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Abstract Background Peppers, bell and chile, are a culturally and economically important worldwide. Domesticated Capsicum spp. are distributed globally and represent a complex of valuable genetic resources. Objectives Explore population structure and diversity in a collection of 467 peppers representing eight species, spanning the spectrum from highly domesticated to wild using 22,916 SNP markers distributed across the twelve chromosomes of pepper. Results These species contained varied levels of genetic diversity, which also varied across chromosomes; the species also differ in the size of genetic bottlenecks they have experienced. We found that levels of diversity negatively correlate to levels of domestication, with the more diverse being the least domesticated.

Abstract Humans have built ports on all the coasts of the world, allowing people to travel, exploit the sea, and develop trade. The proliferation of these artificial habitats and the associated maritime traffic is not predicted to fade in the coming decades. Ports share common characteristics: Species find themselves in novel singular environments, with particular abiotic properties—e.g., pollutants, shading, protection from wave action—within novel communities in a melting pot of invasive and native taxa. Here, we discuss how this drives evolution, including setting up of new connectivity hubs and gateways, adaptive responses to exposure to new chemicals or new biotic communities, and hybridization between lineages that would have never come into contact naturally. There are still important knowledge gaps, however, such as the lack of experimental tests to distinguish adaptation from acclimation processes, the lack of studies to understand the putative threats of port lineages to natural populations or to better understand the outcomes and fitness effects of anthropogenic hybridization. We thus call for further research examining “biological portuarization,” defined as the repeated evolution of marine species in port ecosystems under human‐altered selective pressures. Furthermore, we argue that ports act as giant mesocosms often isolated from the open sea by seawalls and locks and so provide replicated life‐size evolutionary experiments essential to support predictive evolutionary sciences.

Abstract An essential goal in conservation biology is delineating population units that maximize the probability of species persisting into the future and adapting to future environmental change. However, future‐facing conservation concerns are often addressed using retrospective patterns that could be irrelevant. We recommend a novel landscape genomics framework for delineating future “Geminate Evolutionary Units” (GEUs) in a focal species: (1) identify loci under environmental selection, (2) model and map adaptive conservation units that may spawn future lineages, (3) forecast relative selection pressures on each future lineage, and (4) estimate their fitness and likelihood of persistence using geo‐genomic simulations. Using this process, we delineated conservation units for the Yosemite toad (Anaxyrus canorus), a U.S. federally threatened species that is highly vulnerable to climate change. We used a genome‐wide dataset, redundancy analysis, and Bayesian association methods to identify 24 candidate loci responding to climatic selection (R2 ranging from 0.09 to 0.52), after controlling for demographic structure. Candidate loci included genes such as MAP3K5, involved in cellular response to environmental change. We then forecasted future genomic response to climate change using the multivariate machine learning algorithm Gradient Forests. Based on all available evidence, we found three GEUs in Yosemite National Park, reflecting contrasting adaptive optima: YF‐North (high winter snowpack with moderate summer rainfall), YF‐East (low to moderate snowpack with high summer rainfall), and YF‐Low‐Elevation (low snowpack and rainfall). Simulations under the RCP 8.5 climate change scenario suggest that the species will decline by 29% over 90 years, but the highly diverse YF‐East lineage will be least impacted for two reasons: (1) geographically it will be sheltered from the largest climatic selection pressures, and (2) its standing genetic diversity will promote a faster adaptive response. Our approach provides a comprehensive strategy for protecting imperiled non‐model species with genomic data alone and has wide applicability to other declining species.

Abstract Background German-derived ethnicities are one of the largest ethnic groups in Hungary, dating back to the formation of the Kingdom of Hungary, which took place at the beginning of the 11th century. Germans arrived in Hungary in many waves. The most significant immigration wave took place following the collapse of the Ottoman Empire in East-Central Europe which closed the 150 year long Ottoman occupation. To date, there are no comprehensive genome-wide studies investigating the genetic makeup of the Danube Swabians. Here we analyzed 47 Danube Swabian samples collected from elderly Swabian individuals living in the Dunaszekcső-Bár area, in Danube side villages of Southwest Hungary. These Swabians, according to self-declaration, did not admix with other ethnic groups for 3–6 succeeding generations. Using Illumina Infinium 720 K Beadchip genotype data, we applied allele frequency-based and haplotype-based genome-wide marker data analyses to investigate the ancestry and genetic composition of the collected Danube Swabian samples. Results Haplotype-based analyses like identity by descent segment analysis show that the investigated Danube Swabians possess significant German and other West European ancestry, but their Hungarian ancestry is also prominent. Our results suggest that their main source of ancestry can be traced back to Western Europe, presumably to the region of Germany. Conclusion This is the first analysis of Danube Swabian population samples based on genome-wide autosomal data. Our results establish the basis for conducting further comprehensive research on Danube Swabians and on other German ethnicities of the Carpathian basin, which can help reconstruct their origin, and identify their major archaic genomic patterns.

BackgroundMinority groups of African descent experience disproportionately greater asthma morbidity compared with other racial groups, suggesting that genetic variation from a common ancestry could influence exacerbation risk.ObjectiveWe evaluated clinical trial measures in the context of self-reported race and genetic ancestry to identify risk factors for asthma exacerbations.MethodsOne thousand eight hundred forty multiethnic subjects from 12 Asthma Clinical Research Network and AsthmaNet trials were analyzed for incident asthma exacerbations with Poisson regression models that included clinical measures, self-reported race (black, non-Hispanic white, and other), and estimates of global genetic African ancestry in a subgroup (n = 760).ResultsTwenty-four percent of 1840 subjects self-identified as black. Black and white subjects had common risk factors for exacerbations, including a history of 2 or more exacerbations in the previous year and FEV1 percent predicted values, whereas chronic sinusitis, allergic rhinitis, and gastroesophageal reflux disease were only associated with increased exacerbation risk in black subjects. In the combined multiethnic cohort, neither race (P = .30) nor percentage of genetic African ancestry as a continuous variable associated with exacerbation risk (adjusted rate ratio [RR], 1.26 [95% CI, 0.94-1.70; P = .13]; RR per 1-SD change [32% ancestry], 0.97 [95% CI, 0.78-1.19; P = .74]). However, in 161 black subjects with genetic data, those with African ancestry greater than the median (≥82%) had a significantly greater risk of exacerbation (RR, 3.06 [95% CI, 1.09-8.6; P = .03]).ConclusionBlack subjects have unique risk factors for asthma exacerbations, of which global African genetic ancestry had the strongest effect.

Studies of Native South American genetic diversity have helped to shed light on the peopling and differentiation of the continent, but available data are sparse for the major ecogeographic domains. These include the Pacific Coast, a potential early migration route; the Andes, home to the most expansive complex societies and to one of the most widely spoken indigenous language families of the continent (Quechua); and Amazonia, with its understudied population structure and rich cultural diversity. Here, we explore the genetic structure of 176 individuals from these three domains, genotyped with the Affymetrix Human Origins array. We infer multiple sources of ancestry within the Native American ancestry component; one with clear predominance on the Coast and in the Andes, and at least two distinct substrates in neighboring Amazonia, including a previously undetected ancestry characteristic of northern Ecuador and Colombia. Amazonian populations are also involved in recent gene-flow with each other and across ecogeographic domains, which does not accord with the traditional view of small, isolated groups. Long-distance genetic connections between speakers of the same language family suggest that indigenous languages here were spread not by cultural contact alone. Finally, Native American populations admixed with post-Columbian European and African sources at different times, with few cases of prolonged isolation. With our results we emphasize the importance of including understudied regions of the continent in high-resolution genetic studies, and we illustrate the potential of SNP chip arrays for informative regional-scale analysis.

Abstract Background Evolutionary divergence and speciation often occur at a slower rate in the marine realm due to the higher potential for long-distance reproductive interaction through larval dispersal. One common evolutionary pattern in the Indo-Pacific, is divergence of populations and species at the peripheries of widely-distributed organisms. However, the evolutionary and demographic histories of such divergence are yet to be well understood. Here we address these issues by coupling genome-wide SNP data with mitochondrial DNA sequences to test the patterns of genetic divergence and possible secondary contact among geographically distant populations of the highly valuable spiny lobster Panulirus homarus species complex, distributed widely through the Indo-Pacific, from South Africa to the Marquesas Islands. Result After stringent filtering, 2020 SNPs were used for population genetic and demographic analyses, revealing strong regional structure (FST = 0.148, P

Abstract Background Describing how genetic history shapes the pattern of medically relevant variants could improve the understanding of how specific loci interact with each other and affect diseases and traits prevalence. The Qatari population is characterized by a complex history of admixture and substructure, and the study of its population genomic features would provide valuable insights into the genetic landscape of functional variants. Here, we analyzed the genomic variation of 186 newly-genotyped healthy individuals from the Qatari peninsula. Results We discovered an intricate genetic structure using ancestry related analyses. In particular, the presence of three different clusters, Cluster 1, Cluster 2 and Cluster 3 (with Near Eastern, South Asian and African ancestry, respectively), was detected with an additional fourth one (Cluster 4) with East Asian ancestry. These subpopulations show differences in the distribution of runs of homozygosity (ROH) and admixture events in the past, ranging from 40 to 5 generations ago. This complex genetic history led to a peculiar pattern of functional markers under positive selection, differentiated in shared signals and private signals. Interestingly we found several signatures of shared selection on SNPs in the FADS2 gene, hinting at a possible common evolutionary link to dietary intake. Among the private signals, we found enrichment for markers associated with HDL and LDL for Cluster 1(Near Eastern ancestry) and Cluster 3 (South Asian ancestry) and height and blood traits for Cluster 2 (African ancestry). The differences in genetic history among these populations also resulted in the different frequency distribution of putative loss of function variants. For example, homozygous carriers for rs2884737, a variant linked to an anticoagulant drug (warfarin) response, are mainly represented by individuals with predominant Bedouin ancestry (risk allele frequency G at 0.48). Conclusions We provided a detailed catalogue of the different ancestral pattern in the Qatari population highlighting differences and similarities in the distribution of selected variants and putative loss of functions. Finally, these results would provide useful guidance for assessing genetic risk factors linked to consanguinity and genetic ancestry.

The negative genetic impacts of gene flow from domestic to wild populations can be dependent on the degree of domestication and exacerbated by the magnitude of pre‐existing genetic differences between wild populations and the domestication source. Recent evidence of European ancestry within North American aquaculture Atlantic salmon (Salmo salar) has elevated the potential impact of escaped farmed salmon on often at‐risk wild North American salmon populations. Here, we compare the ability of single nucleotide polymorphism (SNP) and microsatellite (SSR) marker panels of different sizes (7‐SSR, 100‐SSR and 220K‐SNP) to detect introgression of European genetic information into North American wild and aquaculture populations. Linear regression comparing admixture predictions for a set of individuals common to the three datasets showed that the 100‐SSR panel and 7‐SSR panels replicated the full 220K‐SNP‐based admixture estimates with low accuracy (r2 of .64 and .49, respectively). Additional tests explored the effects of individual sample size and marker number, which revealed that ~300 randomly selected SNPs could replicate the 220K‐SNP admixture predictions with greater than 95% fidelity. We designed a custom SNP panel (301‐SNP) for European admixture detection in future monitoring work and then developed and tested a python package, salmoneuadmix (https://github.com/CNuge/SalmonEuAdmix), which uses a deep neural network to make de novo estimates of individuals' European admixture proportion without the need to conduct complete admixture analysis utilizing baseline samples. The results demonstrate the mobilization of targeted SNP panels and machine learning in support of at‐risk species conservation and management. [ABSTRACT FROM AUTHOR]

Introduction: Research in the field of pharmacogenomics (PGx) aims to identify genetic variants that modulate response to drugs, through alterations in their pharmacokinetics (PK) or pharmacodynamics (PD). The distribution of PGx variants differs considerably among populations, and whole-genome sequencing (WGS) plays a major role as a comprehensive approach to detect both common and rare variants. This study evaluated the frequency of PGx markers in the context of the Brazilian population, using data from a population-based admixed cohort from Sao Paulo, Brazil, which includes variants from WGS of 1,171 unrelated, elderly individuals. Methods: The Stargazer tool was used to call star alleles and structural variants (SVs) from 38 pharmacogenes. Clinically relevant variants were investigated, and the predicted drug response phenotype was analyzed in combination with the medication record to assess individuals potentially at high-risk of gene-drug interaction. Results: In total, 352 unique star alleles or haplotypeswere observed, of which 255 and 199 had a frequency < 0.05 and < 0.01, respectively. For star alleleswith frequency > 5% (n = 97), decreased, loss-of-function and unknown function accounted for 13.4%, 8.2% and 27.8% of alleles or haplotypes, respectively. Structural variants (SVs) were identified in 35 genes for at least one individual, and occurred with frequencies >5% for CYP2D6, CYP2A6, GSTM1, and UGT2B17. Overall 98.0% of the individuals carried at least one high risk genotype-predicted phenotype in pharmacogenes with PharmGKB level of evidence 1A for drug interaction. The Electronic Health Record (EHR) Priority Result Notation and the cohort medication registry were combined to assess high-risk genedrug interactions. In general, 42.0% of the cohort used at least one PharmGKB evidence level 1A drug, and 18.9% of individualswho used PharmGKB evidence level 1A drugs had a genotype-predicted phenotype of high-risk gene-drug interaction. Conclusion: This study described the applicability of next-generation sequencing (NGS) techniques for translating PGx variants into clinically relevant phenotypes on a large scale in the Brazilian population and explores the feasibility of systematic adoption of PGx testing in Brazil. [ABSTRACT FROM AUTHOR]

Objectives: The increased availability of genome‐wide data allows capturing the fine genetic structure of present days populations. Here we analyze the genetic ancestry at a fine scale of an Argentinean Patagonia population to understand the origins beyond the three‐hybrid model, and to compare these results with volunteers' self‐perceived ancestry in a broad context encompassed by historical and familiar information. Materials and Methods: We compare high‐throughput genotyping data for 92 individuals that we generated to data sets from the literature by applying fully haplotype‐based methods to examine patterns of human population substructure. The volunteers filled out a semi‐structured questionnaire, including questions about their history, ancestors, and self‐perceived ancestry. Finally, we used non‐parametric tests in order to compare genomic ancestry against self‐perception. Results: Genetic ancestry from Iberian populations accounted for 0.176 (Spain and Basque origins), while the component associated with Italian populations accounted for 0.140. We observed a 0.169 Native American genetic ancestry. Participants significantly over‐ and under‐ self‐perceived Native American and European origins, respectively. Components of origins from North Africa to Central South Asia accounted for 0.225 of the genetic ancestry in the sample, with significantly higher proportions for people that mentioned such origins in their genealogical history. Discussion: We captured the fine‐genetic architecture of a Puerto Madryn population sample in Chubut province, showing that self‐perceived ancestry remains a poor proxy for genetic ancestry. The presence of North Africa to Central South Asia components and its correlate with self‐perception of these origins justifies its inclusion in future miscegenation studies in Argentina. [ABSTRACT FROM AUTHOR]

Humans have had a major influence on the dissemination of crops beyond their native range, thereby offering new hybridization opportunities. Characterizing admixed genomes with mosaic origins generates valuable insight into the adaptive history of crops and the impact on current varietal diversity. We applied the ELAI tool—an efficient local ancestry inference method based on a two-layer hidden Markov model to track segments of wild origin in cultivated accessions in the case of multiway admixtures. Source populations—which may actually be limited and partially admixed—must be generally specified when using such inference models. We thus developed a framework to identify local ancestry with admixed source populations. Using sequencing data for wild and cultivated Coffea canephora (commonly called Robusta), our approach was found to be highly efficient and accurate on simulated hybrids. Application of the method to assess elite Robusta varieties from Vietnam led to the identification of an accession derived from a likely backcross between two genetic groups from the Congo Basin and the western coastal region of Central Africa. Admixtures resulting from crop hybridization and diffusion could thus lead to the generation of elite high-yielding varieties. Our methods should be widely applicable to gain insight into the role of hybridization during plant and animal evolutionary history. [ABSTRACT FROM AUTHOR]

Admixture, the genetic merging of parental populations resulting in mixed ancestry, has occurred frequently throughout the course of human history. Numerous admixture events have occurred between human populations across the world, which have shaped genetic ancestry in modern humans. For example, populations in the Americas are often mosaics of different ancestries due to recent admixture events as part of European colonization. Admixed individuals also often have introgressed DNA from Neanderthals and Denisovans that may have come from multiple ancestral populations, which may affect how archaic ancestry is distributed across an admixed genome. In this study, we analyzed admixed populations from the Americas to assess whether the proportion and location of admixed segments due to recent admixture impact an individual's archaic ancestry. We identified a positive correlation between non-African ancestry and archaic alleles, as well as a slight increase of Denisovan alleles in Indigenous American segments relative to European segments in admixed genomes. We also identify several genes as candidates for adaptive introgression, based on archaic alleles present at high frequency in admixed American populations but low frequency in East Asian populations. These results provide insights into how recent admixture events between modern humans redistributed archaic ancestry in admixed genomes. [ABSTRACT FROM AUTHOR]

Simple Summary: The human management of honey bees (Apis mellifera) has led to a reduction in the range and integrity of native subspecies, as they are replaced by foreign subspecies with traits that are perceived to be more desirable. Introgression—the transfer of alleles (gene variants) between genetically distinct lineages via hybridisation and repeated backcrossing—can lead to the loss of combinations of alleles that have built up over time as a result of adaptation. Measuring introgression is important for assessing the genetic integrity of colonies for breeders and conservationists. However, there is no agreed upon approach for measuring introgression in honey bee colonies. Here, we compare two commonly applied statistical methods for estimating introgression in honey bees from both individual and colony-pooled genetic data: a clustering approach (ADMIXTURE) and an allele pattern approach (ABBA BABA). Overall, data from a single individual from a colony resulted in lower introgression estimates than those from pooled colony samples using ADMIXTURE. However, ABBA BABA consistently yielded lower introgression estimates than ADMIXTURE. This study highlights that sometimes one individual is not enough to assess colony-level introgression and future studies using pooled colony approaches should not be solely dependent on ADMIXTURE for introgression estimates. The human management of honey bees (Apis mellifera) has resulted in the widespread introduction of subspecies outside of their native ranges. One well known example of this is Apis mellifera mellifera, native to Northern Europe, which has now been significantly introgressed by the introduction of C lineage honey bees. Introgression has consequences for species in terms of future adaptive potential and long-term viability. However, estimating introgression in colony-living haplodiploid species is challenging. Previous studies have estimated introgression using individual workers, individual drones, multiple drones, and pooled workers. Here, we compare introgression estimates via three genetic approaches: SNP array, individual RAD-seq, and pooled colony RAD-seq. We also compare two statistical approaches: a maximum likelihood cluster program (ADMIXTURE) and an incomplete lineage sorting model (ABBA BABA). Overall, individual approaches resulted in lower introgression estimates than pooled colonies when using ADMIXTURE. However, the pooled colony ABBA BABA approach resulted in generally lower introgression estimates than all three ADMIXTURE estimates. These results highlight that sometimes one individual is not enough to assess colony-level introgression, and future studies that do use colony pools should not be solely dependent on clustering programs for introgression estimates. [ABSTRACT FROM AUTHOR]

Genome-wide association studies (GWAS) of psychiatric disorders have focused primarily on individuals of European ancestry, excluding other ancestries, including Latin American populations. We explore representation of Latin American populations in psychiatric genetics, with a focus on eating disorders. Latin America is "admixed," representing the rich migration history from Africa, Europe, and Asia. Early GWAS technology and analytic strategies performed best in European-ancestry populations. New technology and statistical methods are designed to be inclusive of the genetic richness of admixed populations. Failure to include Latin American and other underrepresented ancestries in genetic studies could lead to incomplete or faulty conclusions about genetic and environmental contributions to psychiatric disease. This raises ethical questions and has critical scientific repercussions, as GWAS findings may not fully replicate across ancestries, ultimately exacerbating health disparities. We review efforts to accelerate genetic research by the Latin American Genetics Consortium (LAGC); highlight strategies to increase transparency and willingness of Latin American individuals to participate in research; and efforts to build capacity throughout Latin America. Achieving these goals advance etiological understanding of psychiatric disorders and assure that future treatments will serve people across all ancestries. [ABSTRACT FROM AUTHOR]

In this study, the effect of microbead dosages (0%, 5%, 10%, 15%, and 20%) on the carbonation resistance of expanded polystyrene (EPS) concrete was investigated. Five groups of EPS concrete specimens were produced and underwent rapid carbonation testing. The carbonation depth and strength after carbonation of the specimens were measured at different carbonation ages (7 days, 14 days, and 28 days) and analyzed to determine the effect of microbead dosages and compressive strength on carbonation resistance. Results indicated that the carbonation depth increased with the progression of carbonation time. The introduction of microbeads was found to significantly improve the carbonation resistance of EPS concrete, leading to a reduction in carbonation depth of over 50% after 28 days and an increase in strength after carbonation by 18–56%. A relative compressive strength model for EPS concrete after carbonation was developed, which could accurately characterize the growth of compressive strength. Based on the analysis of EPS concrete carbonation depth data, a prediction model for the carbonation depth of EPS concrete with microbead dosage was established through fitting, providing improved accuracy in predicting carbonation resistance. The microstructure of EPS concrete was also examined using scanning electron microscopy to uncover the underlying mechanisms of microbead enhancement on carbonation resistance. These findings have potential implications for future research and engineering applications in the carbonation resistance of EPS concrete. [ABSTRACT FROM AUTHOR]

Setophaga townsendi is a species of wood warbler (family Parulidae) in northwestern North America that has geographic structure in the mitochondrial and nuclear genomes: while interior populations have differentiated mitonuclear ancestry from the sister species S. occidentalis, coastal populations have a mix of inland and S. occidentalis mitonuclear ancestries. This coastal to inland transition in genomic ancestry raises the possibility of similar geographic structure in phenotypic traits, especially those involved in mate choice. Using qualitative and multivariate approaches, we investigated whether there is a sharp transition between coastal and inland populations in both song and in nuclear DNA. We find there is a shallow geographic cline in Type I song but not in Type II song. Nuclear DNA shows a gradient between coast and inland. There is little correlation between variation in song and the isolation-by-distance pattern in the nuclear DNA. Learned songbird song is shaped by both genetic and cultural processes. There has been a debate on whether song learning promotes or slows down population differentiation. By comparing the within-species variation in song and genetic structures, we can expand our understanding of the dynamic interplay between mating signals and population differentiation. [ABSTRACT FROM AUTHOR]

Translocation is becoming an increasingly important approach to threatened species conservation. Coupled with the knowledge that maximizing genetic diversity aids population establishment, the growing use of translocations can place unsustainable harvesting pressure on critical and vulnerable source populations. However, adaptive, genetically informed modelling tools such as Population Viability Analysis (PVA) can be used to predict translocation outcomes and optimize harvesting strategies. In this study, we use PVAs for the frequently translocated greater stick‐nest rat (Leporillus conditor) to demonstrate the value of admixing founder populations for translocation, even when one source population is deemed genetically depauperate. This approach not only maximizes genetic diversity in the translocated population but reduces harvesting pressure on critical populations. Further, we show that admixed harvesting ratios can be skewed significantly towards the genetically depauperate population in order to further protect the critical population while still producing favourable outcomes, providing adequate founder numbers are used. As many threatened species are limited to fragmented and bottlenecked populations, these results are broadly applicable to the science of reintroduction biology, and demonstrate the value of PVAs for preliminary translocation planning and species management. [ABSTRACT FROM AUTHOR]

Background. Vasopressin is frequently utilized for a variety of shock states in critically ill patients. Short stability (≤24 hours) after intravenous admixture with current manufacturer labeling requires just in time preparation and may lead to delays in therapy and increased medication waste. We aimed to evaluate vasopressin stability in 0.9% sodium chloride stored in polyvinyl chloride bags and polypropylene syringes for up to 90 days. Additionally, we evaluated the impact of extended stability on the time to administration and cost savings from reduced medical waste at an academic medical center. Methods. Dilutions of vasopressin to concentrations of 0.4 and 1.0 unit/mL were performed under aseptic conditions. The bags and syringes were stored at room temperature (23°C-25°C) or under refrigeration (3°C-5°C). Three samples of each preparation and storage environment were analyzed on days 0, 2, 14, 30, 45, 60, and 90. Physical stability was performed by visual examination. The pH was assessed at each point and upon final degradation evaluation. Sterility of the samples was not assessed. Chemical stability of vasopressin was evaluated using liquid chromatography with tandem mass spectrometry. Samples were considered stable if there was <10% degradation of the initial concentration. Results. Vasopressin diluted to 0.4 and 1.0 unit/mL with 0.9% sodium chloride injection was physically stable throughout the study. No precipitation was observed. At days 2, 14, 30, 45, 60, and 90 all bags and syringes diluted to 0.4 units/mL had <10% degradation. Vasopressin diluted to 1 unit/mL and stored under refrigeration had <10% degradation at all measured days, but when stored under room temperature was found to have >10% degradation at day 30. Implementation of a batching process resulted in reduced waste ($185 300) and improved time to administration (26 vs 4 minutes). Conclusion. Vasopressin diluted to a concentration of 0.4 units/mL with 0.9% sodium chloride injection is stable for 90 days at room temperature and under refrigeration. When diluted to 1.0 unit/mL with 0.9% sodium chloride injection it is stable for 90 days under refrigeration. Use of extended stability and sterility testing to batch prepare infusions may lead to improved time to administration and cost savings from reduced medication waste. [ABSTRACT FROM AUTHOR]

Understanding landscape connectivity and population genetic parameters is imperative for threatened species management. However, such information is lacking for the snow leopard (Panthera uncia). This study sought to explore hierarchical snow leopard gene flow patterns and drivers of genetic structure in Mongolia and China. A total of 97 individuals from across Mongolia and from the north-eastern edge of the Qinghai-Tibetan Plateau in Gansu Province to the middle of Qinghai Province in China were genotyped across 24 microsatellite loci. Distance-based frameworks were used to determine a landscape scenario best explaining observed genetic structure. Spatial and non-spatial methods were used to investigate fine-scale autocorrelation and similarity patterns as well as genetic structure and admixture. A genetic macro-division between populations in China and Mongolia was observed, suggesting that the Gobi Desert is a substantial barrier to gene flow. However, admixture and support for a resistance-based mode of isolation suggests connective routes that could facilitate movement. Populations in Mongolia had greater connectivity, indicative of more continuous habitat. Drivers of genetic structure in China were difficult to discern, and fine-scale sampling is needed. This study elucidates snow leopard landscape connectivity and helps to prioritize conservation areas. Although contact zones may have existed and occasional crossings can occur, establishing corridors to connect these areas should not be a priority. Focus should be placed on maintaining the relatively high connectivity for snow leopard populations within Mongolia and increasing research efforts in China. [ABSTRACT FROM AUTHOR]

Gene flow between previously differentiated populations during the founding of an admixed or hybrid population has the potential to introduce adaptive alleles into the new population. If the adaptive allele is common in one source population, but not the other, then as the adaptive allele rises in frequency in the admixed population, genetic ancestry from the source containing the adaptive allele will increase nearby as well. Patterns of genetic ancestry have therefore been used to identify post-admixture positive selection in humans and other animals, including examples in immunity, metabolism, and animal coloration. A common method identifies regions of the genome that have local ancestry "outliers" compared with the distribution across the rest of the genome, considering each locus independently. However, we lack theoretical models for expected distributions of ancestry under various demographic scenarios, resulting in potential false positives and false negatives. Further, ancestry patterns between distant sites are often not independent. As a result, current methods tend to infer wide genomic regions containing many genes as under selection, limiting biological interpretation. Instead, we develop a deep learning object detection method applied to images generated from local ancestry-painted genomes. This approach preserves information from the surrounding genomic context and avoids potential pitfalls of user-defined summary statistics. We find the method is robust to a variety of demographic misspecifications using simulated data. Applied to human genotype data from Cabo Verde, we localize a known adaptive locus to a single narrow region compared with multiple or long windows obtained using two other ancestry-based methods. [ABSTRACT FROM AUTHOR]

Southeastern Canada is inhabited by an amalgam of hybridizing wolf-like canids, raising fundamental questions regarding their taxonomy, origins, and timing of hybridization events. Eastern wolves (Canis lycaon), specifically, have been the subject of significant controversy, being viewed as either a distinct taxonomic entity of conservation concern or a recent hybrid of coyotes (C. latrans) and grey wolves (C. lupus). Mitochondrial DNA analyses show some evidence of eastern wolves being North American evolved canids. In contrast, nuclear genome studies indicate eastern wolves are best described as a hybrid entity, but with unclear timing of hybridization events. To test hypotheses related to these competing findings we sequenced whole genomes of 25 individuals, representative of extant Canadian wolf-like canid types of known origin and levels of contemporary hybridization. Here we present data describing eastern wolves as a distinct taxonomic entity that evolved separately from grey wolves for the past ∼67,000 years with an admixture event with coyotes ∼37,000 years ago. We show that Great Lakes wolves originated as a product of admixture between grey wolves and eastern wolves after the last glaciation (∼8,000 years ago) while eastern coyotes originated as a product of admixture between "western" coyotes and eastern wolves during the last century. Eastern wolf nuclear genomes appear shaped by historical and contemporary gene flow with grey wolves and coyotes, yet evolutionary uniqueness remains among eastern wolves currently inhabiting a restricted range in southeastern Canada. [ABSTRACT FROM AUTHOR]

The concept of admixture is currently widely being used, both in population genetics research and in DNA ancestry testing discourse. It is assumed to describe the process of gene flow between 2 previously distinct populations that eventually become admixed because of this flow. The concept per se does not require pure or unadmixed populations; the changes are relative and what matters is the level of admixture before and after the event under consideration. However, in this paper, we argue that the concept of admixture as currently used assumes the existence of pure or unadmixed categories. These do not need to have actually existed but to be able to exist in principle. We argue that this is a problematic notion that accrues from the racialist origins of the term admixture, which, as a result, is based on assumptions about purity. We suggest that scientists should be very cautious in their use of this term, especially in science education and communication. We also suggest that the term admixture should be better replaced by terms denoting similarity rather than difference. [ABSTRACT FROM AUTHOR]

The admixture between modern humans and Neandertals has resulted in ∼2% of the genomes of present-day non-Africans being composed of Neandertal DNA. Introgressed Neandertal DNA has been demonstrated to significantly affect the transcriptomic landscape in people today and via this molecular mechanism influence phenotype variation as well. However, little is known about how much of that regulatory impact is mediated through long-range regulatory effects that have been shown to explain ∼20% of expression variation. Here we identified 60 transcription factors (TFs) with their top cis-eQTL SNP in GTEx being of Neandertal ancestry and predicted long-range Neandertal DNA-induced regulatory effects by screening for the predicted target genes of those TFs. We show that the TFs form a significantly connected protein–protein interaction network. Among them are JUN and PRDM5, two brain-expressed TFs that have their predicted target genes enriched in regions devoid of Neandertal DNA. Archaic cis-eQTLs for the 60 TFs include multiple candidates for local adaptation, some of which show significant allele frequency increases over the last ∼10,000 years. A large proportion of the cis-eQTL-associated archaic SNPs have additional associations with various immune traits, schizophrenia, blood cell type composition and anthropometric measures. Finally, we demonstrate that our results are consistent with those of Neandertal DNA-associated empirical trans-eQTLs. Our results suggest that Neandertal DNA significantly influences regulatory networks, that its regulatory reach goes beyond the 40% of genomic sequence it still covers in present-day non-Africans and that via the investigated mechanism Neandertal DNA influences the phenotypic variation in people today. [ABSTRACT FROM AUTHOR]

Robert (Bob) Keith Wayne lost his battle with cancer in his home on 26 December 2022 with his wife, Dr. Blaire Van Valkenburgh, by his side. This essay, written by his former graduate students, highlights the foundation that survives Bob and our vision of continuing his efforts in building a future for endangered species. [ABSTRACT FROM AUTHOR]

Forest trees growing in high altitude conditions offer a convenient model for studying adaptation processes. They are subject to a whole range of adverse factors that are likely to cause local adaptation and related genetic changes. Siberian larch (Larix sibirica Ledeb.), whose distribution covers different altitudes, makes it possible to directly compare lowland with highland populations. This paper presents for the first time the results of studying the genetic differentiation of Siberian larch populations, presumably associated with adaptation to the altitudinal gradient of climatic conditions, based on a joint analysis of altitude and six other bioclimatic variables, together with a large number of genetic markers, single nucleotide polymorphisms (SNPs), obtained from double digest restriction-site-associated DNA sequencing (ddRADseq). In total, 25,143 SNPs were genotyped in 231 trees. In addition, a dataset of 761 supposedly selectively neutral SNPs was assembled by selecting SNPs located outside coding regions in the Siberian larch genome and mapped to different contigs. The analysis using four different methods (PCAdapt, LFMM, BayeScEnv and RDA) revealed 550 outlier SNPs, including 207 SNPs whose variation was significantly correlated with the variation of some of environmental factors and presumably associated with local adaptation, including 67 SNPs that correlated with altitude based on either LFMM or BayeScEnv and 23 SNPs based on both of them. Twenty SNPs were found in the coding regions of genes, and 16 of them represented non-synonymous nucleotide substitutions. They are located in genes involved in the processes of macromolecular cell metabolism and organic biosynthesis associated with reproduction and development, as well as organismal response to stress. Among these 20 SNPs, nine were possibly associated with altitude, but only one of them was identified as associated with altitude by all four methods used in the study, a nonsynonymous SNP in scaffold_31130 in position 28092, a gene encoding a cell membrane protein with uncertain function. Among the studied populations, at least two main groups (clusters), the Altai populations and all others, were significantly genetically different according to the admixture analysis based on any of the three SNP datasets as follows: 761 supposedly selectively neutral SNPs, all 25,143 SNPs and 550 adaptive SNPs. In general, according to the AMOVA results, genetic differentiation between transects or regions or between population samples was relatively low, although statistically significant, based on 761 neutral SNPs (FST = 0.036) and all 25,143 SNPs (FST = 0.017). Meanwhile, the differentiation based on 550 adaptive SNPs was much higher (FST = 0.218). The data showed a relatively weak but highly significant linear correlation between genetic and geographic distances (r = 0.206, p = 0.001). [ABSTRACT FROM AUTHOR]

Natural hybridization between closely related species in sympatry is an evolutionary process that is common in orchids. Once seen as a threat to parent species, interspecific genetic change is increasingly viewed as a source of novel variation in some ecological contexts. Terrestrial fringed orchids in the genus Platanthera contain several clades with high genetic compatibility among species and many putative hybrids. We used biallelic SNPs generated with 3RAD sequencing to study the hybrid complex formed from the parent species P. blephariglottis, P. ciliaris, and P. cristata with high resolution. The genetic structure and phylogenetic relationship of the hybrid complex revealed site-dependent gene flow between species. We documented extensive hybridization and cryptic hybrids in sympatric sites. Interspecific genetic exchange is particularly common between P. blephariglottis and P. ciliaris, with cryptic hybrids among putative P. ciliaris samples being more common than parental assignments in sympatric sites. Hybridization across the triad species complex can reticulate lineages and introduce adaptive alleles. Conversely, it can reduce diversification rates and introduce maladaptive alleles. Investigation into whether anthropogenic forces are eroding species boundaries, particularly the permeable P. blephariglottis and P. ciliaris boundary, is appropriate for conservation efforts. [ABSTRACT FROM AUTHOR]

Estimating contemporary effective population size (Ne), sibship and parentage can be useful for designing and monitoring plant translocations. Contemporary Ne is an important indicator of population viability, as it considers several demographic factors, e.g. sex ratio, mate compatibility, inbreeding, nonrandom mating, and family size. Sibship and parentage analyses allow not only estimating genetic relatedness of transplants and post‐translocation generations, but also selfing rates, parent contributions to offspring and contemporary seed and pollen dispersal. Sibship assignment method was used to reconstruct offspring pedigree and parentage and to estimate contemporary Ne, selfing rate, and contemporary seed and pollen dispersal in wild (used as seed sources for translocation) and translocated populations of the self‐compatible, insect‐pollinated Dianthus deltoides (Caryophyllaceae). Source populations show very small Ne estimates (5–21) and high selfing rates (28.6–68.9%), despite high census sizes. The first post‐translocation generation (recruits and transplant seed progeny) showed small contemporary Ne estimates (19–53) and substantial selfing rates (8.4–22.3%), despite high flowering sizes, overall genetic diversity and multiple paternity. Parentage assignments revealed high levels of admixture between sources, restricted seed dispersal and successful—often restricted—pollen dispersal in the post‐translocation generation. Pollinator service, crosses between selfed or related transplants and floral display, may have contributed to selfing and pollen dispersal patterns in translocated populations. The present findings support the interest of sibship and parentage reconstruction as genetic tool for designing and monitoring plant translocations, emphasizing the importance of assessing the genetic quality of the transplants, and contributing to a more precise evaluation of population extinction risk. [ABSTRACT FROM AUTHOR]

We analyzed mitochondrial DNA polymorphisms to search for evidence of the genetic structure and patterns of admixture in 124 populations (N = 1407 trees) across the distribution of Scots pine in Europe and Asia. The markers revealed only a weak population structure in Central and Eastern Europe and suggested postglacial expansion to middle and northern latitudes from multiple sources. Major mitotype variants include the remnants of Scots pine at the north‐western extreme of the distribution in the Scottish Highlands; two main variants (western and central European) that contributed to the contemporary populations in Norway and Sweden; the central‐eastern European variant present in the Balkan region, Finland, and Russian Karelia; and a separate one common to most eastern European parts of Russia and western Siberia. We also observe signatures of a distinct refugium located in the northern parts of the Black Sea basin that contributed to the patterns of genetic variation observed in several populations in the Balkans, Ukraine, and western Russia. Some common haplotypes of putative ancient origin were shared among distant populations from Europe and Asia, including the most southern refugial stands that did not participate in postglacial recolonization of northern latitudes. The study indicates different genetic lineages of the species in Europe and provides a set of genetic markers for its finer‐scale population history and divergence inference. [ABSTRACT FROM AUTHOR]

The study is aimed at improving the permeability aspect of concrete durability. The main reason for black olive oil (BLO) as the choice material relies on its inherent hydrophobic properties. The effect of BLO admixture on strength and permeability properties of concrete grade C30 was experimentally examined. BLO was integrated into the fresh concrete mix at percentages of 0.3%, 0.5%, 0.7% and 1% by weight of cement content and a water-cement ratio of 0.5 was used throughout the study. Compressive and flexural strength, permeability properties in terms of water adsorption, porosity, coefficient of permeability and sorptivity of the concrete samples were investigated after curing in water at 3, 7, 28, 60, 90 and 180days hydration period. The BLO test admixture acted as a workability improving admixture and air entraining admixture in the fresh concrete. The various water permeability parameters of BLO-concrete samples were significantly improved for all the percentage inclusion of BLO. However, the mechanical strength properties of concrete sample containing the admixture decreased steadily with increase in BLO content. The 28days compressive strength of 03%, 05%, 0.7% and 1% BLO concrete samples decreased approximately by 3%, 13%, 6% and 13% respectively.The adverse impact on the strength properties of BLO-concrete mixes attributed to the effect of increased air content and workability induced by the BLO admixture can be compensated by reducing the water-cement ratio. The 0.3% BLO-concrete which exhibited the least reduction in strength and also meeting the design strength required for residential buildings is considered the optimum content. [ABSTRACT FROM AUTHOR]

Abstract A nomenclatural type is the element to which a name is permanently linked and must consist of a gathering, or part of a gathering, of a single species or infraspecific taxon. However, sometimes more than one species may be mounted on a single herbarium sheet (‘Frankenstein type’), causing a nomenclatural confusion (admixture) in the use of a name, which creates difficulties on the delimitation of the species and application of its name (‘taxonomic headache’). This is the case of the assigned holotype to Mimosa asperoides Izag. & Beyhaut that is composed also of other Mimosa species. To solve the ‘Frankenstein type’ of Mimosa asperoides, we analyzed the original material, the protologue, and performed a morphological comparative analysis to distinguish the species involved in the admixture. These analyses allowed us to identify which of the fragments of the ‘Frankenstein type’ correspond to M. asperoides, enabling its lectotypification and providing new diagnostic features to amend its description. Finally, we reported the first citation of M. asperoides for Brazil and discussed the link between nomenclature and taxonomy to solve a taxonomic headache due to admixture.

The preparation and development of eco-friendly building materials have emerged as feasible options for large-scale solid waste management. This research prepared a high-performance three-dimensional (3D) printing material and printed building components using the two-stage conversion of solid waste. In the first transition process, a sulphoaluminate cementitious material was produced by calcination at 1270 ℃ using industrial solid waste, including municipal solid waste incineration fly ash, flue-gas desulfurization gypsum, and aluminum ash. Then, four admixtures, namely, water-reducing agent, sodium gluconate, dispersible latex powder, and hydroxypropyl methylcellulose, were selected to improve its performance and achieve a further transition of solid waste. The effect of admixtures, standard sand, and fiber on the properties of cementitious materials was studied. It was found that the addition of appropriate proportion admixtures increased the fluidity, extended the initial setting time, and controlled the decrease of compressive strength of the materials. A 1:1 ratio of cementitious material to standard sand with a fiber length of 12 mm, generated a high-performance sulfoaluminate-based cementitious material suitable for the preparation of 3D building components. The material has a fluidity of 188 mm, an initial setting time of 53 min, one-day compressive strength of 37.8 MPa, and one-day flexural strength of 7.6 MPa. Therefore, utilizing solid waste through this two-stage transition to prepare 3D printing materials has significant economic benefits, providing valuable ideas for large-scale solid waste treatment.

Our interest in the genetic basis of skin color variation between populations led us to seek a Native American population with genetically African admixture but low frequency of European light skin alleles. Analysis of 458 genomes from individuals residing in the Kalinago Territory of the Commonwealth of Dominica showed approximately 55% Native American, 32% African, and 12% European genetic ancestry, the highest Native American genetic ancestry among Caribbean populations to date. Skin pigmentation ranged from 20 to 80 melanin units, averaging 46. Three albino individuals were determined to be homozygous for a causative multi-nucleotide polymorphism OCA2NW273KV contained within a haplotype of African origin; its allele frequency was 0.03 and single allele effect size was –8 melanin units. Derived allele frequencies of SLC24A5A111T and SLC45A2L374F were 0.14 and 0.06, with single allele effect sizes of –6 and –4, respectively. Native American genetic ancestry by itself reduced pigmentation by more than 20 melanin units (range 24–29). The responsible hypopigmenting genetic variants remain to be identified, since none of the published polymorphisms predicted in prior literature to affect skin color in Native Americans caused detectable hypopigmentation in the Kalinago.

Tailings from gold mines gradually approach ultra-fine, making mine backfill costs higher and strength lower, which poses a serious threat to the safety of underground personnel and equipment. It is well known that suitable chemical admixtures can enhance the working properties of mortar materials. Therefore, in order to achieve the purpose of reducing the cost of ultra-fine tailings backfill and improving the working performance of ultra-fine tailings filling slurry, this paper provides a study on the effect of sodium silicate and calcium chloride on the properties of ultra-fine tailings cemented backfill materials. The results of experimental studies through rheology, strength, and microstructural tests, etc., showed that the optimal proportioning parameters of cementitious materials are 76.92% blast furnace slag, 19.24% carbide slag, and admixtures of 2.88% sodium silicate and 0.96% calcium chloride. The 3, 7, and 28-day uniaxial compressive strength of the ultra-fine tailings cemented paste backfill with the newly formulated blast furnace slag-based cementitious material increased by 124%, 142%, and 14%, respectively, compared to that of the ultra-fine tailings cemented paste backfill with the P. O42.5 cement. The setting time for ultra-fine tailings cemented backfill slurry is shortened by the addition of admixtures, and the shear stress of the slurry is correlated with the amount of hydration product generation and its formation of flocculating structure. Moreover, the cost of the newly prepared cementitious material is much lower than that of traditional cement, which lays a good foundation for the cemented filling of ultra-fine tailings.

This study investigates the hydration, microstructure, autogenous shrinkage, electrical resistivity, and mechanical properties of Portland cement pastes modified with PEG-PPG triblock copolymers with varied molecular weights. The early age properties including setting time and hydration heat were examined using the Vicat test and isothermal calorimetry. The hydration products and pore size distribution were analyzed using thermogravimetric analysis (TGA) and nitrogen adsorption, respectively. Mechanical properties and electrical resistivity were evaluated using the compressive strength test and electrochemical impedance spectroscopy (EIS). It was shown that the addition of the copolymers reduced the surface tension of the cement paste pore solution due to the presence of a hydrophobic block (PPG) in the molecular structure of the copolymers. The setting time and hydration heat were relatively similar in the control paste as well as the pastes modified with the copolymers. The results showed that copolymers were able to reduce the autogenous shrinkage in the paste due primarily to a reduction in pore solution surface tension. TGA showed a slight increase in the hydration degree of the paste modified with the copolymers. The compressive strength was reduced in the pastes modified with the copolymers that showed an increased volume of air voids. The addition of copolymers did not affect the electrical resistivity of the pastes except in the case where there was a large volume of air voids, which acted as electrical insulators.

Runs of homozygosity (ROH) are important genomic features that manifest when an individual inherits two haplotypes that are identical by descent. Their length distributions are informative about population history, and their genomic locations are useful for mapping recessive loci contributing to both Mendelian and complex disease risk. We have previously shown that ROH, and especially long ROH that are likely the result of recent parental relatedness, are enriched for homozygous deleterious coding variation in a worldwide sample of outbred individuals. However, the distribution of ROH in admixed populations and their relationship to deleterious homozygous genotypes is understudied. Here we analyze whole-genome sequencing data from 1,441 unrelated individuals from self-identified African American, Puerto Rican, and Mexican American populations. These populations are three-way admixed between European, African, and Native American ancestries and provide an opportunity to study the distribution of deleterious alleles partitioned by local ancestry and ROH. We re-capitulate previous findings that long ROH are enriched for deleterious variation genome-wide. We then partition by local ancestry and show that deleterious homozygotes arise at a higher rate when ROH overlap African ancestry segments than when they overlap European or Native American ancestry segments of the genome. These results suggest that, while ROH on any haplotype background are associated with an inflation of deleterious homozygous variation, African haplotype backgrounds may play a particularly important role in the genetic architecture of complex diseases for admixed individuals, highlighting the need for further study of these populations.

Natural populations often exist in spatially diverse environments and may experience variation in the strength and targets of natural selection across their ranges. Drosophila provides an excellent opportunity to study the effects of spatially varying selection in natural populations, as both Drosophila melanogaster and Drosophila simulans live across a wide range of environments in North America. Here, we characterize patterns of variation in transposable elements (TEs) from six populations of D. melanogaster and nine populations of D. simulans sampled from multiple latitudes across North America. We find a nearly twofold excess of TEs in D. melanogaster relative to D. simulans, with this difference largely driven by TEs segregating at the lowest and highest allele frequencies. We find no effect of latitude on either total TE abundance or average TE allele frequencies in either species. Moreover, we show that, as a class of mutations, the most common patterns of TE variation do not coincide with the sampled latitudinal gradient, nor are they consistent with local adaptation acting on environmental differences found in the most extreme latitudes. We also do not find a cline in ancestry for North American D. melanogaster-for either TEs or single nucleotide polymorphisms-suggesting a limited role for demography in shaping patterns of TE variation. Though we find little evidence for widespread clinality among TEs in Drosophila, this does not necessarily imply a limited role for TEs in adaptation. We discuss the need for improved models of adaptation to large-scale environmental heterogeneity, and how these might be applied to TEs.

Abstract 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.

Sustainability is a growing area of concern, especially amid the concrete industry. Concrete, especially traditional concrete, which contains Portland cement, is extremely harmful to the environment producing mass amounts of carbon dioxide. Additionally, the harvesting of these materials, like lime, cause significant damage to waterways and the ecosystem. For years, studies have found numerous, more sustainable, alternatives that are structurally equivalent to traditional concrete. The Connecticut Department of Transportation does allow for the use of alternative “green” concretes as long as the mix designs meet the required specifications. Nevertheless, heavy highway construction seems reluctant to dabble with new substances and continues to falls back on the use of fly ash concrete. This solution, however, is not perfect, as fly ash is a finite material. By conducting a nationwide survey to the Departments of Transportation (DOT), the reliance on fly ash was evident. It was also found that the biggest concerns for DOTs would be the cost and availability of the material. This study investigates presently accepted alternative concrete mixture designs and also explores the solutions of volcanic ash concrete and ground glass concrete. Based off the results of the survey and practicality, this study suggests the incorporation of ground glass concrete for heavy highway construction. This solution provides the needed strength requirements per DOT specs and is within the same price-range as fly ash concrete.

As the barred owl (Strix varia; Aves: Strigiformes: Strigidae) expands throughout western North America, hybridization between barred and spotted owls (Strix varia and S. occidentalis, respectively), if abundant, may lead to genetic swamping of the endangered spotted owl. We analyzed low-coverage, whole-genome sequence data from fifty-one barred and spotted owls to investigate recent introgression between these two species. Although we obtained genomic confirmation that these species can and do hybridize and backcross, we found no evidence of widespread introgression. Plumage characteristics of western S. varia that suggested admixture with S. occidentalis appear unrelated to S. occidentalis ancestry and may instead reflect local selection.

Introduction: Research in the field of pharmacogenomics (PGx) aims to identify genetic variants that modulate response to drugs, through alterations in their pharmacokinetics (PK) or pharmacodynamics (PD). The distribution of PGx variants differs considerably among populations, and whole-genome sequencing (WGS) plays a major role as a comprehensive approach to detect both common and rare variants. This study evaluated the frequency of PGx markers in the context of the Brazilian population, using data from a population-based admixed cohort from Sao Paulo, Brazil, which includes variants from WGS of 1,171 unrelated, elderly individuals.Methods: The Stargazer tool was used to call star alleles and structural variants (SVs) from 38 pharmacogenes. Clinically relevant variants were investigated, and the predicted drug response phenotype was analyzed in combination with the medication record to assess individuals potentially at high-risk of gene-drug interaction.Results: In total, 352 unique star alleles or haplotypes were observed, of which 255 and 199 had a frequency < 0.05 and < 0.01, respectively. For star alleles with frequency > 5% (n = 97), decreased, loss-of-function and unknown function accounted for 13.4%, 8.2% and 27.8% of alleles or haplotypes, respectively. Structural variants (SVs) were identified in 35 genes for at least one individual, and occurred with frequencies >5% for CYP2D6, CYP2A6, GSTM1, and UGT2B17. Overall 98.0% of the individuals carried at least one high risk genotype-predicted phenotype in pharmacogenes with PharmGKB level of evidence 1A for drug interaction. The Electronic Health Record (EHR) Priority Result Notation and the cohort medication registry were combined to assess high-risk gene-drug interactions. In general, 42.0% of the cohort used at least one PharmGKB evidence level 1A drug, and 18.9% of individuals who used PharmGKB evidence level 1A drugs had a genotype-predicted phenotype of high-risk gene-drug interaction.Conclusion: This study described the applicability of next-generation sequencing (NGS) techniques for translating PGx variants into clinically relevant phenotypes on a large scale in the Brazilian population and explores the feasibility of systematic adoption of PGx testing in Brazil.

From the 15th to the 19th century, the Trans-Atlantic Slave-Trade (TAST) influenced the genetic and cultural diversity of numerous populations. We explore genomic and linguistic data from the nine islands of Cabo Verde, the earliest European colony of the era in Africa, a major Slave-Trade platform between the 16th and 19th centuries, and a previously uninhabited location ideal for investigating early admixture events between Europeans and Africans. Using local-ancestry inference approaches, we find that genetic admixture in Cabo Verde occurred primarily between Iberian and certain Senegambian populations, although forced and voluntary migrations to the archipelago involved numerous other populations. Inter-individual genetic and linguistic variation recapitulates the geographic distribution of individuals’ birth-places across Cabo Verdean islands, following an isolation-by-distance model with reduced genetic and linguistic effective dispersals within the archipelago, and suggesting that Kriolu language variants have developed together with genetic divergences at very reduced geographical scales. Furthermore, based on approximate bayesian computation inferences of highly complex admixture histories, we find that admixture occurred early on each island, long before the 18th-century massive TAST deportations triggered by the expansion of the plantation economy in Africa and the Americas, and after this era mostly during the abolition of the TAST and of slavery in European colonial empires. Our results illustrate how shifting socio-cultural relationships between enslaved and non-enslaved communities during and after the TAST, shaped enslaved-African descendants’ genomic diversity and structure on both sides of the Atlantic.

White cement is characterized by higher tricalcium aluminate (C3A) contents than conventional Portland cement; thus, it can present a reduced setting time, especially under hot weather conditions, limiting the material's application period. An approach to delay these materials' setting time is using retarder admixtures (RA). Nevertheless, there is a knowledge gap regarding the effect of RA on the rheological properties of white cement. This study aimed to evaluate the effect of two types of RA on the mini-slump, rheological parameters, hydration kinetics, and compressive strength of two white cements. Furthermore, the effect of temperatures of 25 and 40 ⁰C on the performance of the admixtures was also assessed. Both RA showed a dispersing effect, reducing cement pastes' dynamic yield stress and plastic viscosity. Moreover, the admixtures extended the induction period of cement hydration by up to 15.4 h without significantly affecting the 72-h cumulative heat at a temperature of 25 ⁰C. At 40 ⁰C, both RA exhibited a lower dispersing and retarding effect. Although RA delayed the initial hydration reactions of the WC, it enhanced the mechanical performance of the mortars after three days of hydration.

The utilization of ultra-high-performance concrete (UHPC) permanent formwork could facilitate the construction of hydraulic concrete structures. However, the joints between UHPC formwork are the vulnerable parts of a whole permanent formwork system. This study aimed to develop a High Strength Cementitious Grout (HSCG) for filling these joints, integrating the formwork system, and minimizing the adverse influence on these joints. The aggregate size for the HSCG was optimized, and four kinds of admixtures (i.e., hydrophobic powder (HP), expansive agent (EA), redispersible polymer powder (RPP), and cellulose ether (CE)) and PVA fibers were used to improve the HSCG. The HSCG with different aggregate sizes, admixture dosages, and PVA fiber contents were experimentally investigated. By evaluating the compressive, tensile, flexural, and adhesive strengths of the prepared grout, the aggregate size range was recommended to be 0.15–0.30 ​mm, while the suggested contents of HP, EA, RPP, and CE were 0%, 6%, 2%, and 0.1%, respectively, by weight of binding materials. In addition, the optimal volume content of PVA fibers was 0.45%. In order to avoid the introduced foams, 0.2% of the defoamers were used in combination with the CE. After that, six combinations were tested to consider the coupled effect of different admixtures and PVA fibers on the HSCG. In consideration of the strengths, shrinkage, and abrasion resistance to water impact, the HSCG with the combination of (EA ​+ ​RPP ​+ ​CE), the aggregate size of 0.15–0.30 ​mm showed the optimal overall performance and was regarded as the most suitable HSCG for grouting.

Background: Peppers, bell and chile, are a culturally and economically important worldwide. Domesticated Capsicum spp. are distributed globally and represent a complex of valuable genetic resources. Objectives: Explore population structure and diversity in a collection of 467 peppers representing eight species, spanning the spectrum from highly domesticated to wild using 22,916 SNP markers distributed across the twelve chromosomes of pepper. Results: These species contained varied levels of genetic diversity, which also varied across chromosomes; the species also differ in the size of genetic bottlenecks they have experienced. We found that levels of diversity negatively correlate to levels of domestication, with the more diverse being the least domesticated. [ABSTRACT FROM AUTHOR]

The Resande are a minority ethnic group in Sweden, who were characterized by an itinerant way of life, and they have been suggested to originate from the mixture between Swedish and Romani populations. Because the population history of the Resande has been scarcely studied, we analyzed genome-wide genotype array data from unrelated Resande individuals in order to shed light on their origins and demographic history for the first time from a genetic perspective. Our results confirm the Romani-related ancestry of this population and suggest an admixture event between a Romani-like population and a general Swedish-like population that occurred approximately between the mid-18th and mid-19th centuries, two centuries after the arrival of the first historically reported Romani families in Sweden. This inferred date suggests that the Romani group involved in the admixture is related to the pre-18th-century arrivals of Romani in Scandinavia. In addition, a reduction in the population size is detected previous to the admixture event, suggesting a subtle signal of isolation. The present work constitutes a step forward toward a better representation of ethnic minorities and underrepresented groups in population genetic analyses. In order to know in more detail the complete history of human populations, it is time to focus on studying populations that have not been previously considered for a general scenario and that can provide valuable information to fill in the gaps that still remain uncovered. [ABSTRACT FROM AUTHOR]

Humans have built ports on all the coasts of the world, allowing people to travel, exploit the sea, and develop trade. The proliferation of these artificial habitats and the associated maritime traffic is not predicted to fade in the coming decades. Ports share common characteristics: Species find themselves in novel singular environments, with particular abiotic properties—e.g., pollutants, shading, protection from wave action—within novel communities in a melting pot of invasive and native taxa. Here, we discuss how this drives evolution, including setting up of new connectivity hubs and gateways, adaptive responses to exposure to new chemicals or new biotic communities, and hybridization between lineages that would have never come into contact naturally. There are still important knowledge gaps, however, such as the lack of experimental tests to distinguish adaptation from acclimation processes, the lack of studies to understand the putative threats of port lineages to natural populations or to better understand the outcomes and fitness effects of anthropogenic hybridization. We thus call for further research examining "biological portuarization," defined as the repeated evolution of marine species in port ecosystems under human‐altered selective pressures. Furthermore, we argue that ports act as giant mesocosms often isolated from the open sea by seawalls and locks and so provide replicated life‐size evolutionary experiments essential to support predictive evolutionary sciences. [ABSTRACT FROM AUTHOR]

Sex-biased admixture can be inferred from ancestry-specific proportions of X chromosome and autosomes. In a paper published in the American Journal of Human Genetics , Micheletti et al. 1 used this approach to quantify male and female contributions following the transatlantic slave trade. Using a large dataset from 23andMe, they concluded that African and European contributions to gene pools in the Americas were much more sex biased than previously thought. We show that the reported extreme sex-specific contributions can be attributed to unassigned genetic ancestry as well as the limitations of simple models of sex-biased admixture. Unassigned ancestry proportions in the study by Micheletti et al. ranged from ∼1% to 21%, depending on the type of chromosome and geographic region. A sensitivity analysis illustrates how this unassigned ancestry can create false patterns of sex bias and that mathematical models are highly sensitive to slight sampling errors when inferring mean ancestry proportions, making confidence intervals necessary. Thus, unassigned ancestry and the sensitivity of the models effectively prohibit the interpretation of estimated sex biases for many geographic regions in Micheletti et al. Furthermore, Micheletti et al. assumed models of a single admixture event. Using simulations, we find that violations of demographic assumptions, such as subsequent gene flow and/or sex-specific assortative mating, may have confounded the analyses of Micheletti et al., but unassigned ancestry was likely the more important confounding factor. Our findings underscore the importance of using complete ancestry information, sufficiently large sample sizes, and appropriate models when inferring sex-biased patterns of demography. This Matters Arising paper is in response to Micheletti et al., 1 published in American Journal of Human Genetics. See also the response by Micheletti et al., 2 published in this issue. [ABSTRACT FROM AUTHOR]

Admixture estimation plays a crucial role in ancestry inference and genome-wide association studies (GWASs). Computer programs such as ADMIXTURE and STRUCTURE are commonly employed to estimate the admixture proportions of sample individuals. However, these programs can be overwhelmed by the computational burdens imposed by the 10 5 to 10 6 samples and millions of markers commonly found in modern biobanks. An attractive strategy is to run these programs on a set of ancestry-informative SNP markers (AIMs) that exhibit substantially different frequencies across populations. Unfortunately, existing methods for identifying AIMs require knowing ancestry labels for a subset of the sample. This supervised learning approach creates a chicken and the egg scenario. In this paper, we present an unsupervised, scalable framework that seamlessly carries out AIM selection and likelihood-based estimation of admixture proportions. Our simulated and real data examples show that this approach is scalable to modern biobank datasets. OpenADMIXTURE, our Julia implementation of the method, is open source and available for free. [ABSTRACT FROM AUTHOR]