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Our knowledge of human evolutionary history has been greatly advanced by paleogenomics. Since the 2020s, the study of ancient DNA has increasingly focused on reconstructing the recent past. However, the accuracy of paleogenomic methods in resolving questions of historical and archaeological importance amidst the increased demographic complexity and decreased genetic differentiation remains an open question. We evaluated the performance and behavior of two commonly used methods, qpAdm and the f3-statistic, on admixture inference under a diversity of demographic models and data conditions. We performed two complementary simulation approaches-firstly exploring a wide demographic parameter space under four simple demographic models of varying complexities and configurations using branch-length data from two chromosomes-and secondly, we analyzed a model of Eurasian history composed of 59 populations using whole-genome data modified with ancient DNA conditions such as SNP ascertainment, data missingness, and pseudohaploidization. We observe that population differentiation is the primary factor driving qpAdm performance. Notably, while complex gene flow histories influence which models are classified as plausible, they do not reduce overall performance. Under conditions reflective of the historical period, qpAdm most frequently identifies the true model as plausible among a small candidate set of closely related populations. To increase the utility for resolving fine-scaled hypotheses, we provide a heuristic for further distinguishing between candidate models that incorporates qpAdm model P-values and f3-statistics. Finally, we demonstrate a significant performance increase for qpAdm using whole-genome branch-length f2-statistics, highlighting the potential for improved demographic inference that could be achieved with future advancements in f-statistic estimations., Competing Interests: Conflicts of interest: The authors declare no conflicts of interest., (© The Author(s) 2024. Published by Oxford University Press on behalf of The Genetics Society of America.)

Admixture refers to the mixing of genetic ancestry from different populations. Admixture is important for genomic medicine because it can affect how an individual responds to certain medications, how they metabolize drugs, and susceptibility to certain diseases. For example, some genetic variants associated with drug metabolism and response may be more common in certain populations, and individuals with admixed ancestry may have a different frequency of these variants than individuals from the ancestral populations. Understanding the patterns of admixture in a population can also help researchers identify new genetic variants associated with diseases or traits and develop more personalized and targeted treatments. In this study, we compared and classified the known and self-reported genetic backgrounds from 1000 Genomes Project and admixed samples from GTEx projects using supervised, unsupervised and statistical classification methodologies. We developed a novel tool called Admix-AI that uses a one-dimensional convolutional neural network to understand and classify admixed genetic backgrounds using 213 DNA-marker based genetic background labels. Admix-AI can be used to discover admixed proportions in samples and ultimately aid personalized genomic medicine by identifying specific biomarker systems. We compared Admix-AI to the existing admixture categorization software and found our tool to be computationally faster with 2× speedup and streamlined usage. Admix-AI is available as open-source code under GPL version 3.0 license at https://github.com/rpauly/Admix-AI., (© 2024 The Authors. Clinical Genetics published by John Wiley & Sons Ltd.)

Abstract Background Thailand is a country with large diversity in rice varieties due to its rich and diverse ecology. In this paper, 300 rice accessions from all across Thailand were sequenced to identify SNP variants allowing for the population structure to be explored. Results The result of inferred population structure from admixture and clustering analysis illustrated strong evidence of substructure in each geographical region. The results of phylogenetic tree, PCA analysis, and machine learning on population identifying SNPs also supported the inferred population structure. Conclusion The population structure inferred in this study contains five subpopulations that tend to group individuals based on location. So, each subpopulation has unique genetic patterns, agronomic traits, as well as different environmental conditions. This study can serve as a reference point of the nation-wide population structure for supporting breeders and researchers who are interested in Thai rice.

Abstract Background Homo sapiens have experienced admixture many times in the last few thousand years. To examine how admixture affects local adaptation, we investigated genomes of modern Polynesians, who are shaped through admixture between Austronesian-speaking people from Southeast Asia (Asian-related ancestors) and indigenous people in Near Oceania (Papuan-related ancestors). Methods In this study local ancestry was estimated across the genome in Polynesians (23 Tongan subjects) to find the candidate regions of admixture-enabled selection contributed by Papuan-related ancestors. Results The mean proportion of Papuan-related ancestry across the Polynesian genome was estimated as 24.6% (SD = 8.63%), and two genomic regions, the extended major histocompatibility complex (xMHC) region on chromosome 6 and the ATP-binding cassette transporter sub-family C member 11 (ABCC11) gene on chromosome 16, showed proportions of Papuan-related ancestry more than 5 SD greater than the mean (> 67.8%). The coalescent simulation under the assumption of selective neutrality suggested that such signals of Papuan-related ancestry enrichment were caused by positive selection after admixture (false discovery rate = 0.045). The ABCC11 harbors a nonsynonymous SNP, rs17822931, which affects apocrine secretory cell function. The approximate Bayesian computation indicated that, in Polynesian ancestors, a strong positive selection (s = 0.0217) acted on the ancestral allele of rs17822931 derived from Papuan-related ancestors. Conclusions Our results suggest that admixture with Papuan-related ancestors contributed to the rapid local adaptation of Polynesian ancestors. Considering frequent admixture events in human evolution history, the acceleration of local adaptation through admixture should be a common event in humans.

Abstract Introgressive hybridization can pose a serious threat to endangered species which have an overlapping distribution such as in the case of two polecat species, Mustela eversmanii and M. putorius, in Europe. The population size of steppe polecat is known to continuously shrink, whereas its sister species, the European polecat, is still somehow widespread. In this study, we perform an analysis using microsatellite (SSR) and genomic (SNP) data sets to identify natural hybrids between polecats. Four populations were genotyped for eight polymorphic SSR loci, and thousands of unlinked SNPs were generated using a reduced‐representation sequencing approach, RADseq, to characterize the genetic make‐up of allopatric populations and to identify hybrids in the sympatric area. We applied standard population genetic analyses to characterize the populations based on their SSR allelic frequency. Only a single sample out of 48 sympatric samples showed exact intermediacy that we identified as an F1 hybrid. Additionally, one specimen was indicated in the genomic data sets as backcrossed. Other backcrosses, indicated by SSRs, were not validated by SNPs, which highlights the higher efficacy of the genomic method to identify backcrossed individuals. The low frequency of hybridization suggests that the difference in habitat preference of the two species may act as a barrier to admixture. Therefore, it is apparently unlikely that polecat populations are threatened by significant introgression. The two species showed a clear genetic differentiation using both techniques. We found higher genetic diversity values in the sympatric steppe polecat population than in the other studies on polecat populations. Although M. putorius is a hunted species in most countries, genetic diversity values indicate worse conditions in Europe than in the protected sibling species M. eversmanii. Suspending hunting and providing protected status of the former seems to be reasonable and timely.

This paper investigates the compressive and flexural properties and corrosion permeability resistance of concrete, using bauxite tailing as supplementary mineral admixtures. The concrete mixes, curing and testing for mechanical properties were conducted in accordance with BS EN 12390, 2019. Chloride permeability test was conducted in accordance with ASTMC 1202, 1997. The results depicted that at the optimum composition of 20% replacement, the compressive strength, flexural strength and static modulus of elasticity increased by 22%, 28% and 13% respectively over the control concrete specimen. These results showed that, generally, there was an increase in the strength properties and subsequently the modulus of elasticity when cement was replaced with bauxite tailing at the latter age. Again the presence of silicate and aluminum in the bauxite tailing might have consumed Ca(OH)2 which was liberated from cement hydration, enriching the microstructure of the concrete (AS2 +3CH+6H=C2ASH8 +C-S-H) with C-S-H gel and crystalline calcium alumino-silicate (C2ASH8) at the latter age than at the earlier age. The mixes with bauxite tailing replacement had low permeability and very low chloride penetration as compared to the control concrete specimen. This study recommends that bauxite tailing should be used as a mineral admixture to concrete not exceeding 20% replacement and in a chloride environment.

Systemic lupus erythematosus (SLE) susceptibility has a strong genetic component. Genome-wide association studies (GWAS) across trans-ancestral populations show both common and distinct genetic variants of susceptibility across European and Asian ancestries, while many other ethnic populations remain underexplored. We conducted the first SLE GWAS on Egyptians–an admixed North African/Middle Eastern population–using 537 patients and 883 controls. To identify novel susceptibility loci and replicate previously known loci, we performed imputation-based association analysis with 6,382,276 SNPs while accounting for individual admixture. We validated the association analysis using adaptive permutation tests (n = 109). We identified a novel genome-wide significant locus near IRS1/miR-5702 (Pcorrected = 1.98 × 10−8) and eight novel suggestive loci (Pcorrected < 1.0 × 10−5). We also replicated (Pperm < 0.01) 97 previously known loci with at least one associated nearby SNP, with ITGAM, DEF6-PPARD and IRF5 the top three replicated loci. SNPs correlated (r2 > 0.8) with lead SNPs from four suggestive loci (ARMC9, DIAPH3, IFLDT1, and ENTPD3) were associated with differential gene expression (3.5 × 10−95 < p < 1.0 × 10−2) across diverse tissues. These loci are involved in cellular proliferation and invasion—pathways prominent in lupus and nephritis. Our study highlights the utility of GWAS in an admixed Egyptian population for delineating new genetic associations and for understanding SLE pathogenesis.

Abstract Panax vietnamensis Ha et Grushv. is a precious medicinal species native to the tropical forests of Vietnam. Due to habitat loss and over-harvesting, this species is endangered in Vietnam. To conserve the species, we investigated genetic variability and population structure using nine microsatellites for 148 individuals from seven populations across the current distribution range of P. vietnamensis in Vietnam. We determined a moderate genetic diversity within populations (HO = 0.367, HE = 0.437) and relatively low population differentiation (the Weir and Cockerham index of 0.172 and the Hedrick index of 0.254) and showed significant differentiation (P < 0.05), which suggested fragmented habitats, over-utilization and over-harvesting of P. vietnamensis. Different clustering methods revealed that individuals were grouped into two major clusters, which were associated with gene flow across the geographical range of P. vietnamensis. This study also detected that ginseng populations can have undergone a recent bottleneck. We recommend measures in future P. vietnamensis conservation and breeding programs.

NorthEast India, with its unique geographic location in the midst of the Himalayas and Bay of Bengal, has served as a passage for the movement of modern humans across the Indian subcontinent and East/Southeast Asia. In this study we look into the population genetics of a unique population called the Khasi, speaking a language (also known as the Khasi language) belonging to the Austroasiatic language family and residing amidst the Tibeto-Burman speakers as an isolated population. The Khasi language belongs to one of the three major broad classifications or phyla of the Austroasiatic language and the speakers of the three sub-groups are separated from each other by large geographical distances. The Khasi speakers are separated from their nearest Austroasiatic language-speaking sub-groups: the “Mundari” sub-family from East and peninsular India and the “Mon-Khmers” in Mainland Southeast Asia. We found the Khasi population to be genetically distinct from other Austroasiatic speakers, i.e. Mundaris and Mon-Khmers, but relatively similar to the geographically proximal Tibeto Burmans. The possible reasons for this genetic-linguistic discordance lie in the admixture history of different migration events that originated from East Asia and proceeded possibly towards Southeast Asia. We found at least two distinct migration events from East Asia. While the ancestors of today’s Tibeto-Burman speakers were affected by both, the ancestors of Khasis were insulated from the second migration event. Correlating the linguistic similarity of Tibeto-Burman and Sino-Tibetan languages of today’s East Asians, we infer that the second wave of migration resulted in a linguistic transition while the Khasis could preserve their linguistic identity.

Crossbreeding is a process in which animals from different breeds are mated together. The animals produced will exhibit a combination of both additive and non-additive genetic improvement from parental breeds that increase heterozygosity and negate inbreeding depression. However, crossbreeding may also break up the unique and often beneficial gene combinations in parental breeds, possibly reducing performance potential as the benefits of heterosis depends on the type of crossbreeding systems used and heritability of the traits. This effect of crossbreeding, especially on the genome architecture, is still poorly understood with respect to 3-breed crossbreeding systems. Thus, this study examined variation in genomic ancestry estimations relative to pedigree-based estimations and correlated breed composition to key production and health traits. Two rotational crossbred populations, referenced as ProCROSS and Grazecross were assessed and totaled 607 crossbred cattle. ProCROSS is a product of rotational crossbreeding of Viking Red (VKR), Holstein (HOL), and Montbeliarde (MON). In contrast, Grazecross consists of Viking Red (VKR), Normande (NOR), and Jersey (JER). Both breeding programs were aimed at capitalizing on the positive effect of heterosis. The VKR is a marketing term for Swedish Red, Danish Red, and Finnish Ayrshire breed which complicated breed determination. Therefore, genomic breed composition estimates were compared using two different representations of VKR, one of which was based on parents used in the crossing system and a second based on genotypes from the ancestral breeds that comprise VKR. Variation of breed composition estimates were assessed between pedigree and genome-based predictions. Lastly, Genomic estimations were correlated with production and health traits by comparing extreme performance groups to identify the relationship between breed ancestry and performance. With the exception of the JER breed composition in Grazecross, all other estimates of the purebred contribution to the ProCROSS and Grazecross showed a significant difference in their genomic breed estimation when using the VKR ancestral versus the VKR parental reference populations for admixture analysis. These observations were expected given the different relationship of each VKR representation to the crossbred cattle. Further analysis showed that regardless of which VKR reference population was used, the degree of MON and HOL breed composition plays a significant role in milk and fat production in ProCROSS, while the degree of VKR and NOR ancestry were related to improved health performance in Grazecross. In all, identifying the most appropriate and informative animals to use as reference animals in admixture analysis is an important factor when interpreting results of relationship and population structure, but some degree of uncertainty exists when assessing the relationship of breed composition to phenotypic performance.

A new era presently dawns for medical genetics featuring individualised whole genome sequencing and promising personalised medical genetics. Accordingly, we direct readers attention to the continuing value of allele frequency data from Genome-Wide Association Surveys (GWAS) and single gene surveys in well-defined ethnic populations as a guide for best practice in diagnosis, therapy, and prescription. Supporting evidence is drawn from our experiences working with Austronesian volunteer subjects across the Western Pacific. In general, these studies show that their gene pool has been shaped by natural selection and become highly diverged from those of Europeans and Asians. These uniquely evolved patterns of genetic variation underlie contrasting schedules of disease incidence and drug response. Thus, recognition of historical bonds of kinship among Austronesian population groups across the Asia Pacific has distinct public health advantages from a One Health perspective. Other than diseases that are common among them like gout and diabetes, Austronesian populations face a wide range of climate-dependent infectious diseases including vector-borne pathogens as they are now scattered across the Pacific and Indian Oceans. However, we caution that the value of genetic survey data in Austronesians (and other groups too) is critically dependent on the accuracy of attached descriptive information in associated metadata, including ethnicity and admixture.

Microsatellites have been a workhorse of evolutionary genetic studies for decades and are still commonly in use for estimating signatures of genetic diversity at the population and species level across a multitude of taxa. Yet, the very high mutation rate of these loci is a double-edged sword, conferring great sensitivity at shallow levels of analysis (e.g. paternity analysis) but yielding considerable uncertainty for deeper evolutionary comparisons. For the present study, we used reduced representation genome-wide data (restriction site-associated DNA sequencing (RADseq)) to test for patterns of interspecific hybridization previously characterized using microsatellite data in a contact zone between two closely related mouse lemur species in Madagascar (Microcebus murinus and Microcebus griseorufus). We revisit this system by examining populations in, near, and far from the contact zone, including many of the same individuals that had previously been identified as hybrids with microsatellite data. Surprisingly, we find no evidence for admixed nuclear ancestry. Instead, re-analyses of microsatellite data and simulations suggest that previously inferred hybrids were false positives and that the program NewHybrids can be particularly sensitive to erroneously inferring hybrid ancestry. Combined with results from coalescent-based analyses and evidence for local syntopic co-occurrence, we conclude that the two mouse lemur species are in fact completely reproductively isolated, thus providing a new understanding of the evolutionary rate whereby reproductive isolation can be achieved in a primate. [ABSTRACT FROM AUTHOR]

Population genetic analyses of local ancestry tracts routinely assume that the ancestral admixture process is identical for both parents of an individual, an assumption that may be invalid when considering recent admixture. Here, we present Parental Admixture Proportion Inference (PAPI), a Bayesian tool for inferring the admixture proportions and admixture times for each parent of a single admixed individual. PAPI analyzes unphased local ancestry tracts and has two components: a binomial model that leverages genome-wide ancestry fractions to infer parental admixture proportions and a hidden Markov model (HMM) that infers admixture times from tract lengths. Crucially, the HMM accounts for unobserved within-ancestry recombination by approximating the pedigree crossover dynamics, enabling inference of parental admixture times. In simulations, we find that PAPI's admixture proportion estimates deviate from the truth by 0.047 on average, outperforming ANCESTOR and PedMix by 46.0% and 57.6%, respectively. Moreover, PAPI's admixture time estimates were strongly correlated with the truth (R = 0.76) but have an average downward bias of 1.01 generations that is partly attributable to inaccuracies in local ancestry inference. As an illustration of its utility, we ran PAPI on African American genotypes from the PAGE study (N = 5,786) and found strong evidence of assortative mating by ancestry proportion: couples' ancestry proportions are highly correlated (R = 0.87) and are closer to each other than expected under random mating (p < 10−6). We anticipate that PAPI will be useful in studying the population dynamics of admixture and will also be of interest to individuals seeking to learn about their personal genealogies. [ABSTRACT FROM AUTHOR]

Iron tailing solid waste not only has a high annual output but also has a low comprehensive utilization rate. Low utilization rate of iron tailings seriously restricts the development of comprehensive utilization of solid waste. In order to prepare an iron tailings-based ternary solid waste admixture and to verify its application to concrete, first, the effect of solid waste synergy on the strength of an iron tailings-steel slag-desulfurization ash admixture (ISD) system was investigated. Second, the effect of chemical activator dosing on the strength of an ISD system was studied and the mechanism of chemical activator action on the ISD system was investigated by thermogravimetric analysis (TG-DTA) Then, the effect of this admixture on the strength of concrete was studied. Finally, the mechanism of the effect of this admixture on the strength of concrete was clarified by mercury intrusion porosimetry (MIP) and backscattering electron tests (BSE). The results showed that the 7 d and 28 d compressive strengths of the ISD admixture were significantly higher than those of iron tailings single admixture. The 7 d and 28 d compressive strengths of the ISD system reached 24.9 MPa and 36.1 Mpa, respectively, when the ratio of iron tailings:steel slag:desulfurization ash = 1:1:1. Na2SiO3 is suitable for the early strength agent of the ISD admixture, but the amount of admixture should not exceed 0.6% of the admixture. TG-DTA shows that Na2SiO3 is enhancing the early strength of the ISD system by promoting the consumption of Ca(OH)2 in the ISD system to produce C-S-H. However, in the late reaction of the ISD system, Na2SiO3 inhibits the late strength development of the ISD system by suppressing Ca(OH)2 production. Concrete with ISD dosing of 30% or less meets the C40 requirement. MIP and BSE show that ISD provides a filling effect to concrete, but also causes a reduction in the active reactants of concrete and the combined effect of microfilling and active effects affects the strength development of ISD concrete. This study provides a theoretical and scientific basis for the preparation of iron tailings-based ternary solid waste dopants, and, in addition, the study promotes the consumption of iron tailings solid waste and the development of multiple solid waste dopants. [ABSTRACT FROM AUTHOR]

Creole sheep represent a strategic genetic resource for populations living in marginal areas under financial restrictions on the American continent. Six Colombian sheep breeds (two wool (BCL-Boyacá and NCL-Nariño, 12 and 14 samples) and four hair (OPCE-Ethiopian, 54 samples; OPCS-Sudan, 74 samples; OPCP-Pelibeuy, 59 samples; OPCW-Wayúu, 24 samples) were genotyped using the Illumina Ovine SNP50 BeadChip. Data was also included from international 44 breeds from International Sheep Genomics Consortium (ISGC) and from data published in previous a previous work on the Caribbean and African breeds. Although geographically separated, wool (NCL, BCL) and hair types (OPCE, OPCS, OPCW) presented little genetic differentiation (FST 0.05) at a global level but several groups of animals separated suggesting local clustering due to geographical isolation. The OPCP underwent a recent crossing with Mexican Pelibuey, explaining its differentiation. Findings in this work such as the proximity to West African Djallonké (WAD) and Barbados Black Belly (BBB), suggest different introductions of African type animals from the Caribbean region on a pre-existing genetic basis formed by animals deriving from the first importations coming from Europe in colonial times. As expected, Colombian wool breeds showed, in particular in Admixture software results, a greater genomic component in common with European breeds and in particular with Iberian ones (Churra). This study provides a basis for future research into the genetic diversity within and between the Colombian sheep breeds analysed, and scientific data for policy decisions on Farm Animal Genetic Resources (FAnGR). [ABSTRACT FROM AUTHOR]

We have fabricated two different concrete based on polypropylene fibers with three different percentage admixture and water repellent dosages. The mortar mixtures were proportioned with cement to sand ratio of 1:3 and 1:4. The important FTIR peaks indicates that the presence of polypropylene fibers, and water repellent silicon in concrete mixture. The XRD spectra confirmed that the angle 2θ value with corresponding planes are because of mainly tetrahedrally arranged silicate and octahedrally arrangement of aluminate groups in mixed concrete. The reinforced concretes were cast for the same flow level but different percentages of polypropylene fibers (0, 5, 10 & 15%) dosage. The mechanical study proves that the compressive strength and tensile strength of the concretes increases with increase in polypropylene based concrete mixtures up to 10 wt %. However, it is also noted that the admixture significantly enhances the mechanical strength and decreases the early shrinkage of the concrete. [ABSTRACT FROM AUTHOR]

The mortar mixtures were prepared in various proportioned with cement to sand ratio of 1:3 and 1:4. The reinforced concretes were cast for the same flow level but different percentages of clay (0, 5, 10 & 15%) dosage. The prepared motor concrete subjected for structural study and mechanical property analysis. In FTIR spectra shows predominant peaks are observed the presence of admixture and clay in the concrete motor. The XRD spectra indicates the formation tetrahedrally arrangement of silicate and octahedrally arrangement of aluminate groups in clay mixed concrete. The surface morphology significantly improved upon adding of different admixture as examined in SEM image. The mechanical study revealed that the compressive strength increases with increase in clay percentages up to C-2 (10 wt %) due to the strong adhesion because of mixture of water reduce and water repellent which makes better compact and reduce porosity. The addition of slump flow improved due to presence of polycarboxylate ether and the evident workability loss started after the resting time of 25 min. [ABSTRACT FROM AUTHOR]

In this study, the effect of main and side chain lengths of polycarboxylate ether-based high-range water-reducing admixtures (WRAs) on the fresh properties, compressive strength and water absorption of cementitious systems containing 0, 15, 30 and 45 wt% fly ash was investigated. For this purpose, three WRAs with the same molecular weight but different chain lengths were produced. According to the test results, the flowability of the paste and mortars was negatively affected when the length of the main and side chains of the admixture was longer or shorter than a certain value. This adverse effect is thought to arise from weakening of the adsorption of the admixture with an increase in its chain lengths. However, when the main and side chain lengths of the admixture were shorter or longer than a certain value, the time-dependent flow properties of the mortar mixtures improved. The main and side chain lengths of the WRAs did not have a significant effect on the compressive strength and water absorption capacity of the mortar mixtures. However, irrespective of the admixture characteristics, with an increase in fly ash substitution, the flow and time-dependent flow properties of the mixtures were negatively affected but their water absorption decreased. [ABSTRACT FROM AUTHOR]

Foamed concrete is mostly used for backfilling of long-distance tunnels and compressive strength is an important technical index to control the quality of foamed concrete. The influence factors on compressive strength of low-density foamed concrete were obtained by the single factor test method based on the targeted dry density and compressive strength. The results show that the HT composed of pollution-free animal protein oil and vegetable oil is an efficient foaming agent and can produce stable foams. The cementation ability of cement can be fully expressed when a water to cement ratio of 0.45~0.5 is employed, making foamed concrete have a compressive strength higher than 2 MPa. The foam content is inversely proportional to the compressive strength and dry density of foamed concrete, and the volume ratio of slurry to foam should be 2:1~3:1. The content of fly ash is also inversely proportional to the compressive strength but positively proportional to the dry density. When the content of admixture is 40~55%, the compressive strength of foamed concrete with low density is not less than 2 MPa. The mixing proportion can be changed in the reasonable range to meet the requirements of different projects. [ABSTRACT FROM AUTHOR]

Human evolutionary theory has a history rife with racial biases in what might be considered its distant past that can appear glaringly obvious from our current vantage point. Despite the recognition that as a social activity science is always vulnerable to such biases (and science that attempts to uncover human origin stories all the more so), commitment to the scientific method can lead us to believe that we have improved on, overcome, or otherwise escaped these tendencies in our contemporary practices, whether through scientific contrition, changing social context, or better training and composition of research teams or as a result of advances in technologies and methodologies. This article adapts the evolutionary biology concept of introgression, which refers to the hybridization and repeated bidirectional backcross exchange of information between species, as a metaphorical frame to examine science itself and to trace the ways in which historic race biases from earlier, disowned human evolution research have been retained and selected for beneath the surface of current genomic research today. It takes as its focus the sequencing of the Neanderthal genome, first announced in 2006 and refined since, and the explosion of scientific research comparing that sequence to present-day human DNA from individuals around the world to illustrate the ways in which current research questions and findings in comparative evolutionary genomics draw on and dredge up earlier biases, albeit adapted to and disguised within contemporary social relations and power differentials. [ABSTRACT FROM AUTHOR]

The admixture of domestic pig into French wild boar populations has been monitored since the 1980s thanks to the existence of a cytogenetic difference between the two sub‐species. The number of chromosomes is 2n = 36 in wild boar and 2n = 38 in pig, respectively. This difference makes it possible to assign the "hybrid" status to wild boar individuals controlled with 37 or 38 chromosomes. However, it does not make it possible to determine the timing of the hybridization(s), nor to guarantee the absence of domestic admixture in an animal with 2n = 36 chromosomes. In order to analyze hybridization in greater detail and to avoid the inherent limitations of the cytogenetic approach, 362 wild boars (WB) recently collected in different French geographical areas and in different environments (farms, free ranging in protected or unprotected areas, animals with 2n = 36, 37 or 38 chromosomes) were genotyped on a 70K SNP chip. Principal component analyses allowed the identification of 13 "outliers" (3.6%), for which the proportion of the genome of "domestic" origin was greater than 40% (Admixture analyses). These animals were probably recent hybrids, having Asian domestic pig ancestry for most of them. For the remaining 349 animals studied, the proportion of the genome of "wild" origin varied between 83% and 100% (median: 94%). This proportion varied significantly depending on how the wild boar populations were managed. Local ancestry analyses revealed adaptive introgression from domestic pig, suggesting a critical role of genetic admixture in improving the fitness and population growth of WB. Overall, our results show that the methods used to monitor the domestic genetic contributions to wild boar populations should evolve in order to limit the level of admixture between the two gene pools. [ABSTRACT FROM AUTHOR]

The Chukar Partridge (Alectoris chukar, Galliformes) is one of the most important game birds in its native range, spanning from the Balkans to eastern Asia, and the regions of Europe, North America and New Zealand where it was introduced. Previous studies found two main genetic lineages of the species forming an eastern and a western clade. Chukar Partridges are raised in game farms and released to supplement natural populations for shooting in the USA, Canada, Greece, and Turkey. To explore intraspecific genetic structure, phylogeography, and possible genetic admixture events of A. chukar in Turkey, we genotyped individuals from fourteen wild and five captive populations at two mitochondrial and ten microsatellite DNA loci in. Wild and farmed Chukar Partridge samples were analyzed together to investigate possible influences of intraspecific hybridizations. We found that the farmed chukars, which mainly (85%) cluster into the eastern clade, and wild ones were genetically distinct. The latter could be separated into six management units (MUs), with partridges from Gökçeada Island in the Aegean Sea forming the most divergent population. Intraspecific hybridization was detected between wild and captive populations. This phenomenon causes rampant introgression and homogenization. The phylogeographic analysis revealed admixture among wild populations; nevertheless, this did not impair pointing to Anatolia as likely having a "refugia-within-refugia" structure. We recommend that the genetic structure of Chukar Partridge and its MUs be taken into account when developing the policy of hunting, production, and release to preserve the genetic integrity of this species. [ABSTRACT FROM AUTHOR]

This article examines twentieth-century northern Swedish geographical isolate studies in Norrbotten Province involving Torne-Finns and northern Sámi,who have historically shared pronatalist Laestadian religious beliefs pathologized by mainstream eugenicists. Deemed a sign of religious fanaticism, Laestadianism wasassociated with the eugenic stigmatization of Torne-Finns and Sámi people and beliefs were conceptualized as an early sign of schizophrenia. Geneticists,as an outgrowth of early twentieth-century eugenics, structured schizophrenia as a genetic disease caused by first-cousin marriage. These consanguineous marriages thatwerereported as prevalent in Tornedalian and Sámi reindeer-herding communities practicing Laestadianism, legitimated race-based sterilization of psychitrized Torne-Finn and Sámi women. Similarly, the Swedish State Institute for Race Biology, established in 1922 by Herman Lundborg, advanced reorganizing race along family lines and populations,which supported gendered disability and Sámi genocide. Torne-Finn, aswell as Sámi, religious minority women, who were sterilized at first admission to psychiatric facilities,require redress for colonial violence. Current academic and directto-consumer admixture research on Finnish and Sámi peoples is recognized as upholding colonial logics of difference in Swedish multicultural policies. This, in turn, resultsin ongoing gendered genocide. It is concluded that in a radical break from eugenic theories, major psychoses associated with common infections lie in the neglected half of the human genome rather than according to classical genetic rules. [ABSTRACT FROM AUTHOR]

Context: To establish translocated populations of threatened plants with the genetic resources to adapt to changing environmental conditions, the source of propagation material is an important consideration. Aim: We investigated the fitness consequences of genetic rescue and admixture for the threatened annual daisy Schoenia filifolia subsp. subulifolia, and the common S. filifolia subsp. filifolia, to inform seed-sourcing strategies for translocations of the threatened subspecies. Methods: We evaluated genetic diversity of two populations of S. filifolia subsp. subulifolia and four populations of S. filifolia subsp. filifolia by using microsatellite markers. We grew seedlings from each study population and cross-pollinated inflorescences within and among populations of the same subspecies, and between subspecies. We evaluated the fitness consequences of each cross by using seed set, seed weight and seed viability. Key results: There was a lower genetic diversity in the small (<50 plants, N[sub ar] = 3.28, H[sub e] = 0.42) compared to the large (>10 000 plants, N[sub ar] = 4.42, H[sub e] = 0.51) population of S. filifolia subsp. subulifolia, although none of the measures was significantly different, and seed fitness was slightly, although not significantly, reduced in interpopulation crosses compared with the small population. Genetic diversity was similar between the threatened and widespread subspecies; however, the subspecies were genetically divergent (F[sub st] = 0.242-0.294) and cross-pollination between subspecies produced negligible amounts of seeds (<3% seed set). Conclusions: Although genetic rescue or admixture of S. filifolia subsp. subulifolia would not necessarily result in greatly increased levels of genetic diversity or seed fitness, we still consider it a potential option. Negligible seed set in crosses between subspecies indicates that deliberate hybridisation is not a possibility. Implications: Studies of fitness consequences of admixture or genetic rescue are rare yet critical to assessing the benefits of different translocation strategies. Translocations, the augmentation or establishment of new populations, are a valuable management tool for plants at a risk of extinction. The source of propagation material is an important consideration to ensure that these populations persist. Using a mix of source populations didn't necessarily increase genetic diversity or improve seed fitness for the threatened daisy Schoenia filifolia subsp. filifolia. Whilst planting more seedlings from the same source population is a suitable management strategy, mixing source populations should also be considered. [ABSTRACT FROM AUTHOR]

The population of Mexico has a considerable genetic substructure due to both its pre-Columbian diversity and due to genetic admixture from post-Columbian trans-oceanic migrations. The latter primarily originated in Europe and Africa, but also, to a lesser extent, in Asia. We analyze previously understudied genetic connections between Asia and Mexico to infer the timing and source of this genetic ancestry in Mexico. We identify the predominant origin within Southeast Asia—specifically western Indonesian and non-Negrito Filipino sources—and we date its arrival in Mexico to approximately 13 generations ago (1620 CE). This points to a genetic legacy from the seventeenth century Manila galleon trade between the colonial Spanish Philippines and the Pacific port of Acapulco. Indeed, within Mexico we observe the highest level of this trans-Pacific ancestry in Acapulco, located in the state of Guerrero. This colonial Spanish trade route from East Asia to Europe was centred on Mexico and appears in historical records, but its legacy has been largely ignored. Identities and stories were suppressed due to slavery, assimilation of the immigrants as ‘Indios’ and incomplete historical records. Here we characterize this understudied Mexican ancestry. [ABSTRACT FROM AUTHOR]

Over the past 50 years, geneticists have made great strides in understanding how our species' evolutionary history gave rise to current patterns of human genetic diversity classically summarized by Lewontin in his 1972 paper, ‘The Apportionment of Human Diversity’. One evolutionary process that requires special attention in both population genetics and statistical genetics is admixture: gene flow between two or more previously separated source populations to form a new admixed population. The admixture process introduces ancestry-based structure into patterns of genetic variation within and between populations, which in turn influences the inference of demographic histories, identification of genetic targets of selection and prediction of complex traits. In this review, we outline some challenges for admixture population genetics, including limitations of applying methods designed for populations without recent admixture to the study of admixed populations. We highlight recent studies and methodological advances that aim to overcome such challenges, leveraging genomic signatures of admixture that occurred in the past tens of generations to gain insights into human history, natural selection and complex trait architecture. [ABSTRACT FROM AUTHOR]

Hybridisation has traditionally been considered rare and unimportant in generating biodiversity in the marine environment, particularly in coral reefs ecosystems. Here we review the literature for evidence of hybridisation in coral reef organisms and find that hybridisation is prevalent in well-studied groups, namely fish and hermatypic corals. At least 183 fish and 81 scleractinian coral species are reported to hybridise, with the highest prevalence in angelfishes and psammocorid corals (hybridisation in 46–50% of species in each family). Mapping the geographic location of hybrids revealed that hybridisation was positively associated with proximity to biogeographic borders for fish but not corals, and not linked with areas of low species richness in either group. Molecular studies detected admixture, indicative of past hybridisation, in 30 of 53 cases for fish, and in 22 (possibly 39) out of 47 studies for corals. Patterns of introgression described in the fish studies supported a decrease in lineage diversity in nine cases and the formation of hybrid lineages in seven cases. In the other 14 cases, the two parent species remained genetically distinct despite evidence of introgression. For corals, the evidence of hybrid lineages was rare (5 species), rather there was more support indicating that hybridisation leads to a decrease (36 species), or no change (27 species), in lineage diversity. Collectively, these results show that hybridisation can influence the evolution of fishes and corals in multiple ways and suggests the prevalence of hybridisation is likely to be significantly underestimated for coral reef taxa. The application of new genomic tools will advance our knowledge of the prevalence and evolutionary importance of hybridisation in coral reef organisms. Furthermore, these tools will aid in identifying how natural and assisted hybridisation may help coral reef species adapt to increasing environmental changes. [ABSTRACT FROM AUTHOR]

Abstract In a conservation and sustainable management perspective, we identify the ecological, climatic, and demographic factors responsible for the genetic diversity patterns of the European silver fir (Abies alba Mill.) at its southwestern range margin (Pyrenees Mountains, France, Europe). We sampled 45 populations throughout the French Pyrenees and eight neighboring reference populations in the Massif Central, Alps, and Corsica. We genotyped 1,620 individuals at three chloroplast and ten nuclear microsatellite loci. We analyzed within‐ and among‐population genetic diversity using phylogeographic reconstructions, tests of isolation‐by‐distance, Bayesian population structure inference, modeling of demographic scenarios, and regression analyses of genetic variables with current and past environmental variables. Genetic diversity decreased from east to west suggesting isolation‐by‐distance from the Alps to the Pyrenees and from the Eastern to the Western Pyrenees. We identified two Pyrenean lineages that diverged from a third Alpine–Corsica–Massif Central lineage 0.8 to 1.1 M years ago and subsequently formed a secondary contact zone in the Central Pyrenees. Population sizes underwent contrasted changes, with a contraction in the west and an expansion in the east. Glacial climate affected the genetic composition of the populations, with the western genetic cluster only observed in locations corresponding to the coldest past climate and highest elevations. The eastern cluster was observed over a larger range of temperatures and elevations. All demographic events shaping the current spatial structure of genetic diversity took place during the Mid‐Pleistocene Transition, long before the onset of the Holocene. The Western Pyrenees lineage may require additional conservation efforts, whereas the eastern lineage is well protected in in situ gene conservation units. Due to past climate oscillations and the likely emergence of independent refugia, east–west oriented mountain ranges may be important reservoir of genetic diversity in a context of past and ongoing climate change in Europe.

Abstract Background Local breeds retained unique genetic variability important for adaptive potential especially in light of challenges related to climate change. Our first objective was to perform, for the first time, a genome-wide diversity characterization using Illumina GoatSNP50 BeadChip of autochthonous Drežnica goat breed from Slovenia, and five and one local breeds from neighboring Austria and Italy, respectively. For optimal conservation and breeding programs of endangered local breeds, it is important to detect past admixture events and strive for preservation of purebred representatives of each breed with low or without admixture. In the second objective, we hence investigated the effect of inclusion or exclusion of outliers from datasets on genetic diversity and population structure parameters. Results Distinct genetic origin of the Drežnica goat was demonstrated as having closest nodes to Austrian and Italian breeds. A phylogenetic study of these breeds with other goat breeds having SNP data available in the DRYAD repository positioned them in the alpine, European and global context. Swiss breeds clustered with cosmopolitan alpine breeds and were closer to French and Spanish breeds. On the other hand, the Drežnica goat, Austrian and Italian breeds were closer to Turkish breeds. Datasets where outliers were excluded affected estimates of genetic diversity parameters within the breed and increased the pairwise genetic distances between most of the breeds. Alpine breeds, including Drežnica, Austrian and Italian goats analyzed here, still exhibit relatively high levels of genetic variability, homogeneous genetic structure and strong geographical partitioning. Conclusions Genetic diversity analyses revealed that the Slovenian Drežnica goat has a distinct genetic identity and is closely related to the neighboring Austrian and Italian alpine breeds. These results expand our knowledge on phylogeny of goat breeds from easternmost part of the European Alps. The here employed outlier test and datasets optimization approaches provided an objective and statistically powerful tool for removal of admixed outliers. Importance of this test in selecting the representatives of each breed is warranted to obtain more objective diversity parameters and phylogenetic analysis. Such parameters are often the basis of breeding and management programs and are therefore important for preserving genetic variability and uniqueness of local rare breeds.

Abstract Due to their isolated and often fragmented nature, range margin populations are especially vulnerable to rapid environmental change. To maintain genetic diversity and adaptive potential, gene flow from disjunct populations might therefore be crucial to their survival. Translocations are often proposed as a mitigation strategy to increase genetic diversity in threatened populations. However, this also includes the risk of losing locally adapted alleles through genetic swamping. Human‐mediated translocations of southern lineage specimens into northern German populations of the endangered European fire‐bellied toad (Bombina bombina) provide an unexpected experimental set‐up to test the genetic consequences of an intraspecific introgression from central population individuals into populations at the species range margin. Here, we utilize complete mitochondrial genomes and transcriptome nuclear data to reveal the full genetic extent of this translocation and the consequences it may have for these populations. We uncover signs of introgression in four out of the five northern populations investigated, including a number of introgressed alleles ubiquitous in all recipient populations, suggesting a possible adaptive advantage. Introgressed alleles dominate at the MTCH2 locus, associated with obesity/fat tissue in humans, and the DSP locus, essential for the proper development of epidermal skin in amphibians. Furthermore, we found loci where local alleles were retained in the introgressed populations, suggesting their relevance for local adaptation. Finally, comparisons of genetic diversity between introgressed and nonintrogressed northern German populations revealed an increase in genetic diversity in all German individuals belonging to introgressed populations, supporting the idea of a beneficial transfer of genetic variation from Austria into North Germany.

Abstract Understanding the historical contributions of differing glacial refugia is key to evaluating the roles of microevolutionary forces, such as isolation, introgression, and selection in shaping genomic diversity in present‐day populations. In Europe, where both Mediterranean and extra‐Mediterranean (e.g., Carpathian) refugia of the bank vole (Clethrionomys glareolus) have been identified, mtDNA indicates that extra‐Mediterranean refugia were the main source of colonization across the species range, while Mediterranean peninsulas harbor isolated, endemic lineages. Here, we critically evaluate this hypothesis using previously generated genomic data (>6,000 SNPs) for over 800 voles, focusing on genomic contributions to bank voles in central Europe, a key geographic area in considering range‐wide colonization. The results provide clear evidence that both extra‐Mediterranean (Carpathian) and Mediterranean (Spanish, Calabrian, and Balkan) refugia contributed to the ancestry and genomic diversity of bank vole populations across Europe. Few strong barriers to dispersal and frequent admixture events in central Europe have led to a prominent mid‐latitude peak in genomic diversity. Although the genomic contribution of the centrally located Carpathian refugium predominates, populations in different parts of Europe have admixed origins from Mediterranean (28%–47%) and the Carpathian (53%–72%) sources. We suggest that the admixture from Mediterranean refugia may have provisioned adaptive southern alleles to more northern populations, facilitating the end‐glacial spread of the admixed populations and contributing to increased bank vole diversity in central Europe. This study adds critical details to the complex end‐glacial colonization history of this well‐studied organism and underscores the importance of genomic data in phylogeographic interpretation.

Abstract Background Nile tilapia, Oreochromis niloticus (Linnaeus, 1758) is among the economically most important freshwater fish species in East Africa, and a major source of protein for local consumption. Human induced translocations of non-native stocks for aquaculture and fisheries have been found as a potential threat to the genetic diversity and integrity of local populations. In the present study, we investigate the genetic structure of O. niloticus from 16 waterbodies across Ethiopia using 37 microsatellite loci with SSR-GBAS techniques. Results The samples are structured into three main clusters shaped either by biogeographic factors or stocking activities. High F ST values (Global F ST = 0.438) between populations indicate a high level of genetic differentiation and may suggest long term isolation even within the same drainage systems. Natural populations of the Omo-Turkana system and the lakes in the Southern Main Ethiopian Rift showed the highest genetic variability while low variability was found in stocked populations of lakes Hora, Hashenge and Hayq. Conclusions The results presented herein, may provide an essential basis for the management and conservation of the unique genetic resources in northern East Africa, and advance our understanding of biodiversity, phylogeny, evolution and development towards phylogenetically more accurate taxonomic classifications.

A new admixture is available, to reduce the sludge produced from the cleansing of production and transportation equipment in the fresh concrete industry. The result is agglomerations of hardening concrete, that might be utilised for aggregate. Utilisation depends on adequate properties. This paper reports from investigations on the physical and mechanical properties of the aggregate and discussions on the performance relative to natural and recycled aggregates and towards requirements for utilisation. The findings indicate substantial potential for utilisation, supporting the reduction of waste for deposit and development of the concrete industry towards a circular economy.

• Ladakhi cattle exhibit a distinct genetic admixture of Bos indicus and Bos taurus ancestry, with high genetic diversity and low inbreeding. • The HIF-1 signaling pathway plays a central role in Ladakhi cattle's adaptation to hypobaric hypoxia. • Genes for hypoxia response and energy metabolism show evolutionary adaptation. • Genes within PI3K, mTOR, NF-κB, ERK signaling, and ER stress pathways show significant interaction and crosstalk. • Careful breeding practices are essential in Ladakhi cattle to safeguard adaptive alleles and resilience. Ladakhi cattle, native to the high-altitude region of Ladakh in northern India (ranging from 3,000 to 5,000 m above sea level), have evolved unique genetic adaptations to thrive in harsh environmental conditions, such as hypoxia, extreme cold, and low humidity. This study explored the genome of Ladakhi cattle to investigate genetic structure, selection signatures, and adaptive mechanisms. Whole genome sequencing reads, generated on Illumina NovaSeq 6000 platform, were aligned to the Bos taurus reference genome with BWA-MEM. SNPs were identified and filtered using GATK and bcftools, and functionally annotated with SnpEff. For population genomic analysis, PCA and admixture modeling assessed genetic structure, while Neighbor-Joining trees, LD decay, nucleotide diversity (π), and F ST evaluated phylogenetic relationships and genetic variation. Selective sweeps were detected using RAiSD, and gene-set enrichment and protein–protein interaction analyses were conducted to explore functional pathways related to adaptation. The study revealed 3,759,279 unique SNPs and demonstrated that Ladakhi cattle form a distinct genetic cluster with an estimated admixture of 68 % Bos indicus and 32 % Bos taurus ancestry. Key findings include rapid linkage disequilibrium decay, low inbreeding level, and the identification of selection signatures and genes associated with hypoxia response, energy metabolism, and cold adaptation. Mean nucleotide diversity (π, 0.0037) and F ST values indicated moderate genetic differentiation from other breeds. The analysis highlighted selection signatures for genes like HIF1A, ENO4, ANGPT1, EPO, NOS3, MAPK3, HMOX1, BCL2, CAMK2D, MTOR, AKT2, PIK3CB, and MAP2K1 , among others, including various keratin and heat shock proteins. The interaction between genes associated with hypoxia signaling (HIF-1) and other enriched pathways such as PI3K, mTOR, NFκB, ERK, and ER stress, reveals a complex mechanism for managing hypoxic stress in Ladakhi cattle. These findings offer valuable insights for breeding programs aimed at enhancing livestock resilience in extreme environments and enhance understanding of mammalian adaptation to high-altitude conditions. [ABSTRACT FROM AUTHOR]

The origins and lifeways of the inhabitants of Rapa Nui (Easter Island), a remote island in the southeast Pacific Ocean, have been debated for generations. Archaeological evidence substantiates the widely accepted view that the island was first settled by people of Polynesian origin, as late as 1200 CE [1-4]. What remains controversial, however, is the nature of events in the island's population history prior to the first historic contact with Europeans in 1722 CE. Purported contact between Rapa Nui and South America is particularly contentious, and recent studies have reported genetic evidence for Native American admixture in present-day indigenous inhabitants of Rapa Nui [5-8]. Statistical modeling has suggested that this genetic contribution might have occurred prior to European contact [6]. Here we directly test the hypothesis that the Native American admixture of the current Rapa Nui population predates the arrival of Europeans with a paleogenomic analysis of five individual samples excavated from Ahu Nau Nau, Anakena, dating to pre- and post-European contact, respectively. Complete mitochondrial genomes and low-coverage autosomal genomes show that the analyzed individuals fall within the genetic diversity of present-day and ancient Polynesians, and we can reject the hypothesis that any of these individuals had substantial Native American ancestry. Our data thus suggest that the Native American ancestry in contemporary Easter Islanders was not present on the island prior to European contact and may thus be due to events in more recent history.

This article is a Commentary on Buck et al. (2023), 237: 2435–2449. [ABSTRACT FROM AUTHOR]

Retracing complex population processes that precede extreme bottlenecks may be impossible using data from living individuals. The wisent (Bison bonasus), Europe's largest terrestrial mammal, exemplifies such a population history, having gone extinct in the wild but subsequently restored by captive breeding efforts. Using low coverage genomic data from modern and historical individuals, we investigate population processes occurring before and after this extinction. Analysis of aligned genomes supports the division of wisent into two previously recognized subspecies, but almost half of the genomic alignment contradicts this population history as a result of incomplete lineage sorting and admixture. Admixture between subspecies populations occurred prior to extinction and subsequently during the captive breeding program. Admixture with the Bos cattle lineage is also widespread but results from ancient events rather than recent hybridization with domestics. Our study demonstrates the huge potential of historical genomes for both studying evolutionary histories and for guiding conservation strategies.

A recent study conducted the first genome-wide scan for selection in Inuit from Greenland using single nucleotide polymorphism chip data. Here, we report that selection in the region with the second most extreme signal of positive selection in Greenlandic Inuit favored a deeply divergent haplotype that is closely related to the sequence in the Denisovan genome, and was likely introgressed from an archaic population. The region contains two genes, WARS2 and TBX15, and has previously been associated with adipose tissue differentiation and body-fat distribution in humans. We show that the adaptively introgressed allele has been under selection in a much larger geographic region than just Greenland. Furthermore, it is associated with changes in expression of WARS2 and TBX15 in multiple tissues including the adrenal gland and subcutaneous adipose tissue, and with regional DNA methylation changes in TBX15.

Statistical models in medical and population genetics typically assume that individuals assort randomly in a population. While this simplifies model complexity, it contradicts an increasing body of evidence of nonrandom mating in human populations. Specifically, it has been shown that assortative mating is significantly affected by genomic ancestry. In this work, we examine the effects of ancestry-assortative mating on the linkage disequilibrium between local ancestry tracks of individuals in an admixed population. To accomplish this, we develop an extension to the Wright-Fisher model that allows for ancestry-based assortative mating. We show that ancestry-assortment perturbs the distribution of local ancestry linkage disequilibrium (LAD) and the variance of ancestry in a population as a function of the number of generations since admixture. This assortment effect can induce errors in demographic inference of admixed populations when methods assume random mating. We derive closed form formulae for LAD under an assortative-mating model with and without migration. We observe that LAD depends on the correlation of global ancestry of couples in each generation, the migration rate of each of the ancestral populations, the initial proportions of ancestral populations, and the number of generations since admixture. We also present the first direct evidence of ancestry-assortment in African Americans and examine LAD in simulated and real admixed population data of African Americans. We find that demographic inference under the assumption of random mating significantly underestimates the number of generations since admixture, and that accounting for assortative mating using the patterns of LAD results in estimates that more closely agrees with the historical narrative.

Southern China was the original center of multiple ancestral populations related to modern Hmong-Mien, Tai-Kadai, Austroasiatic, and Austronesian people. More recent genetic surveys have focused on the fine-scale genetic structure and admixture history of southern Chinese populations, but the genetic formation and diversification of Hmong-Mien speakers are far from clear due to the sparse genetic sampling. Here, we reported nearly 700,000 single-nucleotide polymorphisms (SNPs) data from 130 Guizhou Miao and Yao individuals. We used principal component analysis, ADMIXTURE, f-statistics, qpAdm, phylogenetic tree, fineSTRUCTURE, and ALDER to explore the fine-scale population genetic structure and admixture pattern of Hmong-Mien people. The sharing allele patterns showed that our studied populations had a strong genetic affinity with ancient and modern groups from southern and southeastern East Asia. We identified one unique ancestry component maximized in Yao people, which widely existed in other Hmong-Mien-speaking populations in southern China and Southeast Asia and ancient samples of Guangxi. Guizhou Hmong-Mien speakers harbored the dominant proportions of ancestry related to southern indigenous East Asians and minor proportions of northern ancestry related to Yellow River farmers, suggesting the possibility of genetic admixture between Hmong-Mien people and recent southward Sino-Tibetan-related populations. Furthermore, we found a genetic substructure among geographically different Miao and Yao people in Leishan and Songtao. The Yao and Miao people in Leishan harbored more southern East Asian ancestry, but Miao in Songtao received more northern East Asian genetic influence. We observed high mtDNA but low Y-chromosome diversity in studied Hmong-Mien groups, supporting the role of sex-specific residence in influencing human genetic variation. Our data provide valuable clues for further exploring population dynamics in southern China.

Southern China is the birthplace of rice-cultivating agriculture and different language families and has also witnessed various human migrations that facilitated cultural diffusions. The fine-scale demographic history in situ that forms present-day local populations, however, remains unclear. To comprehensively cover the genetic diversity in East and Southeast Asia, we generated genome-wide SNP data from 211 present-day Southern Chinese and co-analyzed them with ∼1,200 ancient and modern genomes. In Southern China, language classification is significantly associated with genetic variation but with a different extent of predictability, and there is strong evidence for recent shared genetic history particularly in Hmong–Mien and Austronesian speakers. A geography-related genetic sub-structure that represents the major genetic variation in Southern East Asians is established pre-Holocene and its extremes are represented by Neolithic Fujianese and First Farmers in Mainland Southeast Asia. This sub-structure is largely reduced by admixture in ancient Southern Chinese since > ∼2,000 BP, which forms a “Southern Chinese Cluster” with a high level of genetic homogeneity. Further admixture characterizes the demographic history of the majority of Hmong–Mien speakers and some Kra-Dai speakers in Southwest China happened ∼1,500–1,000 BP, coeval to the reigns of local chiefdoms. In Yellow River Basin, we identify a connection of local populations to genetic sub-structure in Southern China with geographical correspondence appearing > ∼9,000 BP, while the gene flow likely closely related to “Southern Chinese Cluster” since the Longshan period (∼5,000–4,000 BP) forms ancestry profile of Han Chinese Cline.

Abstract Background Plasmodium falciparum parasite populations in Ethiopia have been experiencing local selective pressures from drugs and immunity, leading to evolutionary adaptation. However, there was a paucity of data on genomic characterization and evolutionary adaptations of P. falciparum isolates from the central area of Ethiopia. Methods Whole-genome analysis of 25 P. falciparum isolates from central Ethiopia, specifically from West Arsi, were studied to determine their genetic diversity, population structures, and signatures of selection in known drug resistance alleles against global isolates from Cambodia, Thailand, DR Congo, and Malawi. Results A total of 18,517 high-quality single-nucleotide polymorphisms (SNPs) were identified in Ethiopian P. falciparum isolates. About 84% of the Ethiopian P. falciparum isolates had a FWS value > 0.95 showing a dominant single genotype infection in most isolates at the time of collection with little potential for out-crossing as expected in areas with low transmission intensity. Within-host diversity of Ethiopian infections was significantly different from East African (p 0.05). A significant population structure has been observed by PCA and population differentiation between Ethiopian parasites and East African (Fst ~ 10%) and Southeast Asian populations (Fst ~ 18%), suggesting limited gene flow and the independent evolution of the Ethiopian parasite population. Moreover, a total of 125 genes under balancing selection was found that include ama1, trap, eba175, and lsa3, previously identified as targets of human host immunity. Recent directional selection analysis using integrated standardized haplotype score (IHS) did not detect any selection signatures in the Pfcrt, Pfdhfr, Pfdhps, Pfmdr1, and PfK13 genes. However, known drug resistance-conferring mutations analysis showed that at least one SNP marker was fixed in these genes, but not in Pfdhps and PfK13. Conclusion Plasmodium falciparum populations in the central region of Ethiopia was structurally diverged from both Southeast Asian and other East African populations. Malaria infections in Ethiopia had low within-host diversity, and parasites carry fixed chloroquine resistance markers despite the withdrawal of this drug for the treatment of P. falciparum.

Abstract Hybridization and admixture can threaten the genetic integrity of populations and be of particular concern to endangered species. Hybridization between grey wolves and dogs has been documented in many wolf populations worldwide and is a prominent example of human‐mediated hybridization between a domesticated species and its wild relative. We analysed whole‐genome sequences from >200 wolves and >100 dogs to study admixture in Fennoscandian wolf populations. A principal component analysis of genetic variation and Admixture showed that wolves and dogs were well‐separated, without evidence for introgression. Analyses of local ancestry revealed that wolves had

Abstract Background The demographic history of South and Southeast Asia (S&SEA) is complex and contentious, with multiple waves of human migration. Some of the earliest footfalls were of the ancestors of modern Austroasiatic (AA) language speakers. Understanding the history of the AA language family, comprising of over 150 languages and their speakers distributed across broad geographical region in isolated small populations of various sizes, can help shed light on the peopling of S&SEA. Here we investigated the genetic relatedness of two AA groups, their relationship with other ethno-linguistically distinct populations, and the relationship of these groups with ancient genomes of individuals living in S&SEA at different time periods, to infer about the demographic history of this region. Results We analyzed 1451 extant genomes, 189 AAs from India and Malaysia, and 43 ancient genomes from S&SEA. Population structure analysis reveals neither language nor geography appropriately correlates with genetic diversity. The inconsistency between “language and genetics” or “geography and genetics” can largely be attributed to ancient admixture with East Asian populations. We estimated a pre-Neolithic origin of AA language speakers, with shared ancestry between Indian and Malaysian populations until about 470 generations ago, contesting the existing model of Neolithic expansion of the AA culture. We observed a spatio-temporal transition in the genetic ancestry of SEA with genetic contribution from East Asia significantly increasing in the post-Neolithic period. Conclusion Our study shows that contrary to assumptions in many previous studies and despite having linguistic commonality, Indian AAs have a distinct genomic structure compared to Malaysian AAs. This linguistic-genetic discordance is reflective of the complex history of population migration and admixture shaping the genomic landscape of S&SEA. We postulate that pre-Neolithic ancestors of today’s AAs were widespread in S&SEA, and the fragmentation and dissipation of the population have largely been a resultant of multiple migrations of East Asian farmers during the Neolithic period. It also highlights the resilience of AAs in continuing to speak their language in spite of checkered population distribution and possible dominance from other linguistic groups.