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A better understanding of the genetic and ecological factors underlying successful invasions is critical to mitigate the negative impacts of invasive species. Here, we study the invasion history of Helianthus annuus populations from Argentina, with particular emphasis on the role of post‐introduction admixture with cultivated sunflower (also H. annuus) and climate adaptation driven by large haploblocks. We conducted genotyping‐by‐sequencing of samples of wild populations as well as Argentinian cultivars and compared them with wild (including related annual Helianthus species) and cultivated samples from the native range. We also characterised samples for 11 known haploblocks associated with environmental variation in native populations to test whether haploblocks contributed to invasion success. Population genomics analyses supported two independent geographic sources for Argentinian populations, the central United States and Texas, but no significant contribution of related annual Helianthus species. We found pervasive admixture with cultivated sunflower, likely as result of post‐introduction hybridization. Genomic scans between invasive populations and their native sources identified multiple genomic regions of divergence, possibly indicative of selection, in the invaded range. These regions significantly overlapped between the two native‐invasive comparisons and showed disproportionally high crop ancestry, suggesting that crop alleles contributed to invasion success. We did not find evidence of climate adaptation mediated by haploblocks, yet outliers of genome scans were enriched in haploblock regions and, for at least two haploblocks, the cultivar haplotype was favoured in Argentina. Our results show that admixture with cultivated sunflower played a major role in the establishment and spread of H. annuus populations in Argentina. [ABSTRACT FROM AUTHOR]

A debate in conservation genomics centers on whether to conserve small, fragmented populations independently or blend them through translocations from larger populations. Translocations of red grouse (Lagopus scotica) from Great Britain to supplement the Irish population have been suggested. We incorporate a variety of genetic datasets to address this. We used genome wide data from 23 contemporary and historic red grouse from Great Britain and Ireland. We also investigate microsatellite data, sequence candidate pigmentation genes, and assess phenotypic color variation. Genomic data indicate higher inbreeding in Irish grouse relative to an English population and significant divergence for genomic (FST = 0.095) and microsatellite (FST = 0.03) markers. Contemporary Ne was seven times smaller in the Irish population compared to the English. We identified divergent regions linked to pigmentation, immune response, and food intake. We show phenotypic differences in plumage color and sequence divergence among coding regions in the melanin pathway including MC1R (FST from genomic data of 0.3). The two populations thus appear locally adapted and this divergence between the source and target population when used for conservation translocations can swamp locally adapted alleles and/or introduce maladapted genotypes, leading to outbreeding depression. While it is important to avoid inbreeding by sustaining larger populations, our research emphasizes the need for practitioners to consider population divergence and local adaptation. We advocate against translocations between Ireland and Britain as a conservation strategy in this particular case and underscore the importance of prioritizing local populations where possible. [ABSTRACT FROM AUTHOR]

Patterson's f -statistics are among the most heavily utilized tools for analyzing genome-wide allele frequency data for demographic inference. Beyond studying admixture, f 3- and f 4-statistics are also used for clustering populations to identify groups with similar histories. However, previous studies have noted an unexpected behavior of f -statistics: multiple populations from a certain region systematically show higher genetic affinity to a more distant population than to their neighbors, a pattern that is mismatched with alternative measures of genetic similarity. We call this counter-intuitive pattern "sister repulsion". We first present a novel instance of sister repulsion, where genomes from Bronze Age East Anatolian sites show higher affinity toward Bronze Age Greece rather than each other. This is observed both using f 3- and f 4-statistics, contrasts with archaeological/historical expectation, and also contradicts genetic affinity patterns captured using principal components analysis or multidimensional scaling on genetic distances. We then propose a simple demographic model to explain this pattern, where sister populations receive gene flow from a genetically distant source. We calculate f 3- and f 4-statistics using simulated genetic data with varying population genetic parameters, confirming that low-level gene flow from an external source into populations from 1 region can create sister repulsion in f -statistics. Unidirectional gene flow between the studied regions (without an external source) can likewise create repulsion. Meanwhile, similar to our empirical observations, multidimensional scaling analyses of genetic distances still cluster sister populations together. Overall, our results highlight the impact of low-level admixture events when inferring demographic history using f -statistics. [ABSTRACT FROM AUTHOR]

The recovery and expansion of formerly isolated wolf populations in Europe raise questions about the nature of their interactions and future consequences for population viability and conservation. Will fragmented populations fuse or maintain a certain level of isolation with migration? Central Europe is suitable for obtaining empirical data in this field as it represents a 'crossroad' with the potential for contact among several phylogeographic lineages. In this study, non‐invasive genetic samples obtained during population monitoring in the Bohemian and Bavarian Forest (BBF) mountain ranges in the Czech Republic and Germany (Bohemian Massif) were analysed at different neutral markers including mitochondrial sequence, nuclear autosomal microsatellites and gonosomal sex markers. Resultant genetic profiles were compared with reference data to study population ancestry. Both cluster analyses of microsatellite genotypes and syntopic occurrence of haplotypes HW01 and HW22 showed genetic admixture between Central European and Alpine populations. This represents secondary contact and interbreeding of formerly allopatric populations with different phylogeographic histories and distant expansion centres in different biomes in the Baltic region versus the Apennine peninsula and Alps. Moreover, the study describes the founding event and genealogy of this admixed deme, inhabiting intermediate environmental conditions compared to parental forms, and emphasises the role of protected areas as stepping stones in the range recolonization process in endangered large mammals. [ABSTRACT FROM AUTHOR]

A good knowledge of the evolutionary history of organisms and an accurate taxonomic framework are keys for efficient biodiversity conservation measures. This is particularly relevant for European butterflies, which are often used as bioindicator organisms and umbrella species for conservation.The Holarctic butterfly genus Agriades includes seven European arctic‐alpine species of which several have a debated taxonomic status. They are localized and allopatric, and at least two of them are of high conservation concern, namely A. aquilo (in Europe, restricted to northern Scandinavia) and A. zullichi (endemic to southern Spain). Despite high conservation value and taxonomic uncertainty, molecular studies on these taxa are limited to DNA barcodes.We investigated the evolutionary history and species delimitation of West Palearctic Agriades using double‐digest RAD sequencing (ddRADseq).Various analyses using genomic data suggested the presence of one species in the glandon species group and one or two in the pyrenaicus species group. The differentiation within the former group (i.e., glandon, aquilo, zullichi) appears to be relatively recent, although the main allopatric populations represent evolutionary significant units (ESUs). Notable geographic structure was found within the pyrenaicus species group, with four allopatric ESUs detected.Wolbachia screening highlighted the presence of several allele combinations, some associated with particular Agriades populations.Genomic data revealed the evolutionary trajectory of European Agriades and a tendency for taxonomic oversplitting within this genus. These findings aid conservation by providing genetic background for region or population prioritization (including ESUs), and for the management of potential population reinforcement or reintroductions. [ABSTRACT FROM AUTHOR]

ABSTRACT Artificial propagation and wild release may influence the genetic integrity of wild populations. This practice has been prevalent in fisheries for centuries and is often termed ‘stocking’. In the Laurentian Great Lakes (Great Lakes here‐on), walleye populations faced declines from the 1950s to the 1970s, prompting extensive stocking efforts for restoration. By the mid‐2010s, walleye populations showed signs of recovery, but the genetic legacy of stocking on population structure at the genomic level remains unclear. Using a dataset of 45,600 genome‐aligned SNP loci genotyped in 1075 walleye individuals, we investigated the genetic impacts of over 50 years of stocking across the Great Lakes. Population structure was associated with both natural geographic barriers and stocking from non‐native sources. Admixture between Lake Erie walleye and walleye from the re‐populated Tittabawassee River indicate that stocking may have re‐distributed putatively adaptive alleles around the Great Lakes. Genome scans identified FST outliers and evidence of selective sweeps, indicating local adaptation of spawning populations is likely. Notably, one genomic region showed strong differentiation between Muskegon River and walleye from the Tittabawassee River, which was re‐populated by Muskegon strain walleye, suggesting admixture and selection both impact the observed genetic diversity. Overall, our study underscores how artificial propagation and translocations can significantly alter the evolutionary trajectory of populations. The findings highlight the complex interplay between stocking practices and population genetic diversity, emphasising the need for careful management strategies to preserve the genetic integrity of wild populations amidst conservation efforts. [ABSTRACT FROM AUTHOR]

Estimation of admixture proportions has become one of the most commonly used computational tools in population genomics. However, there is remarkably little population genetic theory on statistical properties of these variables. We develop theoretical results that can accurately predict means and variances of admixture proportions within a population using models with recombination and genetic drift. Based on established theory on measures of multilocus disequilibrium, we show that there is a set of recurrence relations that can be used to derive expectations for higher moments of the admixture proportions distribution. We obtain closed form solutions for some special cases. Using these results, we develop a method for estimating admixture parameters from estimated admixture proportions obtained from programs such as Structure or Admixture. We apply this method to HapMap 3 data and find that the population history of African Americans, as expected, is not best explained by a single admixture event between people of European and African ancestry. The model of constant gene flow starting at 8 generations and ending at 2 generations before present gives the best fit. [ABSTRACT FROM AUTHOR]

Soil nail walls are effective earth retention systems that reinforce soil masses to mitigate and repair geotechnical hazards, such as slides. A critical component of these structures is the cementitious grout encapsulating the soil nails, which bond the nail to the surrounding earth. A recognized challenge in soil nail wall applications is grout loss into voids and fissures of the in-situ ground conditions. Grout overages, increased costs, and project delays can arise if a site experiences severe grout loss into soil formations. This research investigated the introduction of varying percentages of bentonite, a naturally occurring clay mineral, as an admixture in the neat cement grout to increase the viscosity and potentially reduce the potential losses of grout away from the soil nails. This experimental study consisted of laboratory and field components to assess the impacts of varying bentonite percentages on grout properties. Based on the results of the laboratory tests, a grout mix between 4 and 6% bentonite, by weight of cement, and between 0.5 and 0.6 w/c ratio are recommended for field applications. The findings indicate that the introduction of bentonite into the neat cement grout of soil nails successfully increased the viscosity of the grout mix while also maintaining the strength of the grout. While the field testing of this study could not conclusively measure grout loss reduction, the field results did show a bond capacity increase of the bentonite grout mix and supported the probability of reduced grout loss. Additional research is needed to validate these assertions further. [ABSTRACT FROM AUTHOR]

ABSTRACT Describing naturally occurring genetic variation is a fundamental goal of molecular phylogeography and population genetics. Popular methods for this task include STRUCTURE, a model‐based algorithm that assigns individuals to genetic clusters, and principal component analysis (PCA), a parameter‐free method. The ability of STRUCTURE to infer mixed ancestry makes it popular for documenting natural hybridisation, which is of considerable interest to evolutionary biologists, given that such systems provide a window into the speciation process. Yet, STRUCTURE can produce misleading results when its underlying assumptions are violated, like when genetic variation is distributed continuously across geographic space. To test the ability of STRUCTURE and PCA to accurately distinguish admixture from continuous variation, we use forward‐time simulations to generate population genetic data under three demographic scenarios: two involving admixture and one with isolation by distance (IBD). STRUCTURE and PCA alone cannot distinguish admixture from IBD, but complementing these analyses with triangle plots, which visualise hybrid index against interclass heterozygosity, provides more accurate inference of demographic history, especially in cases of recent admixture. We demonstrate that triangle plots are robust to missing data, while STRUCTURE and PCA are not, and show that setting a low allele frequency difference threshold for ancestry‐informative marker (AIM) identification can accurately characterise the relationship between hybrid index and interclass heterozygosity across demographic histories of admixture and range expansion. While STRUCTURE and PCA provide useful summaries of genetic variation, results should be paired with triangle plots before admixture is inferred. [ABSTRACT FROM AUTHOR]

ABSTRACT Objectives Materials and Methods Results Discussion Previous research using anthropometric data from the west coast of Ireland in the late 19th century showed that two island populations, the Aran Islands and Inishbofin, were phenotypically divergent from the mainland and more similar to England, a pattern consistent with historical evidence for English admixture. The present study extends these analyses by including data from two other island populations in the region that do not have a history of English admixture.Data were taken from published sources for six west coast Irish populations measured in the 1890s: two mainland groups (Connemara and Erris) and four island populations (the Aran Islands, Clare Island, Inishbofin, and the Inishkea Islands). The anthropometric data consist of 13 measures on 317 males. Mahalanobis distances among the six populations were derived as well as distances to a mean based on English anthropometric data.The two island populations with a history of likely English admixture following the garrisoning of English soldiers in previous centuries were the most divergent from the Irish mainland and most similar to the English mean. The other two island populations (Clare Island and the Inishkea Islands) did not have a history of English admixture and were most similar to the Irish mainland.The different patterns of anthropometric similarity among the four island populations show different population histories and support earlier studies suggesting differential English admixture as a factor in the population structure of the region. [ABSTRACT FROM AUTHOR]

Human-induced environmental change and globalization facilitate biological invasions, which can lead to the displacement of native species by non-native ones. 1,2,3,4 Analogously, biodiversity loss may occur within species when habitat modifications facilitate the expansion of a specific population's range, leading to genetic admixture with native local populations. We demonstrate such intraspecific loss in population-level diversity in the Southern Small White (Pieris mannii), an originally sedentary butterfly 5 that recently expanded its range across Central Europe due to urbanization. 6,7,8 Using genome-wide markers from historical museum specimens and contemporary samples, we identify a distinct population initiating this expansion and reveal the genetic homogenization of native local populations by admixture with the expansive one. Our study illustrates how human-made environmental change can simultaneously benefit a species by permitting range expansion and drive cryptic biodiversity loss through the genetic homogenization of conspecific populations. • Range expansion in Pieris mannii butterflies is driven by a distinct population • This population now mixes with formerly isolated local populations • Population mixing causes loss of evolutionary distinctiveness within this species The butterfly Pieris mannii recently expanded its range across Central Europe in response to urbanization. Comparing DNA sequence data from museum and contemporary specimens, Blattner et al. show that this expansion is driven by a distinct lineage and that the mixing of this lineage with local ones results in within-species genetic homogenization. [ABSTRACT FROM AUTHOR]

Four types of archaeogenetic data mining are used to investigate the origin of the Minoans and the Uralic peoples: (1) six SNP mutations related to eye, hair, and skin phenotypes; (2) whole-genome admixture analysis using the G25 system; (3) an analysis of the history of the U5 mitochondrial DNA haplogroup; and (4) an analysis of the origin of each currently known Minoan mitochondrial and y-DNA haplotypes. The uniform result of these analyses is that the Minoans and the Uralic peoples had a common homeland in the lower and middle Danube Basin, as well as the Black Sea coastal regions. This new result helps to reconcile archaeogenetics with linguistics, which have shown that the Minoan language belongs to the Uralic language family. [ABSTRACT FROM AUTHOR]

Glacial periods have been considered as inhospitable environments that consist of treeless vegetation at higher latitudes. The fossil record suggests many species survived the Last Glacial Maximum within refugia, usually at lower latitudes. However, phylogeographic studies have given support to the existence of previously unknown high-latitude refugia that were not detected in the fossil record. Here, we test the hypothesis that cold-tolerant trees of Patagonia survived cold periods in microclimatically favourable locales where hybridization occurred between sister taxa. To study local presence through glacial periods in multiple refugia, we used pollen records and genetic information (isozymes, microsatellites, and combined nuclear and chloroplast DNA sequences) of population pairs of Nothofagus antarctica and N. pumilio that belong to the ancient subgenus Nothofagus which can potentially hybridize in nature, along their entire latitudinal range in Patagonia. Studied species share the N. dombeyi type pollen, which was abundant at >20% in the northernmost latitudinal bands (35–43°S), even during the Last Glacial Maximum. Mid- and southern latitudinal records (44–55°S) yielded lower abundances of ~10% that increased after c. 15.0 cal. ka BP. Therefore, fossil pollen evidence suggests a long-lasting local presence of Nothofagus throughout glacial–interglacial cycles but mostly as small populations between 44°S and 51°S. We found species-specific and shared genetic variants, the latter of which attained relatively high frequencies, thus providing evidence of ancestral polymorphisms. Populations of each species were similarly diverse, suggesting survival throughout the latitudinal range. Estimates of coalescent divergence times were broadly synchronous across latitudes, suggesting that regional climates similarly affected populations and species that hybridized through climate cycles, fostering local persistence. Graphical Abstract [ABSTRACT FROM AUTHOR]

Recent discoveries of sex chromosome diversity across the tree of life have challenged the canonical model of conserved sex chromosome evolution and evoked new theories on labile sex chromosomes that maintain less differentiation and undergo frequent turnover. However, theories of labile sex chromosome evolution lack direct empirical support due to the paucity of case studies demonstrating ongoing sex chromosome turnover in nature. Two divergent lineages (viz. WL & EL) of nine-spined sticklebacks (Pungitius pungitius) with different sex chromosomes (linkage group [LG] 12 in the EL, unknown in the WL) hybridize in a natural secondary contact zone in the Baltic Sea, providing an opportunity to study ongoing turnover between coexisting sex chromosomes. In this study, we first identify an 80 kbp genomic region on LG3 as the sex-determining region (SDR) using whole-genome resequencing data of family crosses of a WL population. We then verify this region as the SDR in most other WL populations and demonstrate a potentially ongoing sex chromosome turnover in admixed marine populations where the evolutionarily younger and homomorphic LG3 sex chromosome replaces the older and heteromorphic LG12 sex chromosome. The results provide a rare glimpse of sex chromosome turnover in the wild and indicate the possible existence of additional yet undiscovered sex chromosome diversity in Pungitius sticklebacks. [ABSTRACT FROM AUTHOR]

Improving the low productivity levels of native cattle breeds in smallholder farming systems is a pressing concern in Pakistan. Crossbreeding high milk-yielding holstein friesian (HF) breed with the adaptability and heat tolerance of Sahiwal cattle has resulted in offspring that are well-suited to local conditions and exhibit improved milk yield. The exploration of how desirable traits in crossbred dairy cattle are selected has not yet been investigated. This study aims to provide the first overview of the selective pressures on the genome of crossbred dairy cattle in Pakistan. A total of eighty-one crossbred, thirty-two HF and twenty-four Sahiwal cattle were genotyped, and additional SNP genotype data for HF and Sahiwal were collected from a public database to equate the sample size in each group. Within-breed selection signatures in crossbreds were investigated using the integrated haplotype score. Crossbreds were also compared to each of their parental breeds to discover between-population signatures of selection using two approaches: cross-population extended haplotype homozygosity and fixation index. We identified several overlapping genes associated with production, immunity, and adaptation traits, including U6, TMEM41B, B4GALT7, 5S_rRNA, RBM27, POU4F3, NSD1, PRELID1, RGS14, SLC34A1, TMED9, B4GALT7, OR2AK3, OR2T16, OR2T60, OR2L3, and CTNNA1. Our results suggest that regions responsible for milk traits have generally experienced stronger selective pressure than others. [ABSTRACT FROM AUTHOR]

Durable building materials are essential for sustainability in construction projects, aiming to reduce environmental damage from the start to the end of a building's life. Reducing the use of Portland cement in concrete production is essential because of the significant CO2 emissions generated globally during its production process. This study investigates the workability, compressive strength, and water absorption of concrete when Portland cement is partially substituted with waste glass powder (WGP) and recycled concrete powder (RCP). These two waste powders can be used to partially substitute Portland cement in order to produce environmentally friendly concrete. The activity of the particles in concrete made from these two waste powders is mostly determined by the type and rate of the powders, as well as the curing methods. Therefore, the current research examines how different curing conditions impact the workability, compressive strength, and water absorption characteristics of this innovative eco-friendly concrete that includes the abovementioned waste powders. According to the experimental results obtained, adequate strength can be achieved using an appropriate replacement level of the powders and curing methods. Therefore, the application of these two recycled mineral admixtures in concrete can save Portland cement and has certain environmental and economic benefits. [ABSTRACT FROM AUTHOR]

Genomic studies of endangered species have primarily focused on describing diversity patterns and resolving phylogenetic relationships, with the overarching goal of informing conservation efforts. However, few studies have investigated genomic diversity housed in captive populations. For tigers (Panthera tigris), captive individuals vastly outnumber those in the wild, but their diversity remains largely unexplored. Privately owned captive tiger populations have remained an enigma in the conservation community, with some believing that these individuals are severely inbred, while others believe they may be a source of now-extinct diversity. Here, we present a large-scale genetic study of the private (non-zoo) captive tiger population in the United States, also known as "Generic" tigers. We find that the Generic tiger population has an admixture fingerprint comprising all six extant wild tiger subspecies. Of the 138 Generic individuals sequenced for the purpose of this study, no individual had ancestry from only one subspecies. We show that the Generic tiger population has a comparable amount of genetic diversity relative to most wild subspecies, few private variants, and fewer deleterious mutations. We observe inbreeding coefficients similar to wild populations, although there are some individuals within both the Generic and wild populations that are substantially inbred. Additionally, we develop a reference panel for tigers that can be used with imputation to accurately distinguish individuals and assign ancestry with ultralow coverage (0.25×) data. By providing a cost-effective alternative to whole-genome sequencing (WGS), the reference panel provides a resource to assist in tiger conservation efforts for both ex-and in situ populations. [ABSTRACT FROM AUTHOR]

Background: Sheep breeds native to the United Kingdom exhibit a striking diversity of different traits. Some of these traits are highly sustainable, such as seasonal wool shedding in the Wiltshire Horn, and are likely to become more important as pressures on sheep production increase in coming decades. Despite their clear importance to the future of sheep farming, the genetic diversity of native UK sheep breeds is poorly characterised. This increases the risk of losing the ability to select for breed-specific traits from native breeds that might be important to the UK sheep sector in the future. Here, we use 50 K genotyping to perform preliminary analysis of breed relationships and genetic diversity within native UK sheep breeds, as a first step towards a comprehensive characterisation. This study generates novel data for thirteen native UK breeds, including six on the UK Breeds at Risk (BAR) list, and utilises existing data from the publicly available Sheep HapMap dataset to investigate population structure, heterozygosity and admixture. Results: In this study the commercial breeds exhibited high levels of admixture, weaker population structure and had higher heterozygosity compared to the other native breeds, which generally tend to be more distinct, less admixed, and have lower genetic diversity and higher kinship coefficients. Some breeds including the Wiltshire Horn, Lincoln Longwool and Ryeland showed very little admixture at all, indicating a high level of breed integrity but potentially low genetic diversity. Population structure and admixture were strongly influenced by sample size and sample provenance – highlighting the need for equal sample sizes, sufficient numbers of individuals per breed, and sampling across multiple flocks. The genetic profiles both within and between breeds were highly complex for UK sheep, reflecting the complexity in the demographic history of these breeds. Conclusion: Our results highlight the utility of genotyping data for investigating breed diversity and genetic structure. They also suggest that routine generation of genotyping data would be very useful in informing conservation strategies for rare and declining breeds with small population sizes. We conclude that generating genetic resources for the sheep breeds that are native to the UK will help preserve the considerable genetic diversity represented by these breeds, and safe-guard this diversity as a valuable resource for the UK sheep sector to utilise in the face of future challenges. [ABSTRACT FROM AUTHOR]

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 f 3-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 f 3-statistics. Finally, we demonstrate a significant performance increase for qpAdm using whole-genome branch-length f 2-statistics, highlighting the potential for improved demographic inference that could be achieved with future advancements in f -statistic estimations. [ABSTRACT FROM AUTHOR]

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. [ABSTRACT FROM AUTHOR]

The macroscopic flow behavior and rheological properties of cemented paste backfill (CPB) are highly impacted by the inherent structure of the paste matrix. In this study, the effects of shear-induced forces and proportioning parameters on the microstructure of fresh CPB were studied. The size evolution and distribution of floc/agglomerate/particles of paste were monitored by focused beam reflection measuring (FBRM) technique, and the influencing factors of aggregation and breakage kinetics of CPB were discussed. The results indicate that influenced by both internal and external factors, the paste kinetics evolution covers the dynamic phase and the stable phase. Increasing the mass content or the cement–tailings ratio can accelerate aggregation kinetics, which is advantageous for the rise of average floc size. Besides, the admixture and high shear can improve breaking kinetics, which is beneficial to reduce the average floc size. The chord length resembles a normal distribution somewhat, with a peak value of approximate 20 µm. The particle disaggregation constant (k2) is positively correlated with the agitation rate, and k2 is five orders of magnitude greater than the particle aggregation constant (k1). The kinetics model depicts the evolution law of particles over time quantitatively and provides a theoretical foundation for the micromechanics of complicated rheological behavior of paste. [ABSTRACT FROM AUTHOR]

Natural regeneration is a crucial factor in improving the economy of forest estates. The presented study analysed the economic parameters of three different approaches to forest regeneration: (i) artificial regeneration with Norway spruce, (ii) a 25% admixture of soil-improving and stabilising species (SSTS), and (iii) natural regeneration. The expenses for these specific operations related to individual regeneration methods were derived. These variants were investigated before the bark beetle calamity (2014) and after the outbreak (2023) for management sets (MS) 531, 551, 571, and 591, i.e. for acidic, nutrient-rich, gleyed, and waterlogged sites of higher elevations. In all cases, natural regeneration decreased expenses by approximately 2 000 EUR.ha-1 (50 000 CZK.ha-1) to 6 000 EUR.ha-1 (150 000 CZK.ha-1). The 25% admixture of SSTS increased the expenses. The proportion of natural regeneration subsequently decreased due to the bark beetle calamity from roughly 40% to 10% in recent years, which is comparable with the Czech Republic as a whole.

Abstract Background Sheep breeds native to the United Kingdom exhibit a striking diversity of different traits. Some of these traits are highly sustainable, such as seasonal wool shedding in the Wiltshire Horn, and are likely to become more important as pressures on sheep production increase in coming decades. Despite their clear importance to the future of sheep farming, the genetic diversity of native UK sheep breeds is poorly characterised. This increases the risk of losing the ability to select for breed-specific traits from native breeds that might be important to the UK sheep sector in the future. Here, we use 50 K genotyping to perform preliminary analysis of breed relationships and genetic diversity within native UK sheep breeds, as a first step towards a comprehensive characterisation. This study generates novel data for thirteen native UK breeds, including six on the UK Breeds at Risk (BAR) list, and utilises existing data from the publicly available Sheep HapMap dataset to investigate population structure, heterozygosity and admixture. Results In this study the commercial breeds exhibited high levels of admixture, weaker population structure and had higher heterozygosity compared to the other native breeds, which generally tend to be more distinct, less admixed, and have lower genetic diversity and higher kinship coefficients. Some breeds including the Wiltshire Horn, Lincoln Longwool and Ryeland showed very little admixture at all, indicating a high level of breed integrity but potentially low genetic diversity. Population structure and admixture were strongly influenced by sample size and sample provenance – highlighting the need for equal sample sizes, sufficient numbers of individuals per breed, and sampling across multiple flocks. The genetic profiles both within and between breeds were highly complex for UK sheep, reflecting the complexity in the demographic history of these breeds. Conclusion Our results highlight the utility of genotyping data for investigating breed diversity and genetic structure. They also suggest that routine generation of genotyping data would be very useful in informing conservation strategies for rare and declining breeds with small population sizes. We conclude that generating genetic resources for the sheep breeds that are native to the UK will help preserve the considerable genetic diversity represented by these breeds, and safe-guard this diversity as a valuable resource for the UK sheep sector to utilise in the face of future challenges.

There is evidence that Murciano Granadina (MG), the most important caprine dairy breed in Spain, has been introgressed by African goats, but the precise geographic origin of such introgression has not been identified yet. Moreover, an accurate estimate of the magnitude of this African introgression is lacking, since current estimates are based on small numbers of sampled individuals. The aim of our work was to tackle these two issues by genotyping 500 MG goats with the Goat SNP50 BeadChip and comparing their genotypes with those of reference populations from Spain (Bermeya), France (Saanen), Morocco (Barcha, Draa, Ghazalia, Noire de Atlas, Nord, Moroccan), Egypt (Barki, Oasis, Saidi), Algeria (Arabia, Makatia, M'Zabite, Kabyle), Tunisia (Tunisian native breeds) and Sudan (Desert, Nilotic, Taggar). The population of 500 MG goats was subdivided into 10 datasets of 50 individuals to ensure that sample sizes of the target (MG) and reference populations are balanced. Performance of an unsupervised ADMIXTURE analysis demonstrated that MG goats have a North African ancestry, with an average proportion of 4.4 ± 2.3%. Next, we did a supervised ADMIXTURE analysis that revealed that the Moroccan genetic component reaches a proportion of 4.01 ± 3.9% in MG goats, while the Algerian (0.001 ± 0.001%), Egyptian (0.2 ± 0.1%), Sudanese (0.1 ± 0.1%) and Tunisian (0.3 ± 0.4%) components are present in extremely small proportions. The historical circumstances of this introgression event are currently unknown, but several plausible scenarios are outlined. Moreover, our results show considerable inter‐individual heterogeneity regarding the magnitude of the Moroccan introgression of MG goats (0%– 12% depending on the MG data set under analysis). This result implies that reliable estimates about the introgression of autochthonous livestock by exotic breeds can only be obtained by extensively sampling target populations. [ABSTRACT FROM AUTHOR]

To investigate the influences of different admixtures on the drying shrinkage of polymer mortar in a metakaolin base, the experiments of VAE (vinyl acetate ethylene copolymer), APAM (anionic polyacrylamide) and CPAM (cationic polyacrylamide) on the drying shrinkage properties of geopolymer mortar were designed under normal temperature curing conditions. An SP-175 mortar shrinkage dilatometer was introduced to measure the dry shrinkage of geopolymer mortar. Meanwhile, the drying shrinkage properties of geopolymer mortar are exhibited by the parameters of water loss rate, drying shrinkage rate, drying shrinkage strain and drying shrinkage coefficient. The experimental data are further fitted to obtain the prediction model of dry shrinkage of geopolymer mortar, which can better reflect the relationship between dry shrinkage rate and time. Finally, the experimental results demonstrate that the dry shrinkage of geopolymer mortar can be significantly increased by adding 4% VAE admixture, meanwhile under the condition that the polymer film formed by VAE reaction can strengthen and toughen the mortar. 2.5% APAM admixture and 1.5% CPAM admixture can enhance the dry shrinkage performance of geopolymer mortar in a certain range. [ABSTRACT FROM AUTHOR]

In Finland, the geographic distribution of domestic reindeer (Rangifer tarandus tarandus) and Finnish wild forest reindeer (Rangifer tarandus fennicus) partly overlap in the vicinity of the southern border of the reindeer herding area. Additionally, domestic reindeer are occasionally kept as pets within the distribution range of the wild forest reindeer. Hybridisation of these two subspecies is one of the major threats for the wild forest reindeer population. Concerns about potential hybridisation served as the catalyst also for this study, which we aimed to clarify the taxonomic status of presumed wild forest reindeer individuals intended as founder individuals for a reintroduction project. To do this, we resequenced genomes of four Rangifer tarandus individuals with unknown taxonomical status and investigated their ancestries by comparing the genomic data with the existing resequenced data of the Finnish domestic reindeer and Finnish wild forest reindeer. The genetic relationship investigations indicated that all individuals we analysed were pure wild forest reindeer, making them suitable as founder individuals for the reintroduction project. Thus, our study provided critical knowledge for practical conservation action, where it was essential to recognise each individual's origin. In the future, it will also offer novel insights into the spread of native wild forest reindeer to new geographic regions in Finland. For subsequent studies, additional resequenced genomic data of Rangifer individuals will be needed to develop an ancestry information marker panel of single nucleotide polymorphisms for rapid and cost-effective identification of hybrid individuals of these subspecies. [ABSTRACT FROM AUTHOR]

Cement and concrete are the most crucial and dominating engineering materials in the construction sector. Cement serves as an excellent binder for concrete and when it is treated under unusual conditions either to satisfy accelerating or retarding requirements by the construction industries, admixtures role comes into the effect. The construction industry has been searching for retarding admixtures and the optimal dosage level, particularly for ready mix concrete applications. Generally the retarding admixtures such as organic retarders (lignosulphonates, hydroxycarboxylic acids and their salts, phosphonates, sugars) or inorganic retarders (phosphonates, borates) were generally used to reduce the speed of the reaction between cement and water by altering the growth of the hydration products and/or limiting the rate of water penetration to the cement particles. The research was still in its infancy stage in terms of determining not just the appropriate dosage amount, but also the ideal retarder materials for the aforementioned uses. In considering this industrial need, an attempt was made on utilizing the usage of sugar in the concrete to study the retarding effect without affecting the strength properties of cement. The sugars usage levels were at 5, 10, 15, and 20% of the usage of cement to investigate consistency, setting time, compressive strength and micro structure properties at the curing age of 7, 14 and 28 days on the mortar specimens. The conclusions of the study reported that setting time was extended with increase of the dosage levels of sugar. However in considering the strength property, less than 5% of sugar dosage level can be better for the application as retarding agent in the industry applications. [ABSTRACT FROM AUTHOR]

Martaban camphor [Cinnamomum parthenoxylon (Jack) Meisn] is a woody tree in India, China, Indonesia, Thailand, and Vietnam and has been widely utilized for commercial purposes. It is threatened due to fragmented habitats, over-deforestation, and oil extraction. To conserve this species, the investigation of genetic diversity and population structure of this species is essential. Herein, we analyzed 192 adult trees from eight populations covering its natural distribution range in Vietnam using ten polymorphic EST-SSR markers. Medium levels of genetic diversity (R = 2.7, Ho = 0.399, He = 0.426) and genetic differences between populations (Fst = 0.223) were determined. Two populations, Cuc Phuong and Xuan Nha have undergone recent bottlenecks. These results indicated that anthropogenic activities may be the major factor for the low heterozygosity and influenced the number of alleles in all C. parthenoxylon populations. Clustering analyses revealed three genetic clusters that related to gene flow between different areas. We proposed in situ conservation for some populations with high levels of allelic richness, genetic diversity, or private alleles. The collecting of the seeds of the remaining populations for ex-situ conservation could be performed.

Simple Summary: Wild horses in the region around Dülmen in Westphalia, Germany, date back to the Middle Ages. These horses ranged the wooden and marsh area in small herds. The Dukes of Croÿ fenced these wild horses in 1856 in an area called Merfelder Bruch, near Dülmen, and managed this herd as a self-contained population. Stallions employed were from the Dülmen wild horse population and, in some breeding seasons, from other primitive horse populations. The Dülmen wild horse population has to cope with harsh natural conditions all year round. The Dülmen wild horse population consists of about 530 horses with around 380 mares. Each year, 2 to 3 stallions sire 50 to 60 foals. In the present study, we characterize, for the first time, the Dülmen wild horse population in comparison to warmblood, coldblood, and primitive horse populations using a highly informative microsatellite marker set. We found a high degree of genetic diversity in the Dülmen wild horse population. Genetic distance measures, principal component analysis, and Bayesian cluster analyses clearly demarcated the Dülmen wild horse population from the other 17 horse populations studied here. In addition, data supported the hypothesis of an early genetic divergence of Dülmen wild horses. The Dülmen wild horse population appeared as an invaluable resource to study the evolution of domesticated horses. The objective of the present study was to analyze the genetic diversity, individual-based assessment of population structure, and admixture in the Dülmen wild horse population in comparison to warmblood, coldblood, and primitive horse populations. The Dülmen wild horse is kept as a unique horse population in the Merfelder Bruch near Dülmen in Westphalia, Germany, and since 1856 has been managed by the Dukes of Croÿ. The Dülmen wild horse population is exposed to the natural conditions of the Merfelder Bruch all year round without human interventions for feeding and veterinary care. In the present study, genetic diversity was estimated for 101 Dülmen wild horses using multilocus genotypic information from a set of 29 autosomal microsatellites and compared with 587 horses from 17 different horse populations. Dülmen wild horses maintained a high degree of genetic diversity, with an average observed heterozygosity of 0.68, a mean number of 6.17 alleles, and heterozygote deficit of −0.035. Pairwise genetic distances (FST, Nei's standard, and Cavalli-Sforza distances) were closest to German coldblood breeds, Polish Konik, and Icelandic horses and most divergent from Sorraia and Przewalski's horses. Neighbor joining dendrogram and PCA plots showed a clear distinction of Dülmen wild horses from other populations, particularly from Przewalski horses. Posterior Bayesian analysis confirmed clear differentiation from other horse populations without an admixture pattern and a high membership index (0.92). It was possible to distinguish Dülmen wild horses from Dülmen and Polish Konik horses. In conclusion, Dülmen wild horses show a notable separation from other German horse breeds and primitive horse populations and may serve as a resource to study evolution of equine domestication. [ABSTRACT FROM AUTHOR]

Human populations have interacted throughout history, and a considerable portion of modern human populations show evidence of admixture. Local ancestry inference (LAI) is focused on detecting the genetic ancestry of chromosomal segments in admixed individuals and has wide applications. In this work, we proposed a new LAI method based on population-specific single-nucleotide polymorphisms (SNPs) and applied it in the analysis of admixed populations in the 1000 Genomes Project (1KGP). Based on population-specific SNPs in a sliding window, we computed local ancestry information vectors, which are moment estimators of local ancestral proportions, for two haplotypes of an admixed individual and inferred the local ancestral origins. Then we used African (AFR), East Asian (EAS), European (EUR) and South Asian (SAS) populations from the 1KGP and indigenous American (AMR) populations from the Human Genome Diversity Project (HGDP) as reference populations and conducted the proposed LAI analysis on African American populations and American populations in the 1KGP. The results were compared with those obtained by RFMix, G-Nomix and FLARE. We demonstrated that the existence of alleles in a chromosomal region that are specific to a particular reference population and the absence of alleles specific to the other reference populations provide reasonable evidence for determining the ancestral origin of the region. Contemporary AFR, AMR and EUR populations approximate ancestral populations of the admixed populations well, and the results from RFMix, G-Nomix and FLARE largely agree with those from the Ancestral Spectrum Analyzer (ASA), in which the proposed method was implemented. When admixtures are ancient and contemporary reference populations do not satisfactorily approximate ancestral populations, the performances of RFMix, G-Nomix and FLARE deteriorate with increased error rates and fragmented chromosomal segments. In contrast, our method provides fair results. [ABSTRACT FROM AUTHOR]

Admixture is a common biological phenomenon among populations of the same or different species. Identifying admixed tracts within individual genomes can provide valuable information to date admixture events, reconstruct ancestry‐specific demographic histories, or detect adaptive introgression, genetic incompatibilities, as well as regions of the genomes affected by (associative‐) overdominance. Although many local ancestry inference (LAI) methods have been developed in the last decade, their performance was accessed using large reference panels, which are rarely available for non‐model organisms or ancient samples. Moreover, the demographic conditions for which LAI becomes unreliable have not been explicitly outlined. Here, we identify the demographic conditions for which local ancestries can be best estimated using very small reference panels. Furthermore, we compare the performance of two LAI methods (RFMix and MOSAIC) with the performance of a newly developed approach (simpLAI) that can be used even when reference populations consist of single individuals. Based on simulations of various demographic models, we also determine the limits of these LAI tools and propose post‐painting filtering steps to reduce false‐positive rates and improve the precision and accuracy of the inferred admixed tracts. Besides providing a guide for using LAI, our work shows that reasonable inferences can be obtained from a single diploid genome per reference under demographic conditions that are not uncommon among past human groups and non‐model organisms. [ABSTRACT FROM AUTHOR]

The Gila topminnow (Poeciliopsis occidentalis) has undergone population recovery actions since being extirpated from much of its historical range in the United States of America (USA) prior to the 1970s. However, it returned to the Santa Cruz River in 2015 independently of these actions, which prompted concerns that a non-native Poeciliopsis lineage had been introduced from Mexico. Some Gila topminnow populations in Mexico are sympatric with P. monacha-occidentalis, which is an exclusively female taxon that originated from historical hybridization between P. occidentalis and headwater livebearer (P. monacha). This hybrid taxon reproduces through hybridogenesis, which is a unique mode of sexual reproduction in which half of one parent's genome is inherited without recombination. This unique property was leveraged to identify hybridogens among 868 individuals from Arizona, USA using common genetic markers (i.e., nuclear microsatellite and mitochondrial sequence data). We described methods for P. monacha-occidentalis identification and conducted population genetic analysis of Santa Cruz River P. occidentalis populations to infer their possible origins. We concluded that human-mediated introduction was the most probable explanation for the current Santa Cruz River P. occidentalis and P. monacha-occidentalis presence. Contemporary diversity may be explained by four introduction events. Population ancestry estimates indicate that P. monacha-occidentalis may have hybridized with two P. occidentalis lineages in the Santa Cruz River. Variable prevalence of P. monacha-occidentalis was noted in two river sections, but the conservation implications of this hybridization are unclear. Public education, targeted removal of P. monacha-occidentalis, and genetic monitoring could mitigate future introductions and potential negative impacts. [ABSTRACT FROM AUTHOR]

Small populations of endangered species risk losing already eroded genetic diversity, important for adaptive potential, through the effects of genetic drift. The magnitude of drift can be mitigated by maximising the effective population size, as is the goal of genetic management strategies. Different mating systems, specifically those leading to reproductive skew, exacerbate genetic drift by distorting contributions. In the absence of an active management strategy, reproductive skew will have long-term effects on the genetic composition of a population, particularly where admixture is present. Here we examine the contrasting effects of conservation management strategies in two ex situ populations of the Critically Endangered eastern black rhino (Diceros bicornis michaeli), one managed as a semi-wild population in South Africa (SAx), and one managed under a mean-kinship breeding strategy in European zoos. We use molecular data to reconstruct pedigrees for both populations and validate the method using the zoo studbook. Using the reconstructed pedigree and studbook we show there is male sex-specific skew in both populations. However, the zoo's mean-kinship breeding strategy effectively reduces reproductive skew in comparison to a semi-wild population with little genetic management. We also show that strong male reproductive skew in SAx has resulted in extensive admixture, which may require a re-evaluation of the population's original intended role in the black rhino meta-population. With a high potential for admixture in many ex situ populations of endangered species, molecular and pedigree data remain vital tools for populations needing to balance drift and selection. [ABSTRACT FROM AUTHOR]

Cultivated potatoes are incredibly diverse, ranging from diploid to pentaploid and encompass four different species. They are adapted to disparate environments and conditions and carry unique alleles for resistance to pests and pathogens. Describing how diversity is partitioned within and among these populations is essential to understanding the potato genome and effectively utilizing landraces in breeding. This task is complicated by the difficulty of making comparisons across cytotypes and extensive admixture within section petota. We genotyped 730 accessions from the US Potato genebank including wild diploids and cultivated diploids and tetraploids using Genotype-by-sequencing. This data set allowed us to interrogate population structure and diversity as well as generate core subsets which will support breeders in efficiently screening genebank material for biotic and abiotic stress resistance alleles. We found that even controlling for ploidy, tetraploid material exhibited higher observed and expected heterozygosity than diploid accessions. In particular group chilotanum material was the most heterozygous and the only taxa not to exhibit any inbreeding. This may in part be because group chilotanum has a history of introgression not just from wild species, but landraces as well. All group chilotanum, exhibits introgression from group andigenum except clones from Southern South America near its origin, where the two groups are not highly differentiated. Moving north, we do not observe evidence for the same level of admixture back into group andigenum. This suggests that extensive history of admixture is a particular characteristic of chilotanum. [ABSTRACT FROM AUTHOR]

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Identifying stages of a species invasion in a new habitat (i.e., colonization, establishment, and landscape spread) and their primary determinants in biological invasion warrants attention, as it provides vital insights for preventing non-native species from becoming pervasive invaders. However, delineating invasion stages and their associated factors can pose significant challenges due to the ambiguous distinctions between these stages. Alliaria petiolata, one of the most noxious weeds in woodland habitats, has recently been introduced to Korea and observed in a few distant locations. Although the plant's spread has been relatively slow thus far, rapid spread is highly likely in the future, given the high invasive potential reported elsewhere. We indirectly diagnose the current status of A. petiolata invasion in Korea through the assessment of genetic diversity and phylogenetic inferences using genome-wide molecular markers and cytological data. We analyzed 86 individual samples collected from two native and six introduced populations, employing 1,172 SNPs. Our analysis estimated within- and among-population genetic diversity and included two clustering analyses. Furthermore, we investigated potential gene flow and reticulation events among the sampled populations. Our data unraveled that Korean garlic mustard exhibits a hexaploid ploidy level with two distinct chromosome numbers, 2n = 36 and 42. The extent of genetic diversity measured in Korean populations was comparable to that of native populations. Using genome-wide SNP data, we identified three distinct clusters with minor gene flow, while failing to detect indications of reticulation among Korean populations. Based on the multifaceted analyses, our study provides valuable insights into the colonization process and stressed the importance of closely monitoring A. petiolata populations in Korea. [ABSTRACT FROM AUTHOR]

To realize the resource utilization of solid waste of iron tailings, steel slag and phosphorus slag, reduce the amount of cement and reduce the adverse impact of iron tailings powder as admixture on concrete, three admixtures of phosphorus slag powder, desulfurization ash powder and steel slag powder were introduced based on high-silicon iron tailings powder. The compressive properties of iron tailing powder-phosphorus slag powder-desulfurization ash powder (IPD), iron tailing powder-phosphorus slag powder-steel slag powder (IPS) and iron tailing powder-steel slag powder-desulfurization ash powder (ISD) concretes were investigated. Mercury injection test and backscattered electron were used to test and analyze the internal pores and interfacial transition zone of concrete. The results show that the 28-day compressive strengthes of IPD system, IPS system and ISD system respectively reach 80.1%, 92.4% and 82.5% of that of pure cement concrete, and the interfacial transition zone between aggregate and cement is more dense after the addition of the admixture with reduced porosity to different degrees. The filling effect of the admixture is well exerted, and the adverse influence of internal porosity on concrete is alleviated. [ABSTRACT FROM AUTHOR]

Introgression of non‐native conspecifics changes the genetic composition of wild populations, potentially leading to loss of local adaptations and fitness declines. However, long‐term data from wild populations are still relatively few. Here, we studied the effects of introgression in a Danish brown trout (Salmo trutta, L.) population, subjected to intensive stocking with domesticated hatchery fish of non‐native origin. We used wild‐caught genetically wild and admixed trout as well as fish from the partly domesticated hatchery strain used for stocking the river up until ~15 years prior to this study, to produce 22 families varying in hatchery/wild admixture. Following a replicated common‐garden experiment conducted in fish tanks from first feeding through 23 weeks at 7, 12, and 16°C, we observed a significant positive relationship between family admixture and fish size upon termination, an effect observed through all levels of admixture. Furthermore, the admixture effect was most distinct at the higher rearing temperatures. Although the hatchery strain used for stocking had been in culture for ~7 generations, it had not been deliberately selected for increased growth. These data thus demonstrate: (i) that growth had increased in the hatchery strain even in the absence of deliberate directional selection for this trait, (ii) that the increasing effect of admixture by temperature could represent inadvertent selection for performance in the hatchery strain at higher temperatures, and most significantly, (iii) that despite undergoing up to five generations of natural selection in the admixed wild population, the genetically increased growth potential was still detectable and thus persistent. Our findings suggest that altered growth patterns and potentially their cascading effects are of importance to the severity of hatchery/wild introgression, especially under changing‐climate scenarios and are of general significance to conservation practitioners seeking to evaluate long‐term effects of intra‐specific hybridization including under recovery. [ABSTRACT FROM AUTHOR]

The hoary fox (Lycalopex vetulus) is the only species of the Canidae (Mammalia: Carnivora) endemic to Brazil, and so far has been the target of few genetic studies. Using microsatellites and mtDNA markers, we investigated its present genetic diversity and population structure. We also tested the hypothesis that this species currently hybridizes with the pampas fox (L. gymnocercus), as suggested by previous mtDNA data from two individuals. We collected tissue and blood samples from animals representing most of the two species' distributions in Brazil (n  = 87), including their recently discovered geographic contact zone in São Paulo state. We observed that the hoary fox exhibits high levels of genetic diversity and low levels of population structure. We identified six individuals from São Paulo state with clear evidence of hybridization based on introgressed pampas fox mitochondrial DNA and/or admixed microsatellite genotypes (three individuals bore both types of evidence). These results demonstrate the existence of admixed individuals between hoary and pampas foxes in southeastern Brazil, representing the first identified case of interspecies admixture between native South American canids. We discuss our findings in the context of the evolutionary history of these foxes and address potential conservation implications of this interspecies hybridization process. [ABSTRACT FROM AUTHOR]

Admixture between populations and species is common in nature. Since the influx of new genetic material might be either facilitated or hindered by selection, variation in mixture proportions along the genome is expected in organisms undergoing recombination. Various graph-based models have been developed to better understand these evolutionary dynamics of population splits and mixtures. However, current models assume a single mixture rate for the entire genome and do not explicitly account for linkage. Here, we introduce TreeSwirl , a novel method for inferring branch lengths and locus-specific mixture proportions by using genome-wide allele frequency data, assuming that the admixture graph is known or has been inferred. TreeSwirl builds upon TreeMix that uses Gaussian processes to estimate the presence of gene flow between diverged populations. However, in contrast to TreeMix , our model infers locus-specific mixture proportions employing a hidden Markov model that accounts for linkage. Through simulated data, we demonstrate that TreeSwirl can accurately estimate locus-specific mixture proportions and handle complex demographic scenarios. It also outperforms related D - and f -statistics in terms of accuracy and sensitivity to detect introgressed loci. [ABSTRACT FROM AUTHOR]

Despite a long presence in the contiguous United States (US), the distribution of invasive wild pigs (Sus scrofa × domesticus) has expanded rapidly since the 1980s, suggesting a more recent evolutionary shift towards greater invasiveness. Contemporary populations of wild pigs represent exoferal hybrid descendants of domestic pigs and European wild boar, with such hybridization expected to enrich genetic diversity and increase the adaptive potential of populations. Our objective was to characterize how genetic enrichment through hybridization increases the invasiveness of populations by identifying signals of selection and the ancestral origins of selected loci. Our study focused on invasive wild pigs within Great Smoky Mountains National Park, which represents a hybrid population descendent from the admixture of established populations of feral pigs and an introduction of European wild boar to North America. Accordingly, we genotyped 881 wild pigs with multiple high‐density single‐nucleotide polymorphism (SNP) arrays. We found 233 markers under putative selection spread over 79 regions across 16 out of 18 autosomes, which contained genes involved in traits affecting feralization. Among these, genes were found to be related to skull formation and neurogenesis, with two genes, TYRP1 and TYR, also encoding for crucial melanogenesis enzymes. The most common haplotypes associated with regions under selection for the Great Smoky Mountains population were also common among other populations throughout the region, indicating a key role of putatively selective variants in the fitness of invasive populations. Interestingly, many of these haplotypes were absent among European wild boar reference genotypes, indicating feralization through genetic adaptation. [ABSTRACT FROM AUTHOR]

Hybridization is of key relevance for conservation of wild species, and yet it is still one of the most controversial issues in conservation. Identifying historical and contemporary factors promoting the formation and maintenance of hybrids is crucial for the management of endangered species, as well as characterizing the environmental factors and patterns of habitat use among parental species and their hybrids. Crocodiles are a conservation priority group since all 23 species recognized worldwide are in a protected category and hybridization occurs between many of their species, particularly between Crocodylus acutus and C. moreletii. Their hybridization system encompasses a geographically extensive hybrid zone, where two distinct hybrids and two C. acutus lineages have diverged and only a few geographically isolated populations of both parental species remain. We used a combined approach of genome‐wide sequencing and ecological niche modeling to discern the geographic and temporal patterns of introgression, migration, and demography, and to assess the ecological niches of the distinct lineages. Our approach enabled us to determine the spatial and temporal components of the divergence and admixture events of hybrids and non‐admixed lineages, to describe the environmental characteristics and geographic extent of areas of sympatry, and to confirm human‐mediated hybridization events. Our findings also showed overall distinct ranges and ecological niches among lineages, where hybrids presented a different set of environmental requirements from both parental species. This approach can be readily applied to different taxa and ecological contexts, providing species information on genetics and the environment with direct conservation relevance. We additionally describe the various conservation challenges that C. acutus and C. moreletii currently face, highlighting that these distinct crocodile species and hybrid lineages warrant recognition and need urgent conservation effort. [ABSTRACT FROM AUTHOR]

Weedy rice, a pervasive and troublesome weed found across the globe, has often evolved through fertilization of rice cultivars with little importance of crop‐weed gene flow. In Argentina, weedy rice has been reported as an important constraint since the early 1970s, and, in the last few years, strains with herbicide‐resistance are suspected to evolve. Despite their importance, the origin and genetic composition of Argentinian weedy rice as well its adaptation to agricultural environments has not been explored so far. To study this, we conducted genotyping‐by‐sequencing on samples of Argentinian weedy and cultivated rice and compared them with published data from weedy, cultivated and wild rice accessions distributed worldwide. In addition, we conducted a phenotypic characterization for weedy‐related traits, a herbicide resistance screening and genotyped accessions for known mutations in the acetolactate synthase (ALS) gene, which confers herbicide resistance. Our results revealed large phenotypic variability in Argentinian weedy rice. Most strains were resistant to ALS‐inhibiting herbicides with a high frequency of the ALS mutation (A122T) present in Argentinian rice cultivars. Argentinian cultivars belonged to the three major genetic groups of rice: japonica, indica and aus while weeds were mostly aus or aus‐indica admixed, resembling weedy rice strains from the Southern Cone region. Phylogenetic analysis supports a single origin for aus‐like South American weeds, likely as seed contaminants from the United States, and then admixture with local indica cultivars. Our findings demonstrate that crop to weed introgression can facilitate rapid adaptation to agriculture environments. [ABSTRACT FROM AUTHOR]

Hybridisation can be an important driver of evolutionary change, but hybridisation with invasive species can have adverse effects on native biodiversity. While hybridisation has been documented across taxa, there is limited understanding of ecological factors promoting patterns of hybridisation and the spatial distribution of hybrid individuals. We combined the results of ecological niche modelling (ENM) and restriction site‐associated DNA sequencing to test theories of niche conservatism and biotic resistance on the success of invasion, admixture, and extent of introgression between native and non‐native fishes. We related Maxent predictions of habitat suitability based on the native ranges of invasive Eastern Banded Killifish (Fundulus diaphanus diaphanus Lesueur 1817) and native Western Banded Killifish (Fundulus diaphanus menona Jordan and Copeland 1877) to admixture indices of individual Banded Killifish. We found that Eastern Banded Killifish predominated at sites predicted as suitable from their ENM, consistent with niche conservatism. Admixed individuals were more common as Eastern Banded Killifish habitat suitability declined. We also found that Eastern Banded Killifish were most common at sites closest to the presumed source of this invasion, whereas the proportion of admixed individuals increased with distance from the source of invasion. Lastly, we found little evidence that habitat suitability for Western Banded Killifish provides biotic resistance from either displacement by, or admixture with, invasive Eastern Banded Killifish. Our study demonstrates that ENMs can inform conservation‐relevant outcomes between native and invasive taxa while emphasising the importance of protecting isolated Western Banded Killifish populations from invasive conspecifics. [ABSTRACT FROM AUTHOR]

The effect of C3A polymorphism, the calcium sulfate source, and the addition of limestone on the hydration kinetics and rheology of cement pastes and their interaction with a lignosulfonate-based admixture were analyzed. Two clinkers produced in industrial cement rotary kilns using the same raw materials and process were produced; their crystallinity was changed by using different fuel sources for research purposes. The cements containing mostly orthorhombic C3A (ORT) had a more extended induction period than cements with mostly cubic C3A (CUB). The phosphogypsum increased apparent viscosity and yield stress, as well as delaying the hydration of both clinkers (with a higher retardation effect on ORT clinker hydration). The limestone increased the apparent viscosity and the yield stress of the samples, besides accelerating the hydration due to the dilution and filler effects. The lignosulfonate admixture delayed the hydration of all cements tested. In ORT cements, the admixture was more efficient in reducing apparent viscosity and yield stress. [ABSTRACT FROM AUTHOR]

The breeding history of the Einsiedler horse is closely connected with the Benedictine cloister Einsiedeln. In the mid‐nineteenth century, it was decided to use European Warmblood stallions for cross‐breeding and to abandon the selection of stallions. Since that time, it has only been possible to trace back the origin of Einsiedler horses using maternal ancestry information. Here, we collected high‐density genotype data for European Warmblood horses (Selle Français, Swiss Warmblood and Einsiedler) and Franches‐Montagnes horses, the last native Swiss horse breed, to unravel the current population structure of the Einsiedler horse. Using commonly applied methods to ascertain fine‐scale population structures, it was not possible to clearly differentiate the Einsiedler from other European Warmblood horses. However, by means of runs of homozygosity (ROH) we were able to detect breed‐specific ROH islands for the Einsiedler horse, including genes involved in domestication and adaptation to high altitude. Therefore, future breeding activities should involve the screening of these breed‐specific ROH segments, the revival of cryopreserved sperm and the selection of Einsiedler stallions. [ABSTRACT FROM AUTHOR]

Genetic data contain a record of our evolutionary history. The availability of large-scale datasets of human populations from various geographic areas and timescales, coupled with advances in the computational methods to analyze these data, has transformed our ability to use genetic data to learn about our evolutionary past. Here, we review some of the widely used statistical methods to explore and characterize population relationships and history using genomic data. We describe the intuition behind commonly used approaches, their interpretation, and important limitations. For illustration, we apply some of these techniques to genome-wide autosomal data from 929 individuals representing 53 worldwide populations that are part of the Human Genome Diversity Project. Finally, we discuss the new frontiers in genomic methods to learn about population history. In sum, this review highlights the power (and limitations) of DNA to infer features of human evolutionary history, complementing the knowledge gleaned from other disciplines, such as archaeology, anthropology, and linguistics.

Genome-wide association studies (GWASs) have identified thousands of variants for disease risk. These studies have predominantly been conducted in individuals of European ancestries, which raises questions about their transferability to individuals of other ancestries. Of particular interest are admixed populations, usually defined as populations with recent ancestry from two or more continental sources. Admixed genomes contain segments of distinct ancestries that vary in composition across individuals in the population, allowing for the same allele to induce risk for disease on different ancestral backgrounds. This mosaicism raises unique challenges for GWASs in admixed populations, such as the need to correctly adjust for population stratification. In this work we quantify the impact of differences in estimated allelic effect sizes for risk variants between ancestry backgrounds on association statistics. Specifically, while the possibility of estimated allelic effect-size heterogeneity by ancestry (HetLanc) can be modeled when performing a GWAS in admixed populations, the extent of HetLanc needed to overcome the penalty from an additional degree of freedom in the association statistic has not been thoroughly quantified. Using extensive simulations of admixed genotypes and phenotypes, we find that controlling for and conditioning effect sizes on local ancestry can reduce statistical power by up to 72%. This finding is especially pronounced in the presence of allele frequency differentiation. We replicate simulation results using 4,327 African-European admixed genomes from the UK Biobank for 12 traits to find that for most significant SNPs, HetLanc is not large enough for GWASs to benefit from modeling heterogeneity in this way.

MethodsUp to 237 individuals belonging to 10 different taurine (Bos taurus), zebu (B. indicus), and taurine × zebu sanga cattle populations sampled in Benin, Burkina Faso, and Niger were typed using the BovineHD BeadChip of Illumina to ascertain the patterns and importance of heterozygosity-rich regions (HRRs) in West African cattle. To account for among-population gene flow, individuals were further classified into three groups (Qtaurine, Qzebu, and admixed) according to maximum likelihood estimates of individual ancestries (q^) obtained using the program Admixture v1.23.Results and discussionThe 967 HRRs identified on 27 out of 29 bovine chromosomes in 231 cattle individuals were further summarized into 103 HRR islands, covering 40.7 Mb of the bovine genome. Only HRR islands identified in at least 10% of the animals typed or 10% of the individuals classified according to cattle type or admixture class were considered relevant to characterize the West African cattle genomic background. Only one and three HRR islands were considered taurine- and zebu-specific, respectively. Most (14) relevant HRR islands identified were present in cattle individuals despite the cattle type or admixture class into which they were classified (waHRR), suggesting that HRR can give advantages for adaptation to harsh environments. A total of 202 potential candidate genes were identified on the 14 waHRR islands. Most of them belonged to gene families coding zinc finger, protocadherin, adhesion G protein-coupled receptors, solute carrier, and arachidonate lipoxygenase proteins, involved in immune response, with a putative role in adaptation. Furthermore, waHRRs were also enriched on 18 and 11 different genes coding olfactory receptors and pregnancy-associated glycoproteins, respectively, giving additional support to the suggested importance of the HRR islands identified for the adaptive ability of West African cattle. Our research identified new genomic areas that can be targeted for further research in cattle adaptive ability.