Admixture Rates Research Articles

Facilitated introgression from domestic goat into Alpine ibex at immune loci.

Hybridization can result in the transfer of adaptive genetic material from one species to another, known as adaptive introgression. Bottlenecked (and hence genetically depleted) species are expected to be particularly receptive to adaptive introgression, since introgression can introduce new or previously lost adaptive genetic variation. The Alpine ibex (Capra ibex), which recently recovered from near extinction, is known to hybridize with the domestic goat (Capra aegagrus hircus), and signals of introgression previously found at the major histocompatibility complex were suggested to potentially be adaptive. Here, we combine two ancient whole genomes of Alpine ibex with 29 modern Alpine ibex genomes and 31 genomes representing six related Capra species to investigate the genome-wide patterns of introgression and confirm the potential relevance of immune loci. We identified low rates of admixture in modern Alpine ibex through various F statistics and screening for putative introgressed tracts. Further results based on demographic modelling were consistent with introgression to have occurred during the last 300 years, coinciding with the known species bottleneck, and that in each generation, 1-2 out of 100 Alpine ibex had a domestic goat parent. The putatively introgressed haplotypes were enriched at immune-related genes, where the adaptive value of alternative alleles may give individuals with otherwise depleted genetic diversity a selective advantage. While interbreeding with domestic species is a prevalent issue in species conservation, in this specific case, it resulted in putative adaptive introgression. Our findings highlight the complex interplay between hybridization, adaptive evolution, and the potential risks and benefits associated with anthropogenic influences on wild species.

#3010 Characteristics of a Brazilian cohort with primary hyperoxaluria type 1 (PH1), an admixed population with different ethnic origins

Abstract Background and Aims Primary Hyperoxaluria type 1 (PH1) is caused by biallelic variants in the AGXT gene, leading to alanine:glyoxylate aminotransferase deficiency, hepatic overproduction of oxalate, hyperoxaluria, nephrolithiasis (NL), and/or nephrocalcinosis (NC), often progressing to chronic kidney disease (CKD) with variable phenotypes. Brazilian population is unique due to its diverse ancestry and high admixture rate, which makes this population an interesting group to expand clinical and genetic profile of PH1. Method A descriptive study of genetic confirmed PH1 patients from various regions of Brazil, involving demographic, clinical-laboratory, and genetic data. Results Twenty-one patients (17 families) were identified; 4 detected by family screening (2 with active disease). Parental consanguinity detected in 4 families (23.5%). Nineteen symptomatic patients (12 males) included. At PH1 diagnosis, 3 patients were on CKD stage 1, 1 on CKD 3 and 15 were on CKD 5. We observed notable clinical heterogeneity, and 3 groups are described according to the age at onset. Table 1 shows data for each group and symptomatic cases. All patients have received pyridoxine since PH1 diagnosis. Conclusion In this Brazilian cohort we observed a high percentage of patients diagnosed on CKD 5, detected by recurrence in the renal graft after isolated renal transplantation, and patients achieving CKD 5 after obstructive kidney stones episode. Several factors, including the broad phenotypic spectrum, the lack of awareness among physicians about the disease and the scarcity of diagnostic tools, may explain this delay in diagnosis. Therefore, there is a need to improve information to the Brazilian medical community. The genetic findings are similar to European and North America genetic descriptions and 2 novel variants were identified expanding the AGXT variants profile. However, it is noteworthy, the high percentage of compound heterozygous variants compared with other cohorts worldwide, which may be characteristic of an admixed population.

Modeling carbonation depth of recycled aggregate concrete containing chlorinated salts

The durability of recycled concrete is susceptible to degradation from both chloride salt attack and carbonation when exposed in service environment. The depth of carbonation in recycled concrete subject to chloride salt attack was studied here. This investigation assessed the effects of mineral admixture, replacement rate of recycled coarse aggregate, and quality of recycled coarse aggregate on the carbonation depth. The carbonation depth Recycled concrete was studied through accelerated simulated carbonation in the laboratory for 7d, 14d and 28d. Based on the results, the correlation analysis was conducted to investigate the relationship between depth of carbonation, mineral admixture, recycled coarse aggregate replacement rate, recycled coarse aggregate quality and the presence of chloride ions. The objective of this study was mainly to investigate the effect of internal chloride ions on the depth of carbonation of recycled concrete subjected to chloride salt attack. The study referred to previous academic research on carbonation in recycled concrete that had not been affected by chloride salts, and conducted a comparative analysis to identify the carbonation depth pattern in recycled concrete influenced by chloride salt exposure. The study discovered a negative correlation between the replacement rate of mineral admixture and recycled coarse aggregate and the carbonation resistance of concrete. Moreover, enhancing the quality of recycled coarse aggregate positively impacted the carbonation resistance of concrete. An improved model was developed that considers the effect of internal chloride salts on the carbonation depth of recycled concrete, in reference to the empirical prediction model presently available. The model demonstrated a high level of agreement with experimental outcomes, displaying an error range of between −4.32% and 8.27%. It enables an in-depth comprehension of the carbonation behavior of recycled aggregate concrete in an environment exposed to chloride salt attack. Based on the model, the service life of recycled concrete structures can be more accurately forecasted, which can provide a theoretical direction for enhancing the durability of engineering structure.

Combine use of 100% thermoactivated recycled cement and recycled aggregate for fully recycled mortar: Properties evaluation and modification

The large-scale recycling of concrete waste and its high-value utilization are key research topic in the field of sustainable building materials. This paper investigated the properties of fully recycled mortar made with thermoactivated recycled cement and recycled fine aggregate (RFA) up to 100%. The 600 °C thermoactivated recycled cement contained active compounds such as C2S and CaO. Substituting recycled cement for ordinary Portland cement reduced the hydration reaction and enlarged the pore structure of paste, but mixing active admixture could improve the micro-structure of recycled cement paste. Incorporating recycled cement and RFA decreased the mechanical strength of mortar, as well as elevated the drying shrinkage and transport properties. The detrimental impact of incorporating recycled cement on the performance degradation was more prominent than that of RFA incorporation. Nevertheless, the properties of fully recycled mortar with both 100% recycled cement and RFA still achieved a relatively satisfactory level. Besides, recycled mortar made with recycled cement derived from cement paste waste exhibited superior performance to that made with recycled cement from concrete waste. Substituting active admixture for 10% recycled cement could obviously improve the strength and permeability resistance of fully recycled mortar. Therefore, optimizing the replacement rate of recycled cement, RFA and active admixture is expected to prepare the fully recycled mortar with good performance. The maximal utilization of concrete waste could be achieved through preparing fully recycled mortar with the use of recycled cement and RFA completely instead of natural sand and ordinary Portland cement. This approach resulted in lower CO2 emissions and provided superior environmental benefits.

A study of the shear strength properties of expansive soil treated with fly ash admixture

The behavior of clay minerals in expansive soils causes them to exhibit shrink-swell characteristics, making them unsuitable for engineering purposes in their natural state. To address this problem, researchers conducted direct shear experiments using fly ash as an admixture and black cotton soil as an expanding soil to explore the strength parameter. The experiments were conducted with varying amounts of fly ash ranging from 2% to 20%. Two arrangements of test series were made, and in the principal series, tests were made utilizing five unique densities and comparing dampness contents. The outcomes showed that the point of inside grating and union expanded directly up to the ideal dampness content and most significant dry thickness before diminishing. The subsequent series showed that the end of inward rubbing grew straightly with the expansion of fly debris admixture, yet attachment reduced after 10% admixture. The decrease in shear strength was because of the diminished passion, as the fly debris' cohesionless attributes took over as the admixture rate increased above 10%. Based on these findings, adding fly ash in small quantities to black cotton soil is recommended to avoid weakening it.

Assessment of genetic diversity, population structure and wolf-dog hybridisation in the Eastern Romanian Carpathian wolf population

The Carpathian Mountains have been constantly inhabited by grey wolves and present one of the largest distribution areas in Europe, comprising between 2300 and 2700 individuals in Romania. To date, however, relatively little is known about the Romanian wolf population. We aimed to provide a first assessment of genetic diversity, population structure and wolf-dog hybridisation based on 444 mostly non-invasively collected samples in the Eastern Romanian Carpathians. Pack reconstruction and analysis of population genetic parameters were performed with mitochondrial DNA control-region sequencing and microsatellite genotyping. We found relatively high levels of genetic diversity, which is similar to values found in previous studies on Carpathian wolves from Poland and Slovakia, as well as to the long-lasting Dinaric-Balkan wolf population. We found no significant population structure in our study region, suggesting effective dispersal and admixture. Analysis of wolf-dog hybridisation using a Single Nucleotide Polymorphism panel optimised for hybrid detection revealed low rates of admixture between wolves and domestic dogs. Our results provide evidence for the existence of a genetically viable wolf population in the Romanian Carpathians. The genetic data obtained in this study may serve as valuable baseline information for the elaboration of monitoring standards and management plans for wolves in Romania.

Experimental and numerical investigation of recycled rubber foam concrete

Processing waste tires into rubber granules for secondary use can effectively alleviate the problem of environmental pollution. Therefore, this paper prepares foam concrete by replacing cementitious materials with recycled rubber granules to recycle resources. The dry density, water absorption, cubic compression, and prismatic flexure tests are carried out with the foam admixture and rubber substitution rate as the test parameters to study the effects of foam admixture and rubber substitution rate on the performance of foam concrete. Using Monte Carlo method simulation and non-linear fitting, a numerical analysis model was developed to predict recycled rubber foam concrete's mechanical properties. The ABAQUS finite element simulation method was used to explore the changes in the stress–strain relationship and damage development of the recycled rubber foam concrete, combined with microscopic observation, SEM, and XRD tests to reveal the specimens' damage mechanism, microscopic morphology, and physical structure. The experimental results show that the foam admixture has a more significant effect on the specimens' dry density, water absorption, and strength index than the effect of the rubber replacement rate. In addition, the strength prediction model, strength conversion model, and uniaxial compression finite element model of recycled rubber foam concrete were established.

Effect of Hydrophobic Water Repellent Admixture on the Compressive Strength of Concrete in Highly Aggressive Water (Dead Sea Water as a Case Study)

The compressive strength of concrete may be affected by seepage of salt water. Dead Sea water is a hazardous environment for concrete due to high concentration of salts. The aim of this study was to investigate the effect of Dead Sea water on the compressive strength of concrete containing hydrophobic water-repellent admixture, and to determine the optimum dosage of admixture to be used to reduce this effect. Three types of cement were used (Ordinary Portland Cement, Pozzolanic Cement, and Sulphate-Resisting Cement) with various dose rate of hydrophobic water repellent admixture (0%, 2%, and 4% of cement weight). An experimental approach, in which the specimens were divided based on the type of cement and the specimen’s age, was adopted. Nine control cubic specimens were cured in plain water to ensure that the required compressive strength was reached and (54) specimens were cured in Dead Sea water. The specimens cured in Dead Sea water were tested at 7 and 28 days to investigate the effect of Dead Sea water on the early and long-term strength. The results showed that a reduction in the 28-day compressive strength occurred in all specimens for the three types of cement used, but with the addition of water repellent, this reduction was alleviated, and the optimum percentage of admixture was 2% of cement weight.

Analyze and simulate an individualized nutritional computing system for multidisciplinary teams in nutritional support therapy

ABSTRACT To explore the efficiency of nutritional support therapy . Pharmacists led the construction of an individualized nutritional computing system and were involved in the process of treatment. After obtaining relevant professional knowledge and instruction on how to operate the system, MDT members intervened in the incorrect treatment process during nutritional support therapy. The Department of Radiation Oncology and the Intensive Care Unit (ICU) were selected as pilot departments to compare and analyze the rationality of nutrition risk screening and the use of enteral nutrition (EN) and parenteral nutrition (PN) in treatment before and after intervention. The individualized nutritional computing system significantly improved work efficiency, promoted nutrition risk screening, and saved 10–15 minutes in the treatment of each patient. After intervention in the Department of Radiation Oncology, the use rate of Total Nutrient Admixture (TNA) increased by 7.17%, and the single-bottle infusion rate of PN preparation decreased by 17.94% in patients at risk of malnutrition. The use rate of EN and single-bottle infusion rate of PN preparation in patients without risk of malnutrition decreased by 15.17% and 20.81%, respectively. Overall, 98.75% of ICU patients were at risk of malnutrition. The use rates of EN and TNA increased by 12.79% and 12.14%, respectively, and the single-bottle infusion rate of PN preparation decreased by 10.06%. Streamlined and mobile MDT, the use of an individualized nutritional computing system, and the effective work of pharmacists in the process significantly improved the efficiency and rationality of nutritional support therapy .

Living on the edge: morphological, karyological and genetic diversity studies of the Hungarian Plantago maxima populations and established ex situ collection

BackgroundThe analysis of genetic diversity of protected plant species can greatly support conservation efforts. Plantago maxima Juss. ex Jacq. is a perennial species distributed along the Eurasian steppe. The westernmost range edge of the species’ distribution is located in the Pannonian basin, in Hungary where it is represented by a few, fragmented and highly endangered populations. We studied population diversity of all Hungarian range edge, natural populations, and one established ex situ population. One population from the centre of distribution (Kazakhstan) was implemented in the cpDNA haplotype study to compare the peripheral vs. central populations. We performed morphometric trait-based analysis, chromosome studies (morphometric analyses and FISH) and genetic diversity evaluations using inter simple sequence repeats (ISSR) and cpDNA trnL-trnF to evaluate differences between the in situ and ex situ populations as well as central vs. peripheral populations.ResultsOur results showed no obvious morphological differences among the in situ and ex situ populations in the period between 2018 and 2020. One ex situ subpopulation develops flowers three years in a row from 2019, which is a favourable indicator of the introduction success. Hungarian populations are exclusively diploids (2n = 2x = 12). The karyogram consists of 5 metacentric and 1 acrocentric chromosome pair. Plantago maxima has one 35S and two 5S rDNA loci, located on the acrocentric chromosome pair. Eight variable ISSR primers yielded 100 fragments, of which 74.6% were polymorphic (mean He = 0.220). A high level of genetic variation within population was observed (92%) while the genetic differentiation among the populations was only 8%. STRUCTURE analysis revealed that the largest Kunpeszér population separated from the rest of the Hungarian populations, indicating a high rate of admixture among the other ones. Based on the trnL-trnF sequence analysis the Hungarian populations represent a single haplotype, which can indicate a reduced diversity due to isolation and recent population decline. By contrast, Kazakh population represents a distinct haplotype compared to the Hungarian samples.ConclusionsThe present study draws the attention to the high conservation value of the Plantago maxima populations from the westernmost range edge of the species’ distribution.

Dynamic properties of the pinyon pine syngameon.

This article is a Commentary on Buck et al. (2023), 237: 2435–2449.

Population genomic insights into invasion success in a polyphagous agricultural pest, Halyomorpha halys.

Invasive species are increasingly threatening ecosystems and agriculture by rapidly expanding their range and adapting to environmental and human-imposed selective pressures. The genomic mechanisms that underlie such rapid changes remain unclear, especially for agriculturally important pests. Here, we used genome-wide polymorphisms derived from native, invasive, and intercepted samples and populations of the brown marmorated stink bug (BMSB), Halyomorpha halys, to gain insights into population genomics processes that have promoted the successful global invasion of this polyphagous pest. Our analysis demonstrated that BMSB exhibits spatial structure but admixture rates are high among introduced populations, resulting in similar levels of genomic diversity across native and introduced populations. These spatial genomic patterns suggest a complex invasion scenario, potentially with multiple bridgehead events, posing a challenge for accurately assigning BMSB incursions to their source using reduced-representation genomic data. By associating allele frequencies with the invasion status of BMSB populations, we found significantly differentiated single nucleotide polymorphisms (SNPs) located in close proximity to genes for insecticide resistance and olfaction. Comparing variations in allele frequencies among populations for outlier SNPs suggests that BMSB invasion success has probably evolved from standing genetic variation. In addition to being a major nuisance of households, BMSB has caused significant economic losses to agriculture in recent years and continues to expand its range. Despite no record of BMSB insecticide resistance to date, our results show high capacity for potential evolution of such traits, highlighting the need for future sustainable and targeted management strategies.

Patterns of Population Structure and Introgression Among Recently Differentiated Drosophila melanogaster Populations.

Despite a century of genetic analysis, the evolutionary processes that have generated the patterns of exceptional genetic and phenotypic variation in the model organism Drosophila melanogaster remains poorly understood. In particular, how genetic variation is partitioned within its putative ancestral range in Southern Africa remains unresolved. Here, we study patterns of population genetic structure, admixture, and the spatial structuring of candidate incompatibility alleles across a global sample, including 223 new accessions, predominantly from remote regions in Southern Africa. We identify nine major ancestries, six that primarily occur in Africa and one that has not been previously described. We find evidence for both contemporary and historical admixture between ancestries, with admixture rates varying both within and between continents. For example, while previous work has highlighted an admixture zone between broadly defined African and European ancestries in the Caribbean and southeastern USA, we identify West African ancestry as the most likely African contributor. Moreover, loci showing the strongest signal of introgression between West Africa and the Caribbean/southeastern USA include several genes relating to neurological development and male courtship behavior, in line with previous work showing shared mating behaviors between these regions. Finally, while we hypothesized that potential incompatibility loci may contribute to population genetic structure across the range of D. melanogaster; these loci are, on average, not highly differentiated between ancestries. This work contributes to our understanding of the evolutionary history of a key model system, and provides insight into the partitioning of diversity across its range.

Comparison of the emission potential of renewable fuels in mono- and bi-fuel systems from the point of view of a car fleet in an incoming circular economy

The aim of the study is to investigate the most effective approach to reduce the emissions of a SI-engine while using a limited amount of renewable fuel. In this study, the renewable fuels ethanol, methanol, 2-ethoxy-2-methylpropane (ETBE), acetone, and dimethylformamide (DMF) were investigated with various fixed admixture rates and with a fully variable on-board fuel mixture (Smart-Fuel concept). One result of the study is that for a Smart-Fuel concept using methanol a reduction in CO2 emissions of approx. 12.5% and a reduction in particulate emissions of approx. 60% can be achieved, when considering an entire car fleet. In terms of engine efficiency, as well as particulate emissions, the pure substances, except DMF, achieved significant improvements compared to standard gasoline. Compared with the pure substances, the Smart-Fuel concept achieved lower advantages; however, it used significantly less scarcely available renewable fuel in the process. Based on the limited availability of renewable fuels within the first stages of a circular economy, the Smart-Fuel concept proves to be a very efficient transition technology to achieve the CO2 reduction targets. The Smart-Fuel concept only uses renewable fuel when it is worthwhile in terms of efficiency or emissions. Predefined fuel blends in a mono-fuel concept offer much less reduction potential in terms of emissions than the Smart-Fuel concept. However, with respect to particulate raw emissions, especially for moderate mixing rates significantly increased particle emissions are sometimes observed, despite the overall very good performance of the pure substances.

F-Statistics estimation and admixture graph construction with Pool-Seq or allele count data using the R package poolfstat.

By capturing various patterns of the structuring of genetic variation across populations, -statistics have proved highly effective for the inference of demographic history. Such statistics are defined as covariances of SNP allele frequency differences among sets of populations without requiring haplotype information and are hence particularly relevant for the analysis of pooled sequencing (Pool-Seq) data. We here propose a reinterpretation of the (and ) parameters in terms of probability of gene identity and derive from this unified definition unbiased estimators for both Pool-Seq data and standard allele count data obtained from individual genotypes. We implemented these estimators in a new version of the R package poolfstat, which now includes a wide range of inference methods: (i) three-population test of admixture; (ii) four-population test of treeness; (iii) -ratio estimation of admixture rates; and (iv) fitting, visualization and (semi-automatic) construction of admixture graphs. A comprehensive evaluation of the methods implemented in poolfstat on both simulated Pool-Seq (with various sequencing coverages and error rates) and allele count data confirmed the accuracy of these approaches, even for the most cost-effective Pool-Seq design involving relatively low sequencing coverages. We further analysed a real Pool-Seq data made of 14 populations of the invasive species Drosophila suzukii, which allowed refining both the demographic history of native populations and the invasion routes followed by this emblematic pest. Our new package poolfstat provides the community with a user-friendly and efficient all-in-one tool to unravel complex population genetic histories from large-size Pool-Seq or allele count SNP data.

Genome analyses revealed genetic admixture and selection signatures in Bos indicus

The genomic diversity and relationship among seven diverse cattle breeds viz. Sahiwal, Tharparkar, Gir, Vechur, Ongole, Kangayam and Hariana were investigated in 132 random samples based on high density SNP array comprising > 777 K SNPs. A total of 1993 SNPs (0.25% of the total) having greater power (FST ≥ 0.20) to differentiate these cattle populations were identified, and utilized to partition genome of each animal into a predefined number of clusters. The structure of these cattle indicated shared ancestry of dairy breeds viz. Gir, Tharparkar and Sahiwal. Most of the animals (> 76%) of different populations under study except Vechur clustered into their own group of animals called breed. Vechur population retained highest rate of admixture, consistent with its crossing with other breeds. Ongole, Kangayam and Hariana shared comparatively less of their genome (≤ 15%) with other breeds. The study indicated that all seven breeds evolved from their independent ancestry but there was intermixing of these breeds in the recent past. The selection signatures identified between draft (Kangayam) and dairy breeds included several genes like FAM19A2, RAB31P, BEST3, DGKA, AHCY, PIGU and PFKP which are involved in immune response, metabolic pathway, transportation of glucose and sugars, signaling pathways, cellular processes, cell division and glycolysis regulation, respectively. Moreover, these genomic regions also harbour QTLs affecting milk performance traits. The signatures were also identified even between the dairy breeds. In comparison to large-sized cattle, there were significant differences in the number of QTLs affecting production (body weight, growth rate etc.) and morphological traits (height) in short-statured Vechur breed. The presence of HMGA2 gene in the selection signature on chromosome 5 may explain the variations in stature between these cattle.

Nitrogen fixation in pulsed microwave discharge studied by infrared absorption combined with modelling

A pulsed microwave surfaguide discharge operating at 2.45 GHz was used for the conversion of molecular nitrogen into valuable compounds in several gas mixtures: N2:O2, N2:O2:CO2 and N2:CO2. The ro-vibrational absorption bands of the molecular species were monitored by a Fourier transform infrared apparatus in the post-discharge region in order to evaluate the relative number density of species, specifically NO production. The effects of specific energy input, pulse frequency, gas flow fraction, gas admixture and gas flow rate were studied for better understanding and optimization of the NO production yield and the corresponding energy cost (EC). By both the experiment and modelling, a highest NO yield is obtained at N2:O2 (1:1) gas ratio in N2:O2 mixture. The NO yield reveals a small growth followed by saturation when pulse repetition frequency increases. The energy efficiency start decreasing after the energy input reaches about 5 eV/molec, whereas the NO yield rises steadily at the same time. The lowest EC of about 8 MJ mol−1 corresponding to the yield and the energy efficiency of about 7% and 1% are found, respectively, in an optimum discharge condition in our case.

Wildcat population density in NE Portugal: A regional stronghold for a nationally threatened felid

AbstractPopulation density data on depleted and endangered wildlife species are essential to assure their effective management and, ultimately, conservation. The European wildcat is an elusive and threatened species inhabiting the Iberian Peninsula, with fragmented populations and living in low densities. We fitted spatial capture–recapture models on camera‐trap data, to provide the first estimate of wildcat density for Portugal and assess the most influential drivers determining it. The study was implemented in Montesinho Natural Park (NE Portugal), where we identified nine individuals, over a total effort of 3,477 trap‐nights. The mean density estimate was 0.032 ± 0.012 wildcat/km2, and density tended to increase with distance to humanized areas, often linked to lower human disturbance and domestic cat presence, with forest and herbaceous vegetation cover and with European rabbit abundance. Although, this density estimate is within the range of values estimated for protected areas elsewhere in the Iberian Peninsula, our estimates are low at the European level. When put in context, our results highlight that European wildcats may be living in low population densities across the Iberian Mediterranean biogeographic region. No phenotypic domestic or hybrid cats were detected, suggesting potentially low admixture rates between the two species, although genetic sampling would be required to corroborate this assertion. We provide evidence that Montesinho Natural Park may be a suitable area to host a healthy wildcat population, and thus be an important protected area in this species' conservation context.

Do phylogeny and habitat influence admixture among four North American chickadee (family: Paridae) species?

Hybridization is an important aspect of speciation, yet questions remain about the ecological and environmental factors that influence hybridization among wild populations. We used microsatellite genotyping data and collected land cover and environmental data for four North American chickadee species: black‐capped Poecile atricapillus, mountain P. gambeli, chestnut‐backed P. rufescens and boreal P. hudsonicus chickadees. Combining these datasets, we sought to examine whether there is evidence of admixture between four widely distributed North American chickadee species; whether admixture takes place more often between more closely related species pairs or between species pairs with more similar ecological preferences; and whether certain habitat types have higher rates of admixture than others. We detected admixture for five of the six species pairs analyzed (chestnut‐backed–mountain chickadee pair showed no evidence of admixture), and found rates of admixture varied geographically, and within taxa pairs. Admixture was higher among less closely related species than more closely related species, although habitat similarity was not a significant predictor. Finally, rates of admixture were higher in urban parkland habitats than deciduous, mixed or coniferous forest habitats. Our work indicates admixture occurs frequently among North American parids, and habitat and environmental variation may play an important role in the frequency and geographic distribution of hybridization.

De novo identification and targeted sequencing of SSRs efficiently fingerprints Sorghum bicolor sub-population identity.

Recent plant breeding studies of several species have demonstrated the utility of combining molecular assessments of genetic distance into trait-linked SNP genotyping during the development of parent lines to maximize yield gains due to heterosis. SSRs (Short Sequence Repeats) are the molecular marker of choice to determine genetic diversity, but the methods historically used to sequence them have been burdensome. The ability to analyze SSRs in a higher-throughput manner independent of laboratory conditions would increase their utility in molecular ecology, germplasm curation, and plant breeding programs worldwide. This project reports simple bioinformatics methods that can be used to generate genome-wide de novo SSRs in silico followed by targeted Next Generation Sequencing (NGS) validation of those that provide the most information about sub-population identity of a breeding line, which influences heterotic group selection. While these methods were optimized in sorghum [Sorghum bicolor (L.) Moench], they were developed to be applied to any species with a reference genome and high-coverage whole-genome sequencing data of individuals from the sub-populations to be characterized. An analysis of published sorghum genomes selected to represent its five main races (bicolor, caudatum, durra, kafir, and guinea; 75 accessions total) identified 130,120 SSR motifs. Average lengths were 23.8 bp and 95% were between 10 and 92 bp, making them suitable for NGS. Validation through targeted sequencing amplified 188 of 192 assayed SSR loci. Results highlighted the distinctness of accessions from the guinea sub-group margaritiferum from all other sorghum accessions, consistent with previous studies of nuclear and mitochondrial DNA. SSRs that efficiently fingerprinted margaritiferum individuals (Xgma1 –Xgma6) are presented. Developing similar fingerprints of other sub-populations (Xunr1 –Xunr182) was not possible due to the extensive admixture between them in the data set analyzed. In summary, these methods were able to fingerprint specific sub-populations when rates of admixture between them are low.