ancestries with an inclination towards West Eurasia. In conclusion, this study, for the first time, concluded the role of rs1981458 in COVID-19 severity among the Indian population and outlined its regulatory potential.This study also highlights that the genetic structure for COVID-19 susceptibilityof South Asia is distinct, however, inclined to the West Eurasian population. We believe this insight may be utilised as a genetic biomarker to identify vulnerable populations, which might be directly relevant for developing policies and allocating resources more effectively during an epidemic.

Malaria resistance-related biological adaptation and complex evolutionary footprints inferred from one integrative Tai-Kadai-related genomic resource

Pathogen‒host adaptative interactions and complex population demographical processes, including admixture, drift, and Darwen selection, have considerably shaped the Neolithic-to-Modern Western Eurasian population structure and genetic susceptibility to modern human diseases. However, the genetic footprints of evolutionary events in East Asia remain unknown due to the underrepresentation of genomic diversity and the design of large-scale population studies. We reported one aggregated database of genome-wide SNP variations from 796 Tai-Kadai (TK) genomes, including that of Bouyei first reported here, to explore the genetic history, population structure, and biological adaptative features of TK people from southern China and Southeast Asia. We found geography-related population substructure among TK people using the state-of-the-art population genetic structure reconstruction techniques based on the allele frequency spectrum and haplotype-resolved phased fragments. We found that the northern TK people from Guizhou harbored one TK-dominant ancestry maximized in the Bouyei people, and the southern TK people from Thailand were more influenced by Southeast Asians and indigenous people. We reconstructed fitted admixture models and demographic graphs, which showed that TK people received gene flow from ancient southern rice farmer-related lineages related to the Hmong-Mien and Austroasiatic people and from northern millet farmers associated with the Sino-Tibetan people. Biological adaptation focused on our identified unique TK lineages related to Bouyei, which showed many adaptive signatures conferring Malaria resistance and low-rate lipid metabolism. Further gene enrichment, the allele frequency distribution of derived alleles, and their correlation with the incidence of Malaria further confirmed that CR1 played an essential role in the resistance of Malaria in the ancient "Baiyue" tribes.

Peculiarities of polyvascular disease and the diagnostic significance of the ankle-brachial index in patients with coronary artery disease: results from the real-world registry KAMMA (Clinical registry on patient population with polyvascular disease in the Russian Federation and Eurasian countries)

Aim. To investigate the prevalence and characteristics of polyvascular disease in the Eurasian region's population with one or more previously established locations of atherosclerotic arterial damage, and to evaluate the diagnostic importance of the ankle-brachial index (ABI) as a marker for polyvascular disease (PVD).Material and methods. A total of 1837 patients were included in the main branch of the KAMMA registry (patients with PVD), among which 91,6% had coronary artery disease (CAD) (n=1683). For further analysis, the group of patients with CAD was combined with 1222 patients included in the second branch of the registry — KAMMA-cardio, forming a patient population (n=2905), in which all patients had verified CAD. The mean age of patients was 66,0 [59,0; 72,0] years, with 60,3% being male. Peripheral arteries was assessed using ultrasound examination.Results. PVD was present in 95,6% of patients with coronary atherosclerosis: dual-region involvement was observed in 51,3% of patients, three-region involvement in 37,1%, four-region involvement in 3,4%, and five-region involvement in 2,0%. Stenoses of the common carotid artery were observed in 71% of patients, internal carotid artery — in 68%, lower limb artery — in 52%, and renal and mesenteric artery — in 8,3%. There were following diagnostic effectiveness of the ABI for detecting patients with lower limb artery stenosis was: sensitivity — 58,0%, specificity — 83,6%. The quality of antithrombotic and lipid-lowering therapy was insufficient.Conclusion. In the overwhelming majority (95,6%) of patients with CAD in the KAMMA registry, PVD was revealed, with nearly half of the patients having involvement in three or more arterial zones. In the patient population with CAD, there should be an active effort to identify patients with PVD, using at least the ABI determination and active modern antithrombotic and lipid-lowering therapy according to current clinical guidelines.

Ancient Mitogenomes Reveal the Maternal Genetic History of East Asian Dogs.

Recent studies have suggested that dogs were domesticated during the Last Glacial Maximum (LGM) in Siberia, which contrasts with previous proposed domestication centers (e.g. Europe, the Middle East, and East Asia). Ancient DNA provides a powerful resource for the study of mammalian evolution and has been widely used to understand the genetic history of domestic animals. To understand the maternal genetic history of East Asian dogs, we have made a complete mitogenome dataset of 120 East Asian canids from 38 archaeological sites, including 102 newly sequenced from 12.9 to 1 ka BP (1,000 years before present). The majority (112/119, 94.12%) belonged to haplogroup A, and half of these (55/112, 49.11%) belonged to sub-haplogroup A1b. Most existing mitochondrial haplogroups were present in ancient East Asian dogs. However, mitochondrial lineages in ancient northern dogs (northeastern Eurasia and northern East Asia) were deeper and older than those in southern East Asian dogs. Results suggests that East Asian dogs originated from northeastern Eurasian populations after the LGM, dispersing in two possible directions after domestication. Western Eurasian (Europe and the Middle East) dog maternal ancestries genetically influenced East Asian dogs from approximately 4 ka BP, dramatically increasing after 3 ka BP, and afterwards largely replaced most primary maternal lineages in northern East Asia. Additionally, at least three major mitogenome sub-haplogroups of haplogroup A (A1a, A1b, and A3) reveal at least two major dispersal waves onto the Qinghai-Tibet Plateau in ancient times, indicating eastern (A1b and A3) and western (A1a) Eurasian origins.

Eurasian Ideologies at Odds. Assessing the Opposing Nature of Eurasianism and Turanism

Eurasianism and Turanism epitomize two antithetical ideologies driven by the ambition of politically and culturally integrating Eurasia. While Eurasianism has never developed an exclusivist nationalist sentiment based on ethnolinguistic foundations, Turanism falls into the category of pan-nationalist ideologies that tend to exclude the appearance and affirmation of other nations within their spatial scope. The mutually incompatibility of the two ideologies rests on the fact that Eurasianism is based on the principle of inclusiveness of the different Eurasian populations, while Turanism on the principle of Ural-Altaic exclusivism and the rejection of a symbiosis with the Slavic element. This article aims to compare the classic variant of Russian Eurasianism with Turanism from an ideological and cultural perspective, through the evaluation of the respective intellectual fathers’ works. While Eurasianism builds its political-ideological project on Russian-Eurasian history, the imperial idea, the primacy of geography and the rejection of the West as a philosophical model, Turanism grounds its raison d’etre on ethnocentric and pan-nationalist postulates designed for the political and cultural union of the Turanian peoples and the exclusion of others. In this frame, the two ideologies embody geographically overlapping mutually exclusive paradigms and idiosyncratic Weltanschauungs.

Thor's hammer: How warfare enables and disables nation formation

AbstractScholars have neglected at a theoretical level the structuring role of warfare in the rise of nations and states. I argue that war‐making has been a constitutive force in the emergence and persistence of many national identities in four ways. First, wars can act as ‘turning points’ for good or ill to become national mythomoteurs. Second, they can create enduring popular we–they stereotypes against significant others. Third, they can generate a gemeinschaft of national sacrifice that anchors the nation after a return to peace. Finally, the outcomes of wars can legitimate ruling establishments or mobilise peoples against them. However, warfare can also disable nation formation. I shall focus on the impact of imperial wars on Eurasian borderland populations. While generating nationalism in these regions, such wars create shatter zones, marked by ethnic diversity and conflict that frustrate the formation of stable national communities.

Population genomics of post-glacial western Eurasia

Western Eurasia witnessed several large-scale human migrations during the Holocene1–5. Here, to investigate the cross-continental effects of these migrations, we shotgun-sequenced 317 genomes—mainly from the Mesolithic and Neolithic periods—from across northern and western Eurasia. These were imputed alongside published data to obtain diploid genotypes from more than 1,600 ancient humans. Our analyses revealed a ‘great divide’ genomic boundary extending from the Black Sea to the Baltic. Mesolithic hunter-gatherers were highly genetically differentiated east and west of this zone, and the effect of the neolithization was equally disparate. Large-scale ancestry shifts occurred in the west as farming was introduced, including near-total replacement of hunter-gatherers in many areas, whereas no substantial ancestry shifts happened east of the zone during the same period. Similarly, relatedness decreased in the west from the Neolithic transition onwards, whereas, east of the Urals, relatedness remained high until around 4,000 bp, consistent with the persistence of localized groups of hunter-gatherers. The boundary dissolved when Yamnaya-related ancestry spread across western Eurasia around 5,000 bp, resulting in a second major turnover that reached most parts of Europe within a 1,000-year span. The genetic origin and fate of the Yamnaya have remained elusive, but we show that hunter-gatherers from the Middle Don region contributed ancestry to them. Yamnaya groups later admixed with individuals associated with the Globular Amphora culture before expanding into Europe. Similar turnovers occurred in western Siberia, where we report new genomic data from a ‘Neolithic steppe’ cline spanning the Siberian forest steppe to Lake Baikal. These prehistoric migrations had profound and lasting effects on the genetic diversity of Eurasian populations.

The association between haemosporidian infection and non-breeding moult location in great reed warblers revisited by combining feather stable isotope profiles and geolocator data

Stable isotope analysis provides valuable insights into the ecology of long-distance migratory birds during periods spent away from a specific study site. In a previous study, Swedish great reed warblers (Acrocephalus arundinaceus) infected with haemosporidian parasites differed in feather isotope ratios compared to non-infected birds, suggesting that infected and non-infected birds spent the non-breeding season in different locations or habitats. Here, we use a novel dataset comprising geolocator data, isotopes, and haemosporidian infection status of 92 individuals from four Eurasian populations to investigate whether parasite transmission varies with geography or habitats. We found that the probability of harbouring Plasmodium and Leucocytozoon parasites was higher in birds moulting in the eastern region of the non-breeding grounds. However, no geographic pattern occurred for Haemoproteus infections or overall infection status. In contrast to the previous study, we did not find any relationship between feather isotope ratios and overall haemosporidian infection for the entire current dataset. Plasmodium-infected birds had lower feather δ15N values indicating that they occupied more mesic habitats. Leucocytozoon-infected birds had higher feather δ34S values suggesting more coastal sites or wetlands with anoxic sulphate reduction. As the composition and prevalence of haemosporidian parasites differed between the old and the current dataset, we suggest that the differences might be a consequence of temporal dynamics of haemosporidian parasites. Our results emphasize the importance of replicating studies conducted on a single population over a restricted time period, as the patterns can become more complex for data from wider geographical areas and different time periods.

What happens in ice age, does not stay in ice age: Phylogeography of Bombus terrestris revealed a low genetic diversity amongst the Eurasian populations

The objective of this research was to assess the genetic diversity and phylogeography of Bombus terrestris and examine the historical events that shaped its contemporary genetic structures using the COI mitochondrial marker. Specimens of the species were collected from its distribution range alongside the Alborz Mountain range, and GenBank sequences from the Eurasian distribution range were incorporated into the dataset. The COI sequences were employed in Bayesian and Maximum Likelihood analyses to generate phylogenetic trees for the species populations and to investigate the evolutionary history of the species. Additionally, species occurrence points and climate data were utilized in Species Distribution Modeling (SDM) analyses to reconstruct the species range under past, present, and future climate conditions. The ML and BI trees yielded similar topologies, indicating extremely low genetic diversity and a homogeneous structure in the species population distribution range in Eurasia. Demographic analyses suggested that the species may have experienced a bottleneck during the last glacial maximum in Eurasia, followed by a recent expansion. The SDM analyses revealed significant fluctuations in the species range in the past and expansion under present conditions. Given the high dispersal ability of the species, the population expansion rate has surpassed the rate of developing new genetic diversity, and the estimated polymorphic sites for the species are likely relatively recent. This low level of genetic variation can also be attributed to the absence of geographical barriers and the excellent flying ability of the queen bee, leading to sustained gene flow throughout the entire continent. Despite the general correlation between larger populations and higher genetic diversity, bumblebees can expand their population size without increasing genetic diversity when residing in resourceful habitats.

The Helicobacter pylori Genome Project: insights into H. pylori population structure from analysis of a worldwide collection of complete genomes

Helicobacter pylori, a dominant member of the gastric microbiota, shares co-evolutionary history with humans. This has led to the development of genetically distinct H. pylori subpopulations associated with the geographic origin of the host and with differential gastric disease risk. Here, we provide insights into H. pylori population structure as a part of the Helicobacter pylori Genome Project (HpGP), a multi-disciplinary initiative aimed at elucidating H. pylori pathogenesis and identifying new therapeutic targets. We collected 1011 well-characterized clinical strains from 50 countries and generated high-quality genome sequences. We analysed core genome diversity and population structure of the HpGP dataset and 255 worldwide reference genomes to outline the ancestral contribution to Eurasian, African, and American populations. We found evidence of substantial contribution of population hpNorthAsia and subpopulation hspUral in Northern European H. pylori. The genomes of H. pylori isolated from northern and southern Indigenous Americans differed in that bacteria isolated in northern Indigenous communities were more similar to North Asian H. pylori while the southern had higher relatedness to hpEastAsia. Notably, we also found a highly clonal yet geographically dispersed North American subpopulation, which is negative for the cag pathogenicity island, and present in 7% of sequenced US genomes. We expect the HpGP dataset and the corresponding strains to become a major asset for H. pylori genomics.