Patterson’s D, also known as the ABBA-BABA statistic, and related statistics such as the f4-ratio, are commonly used to assess evidence of gene flow between populations or closely related species. Currently available implementations often require custom file formats, implement only small subsets of the available statistics, and are impractical to evaluate all gene flow hypotheses across datasets with many populations or species due to computational inefficiencies. Here we present a new software package Dsuite, an efficient implementation allowing genome scale calculations of the D and f4-ratio statistics across all combinations of tens or hundreds of populations or species directly from a variant call format (VCF) file. Our program also implements statistics suited for application to genomic windows, providing evidence of whether introgression is confined to specific loci and it can also aid in interpretation of a system of f4-ratio results with the use of the ‘f-branch’ method. Dsuite ...

The role of interspecific hybridization in the context of diversification dynamics has recently seen increasing attention. Genomic research has now made it abundantly clear that both hybridization and introgression - the exchange of genetic material through hybridization - are far more common than previously thought. Moreover, even highly divergent species were found to hybridize and backcross. These findings raise the question whether commonly used methods for the detection of introgression are applicable to such divergent hybridizing species, given that most of these methods were originally developed for analyses at the level of populations and recently diverged species. In particular, the assumption of constant evolutionary rates, which is implicit in many commonly used approaches, is more likely to be violated as evolutionary divergence increases. To test the limitations of introgression detection methods when being applied to divergent species, we simulated thousands of genomic datasets under a wide range of settings, with varying degrees of among-species rate variation and introgression. Using these simulated datasets, we were able to show that commonly applied statistical methods, including the D-statistic and tests based on sets of phylogenetic trees, produce false-positive signals of introgression between highly divergent taxa when these have different rates of evolution. These misleading signals are caused by the presence of homoplasies that occur at different rates when rate variation is present. To distinguish between the patterns caused by rate variation and genuine introgression, we developed a new test that is based on the expected clustering of introgressed sites and implemented this test in the program Dsuite.

Over the past 15 years, the D-statistic, a four-taxon test for organismal admixture (hybridization, or introgression) which incorporates single nucleotide polymorphism data with allelic patterns ABBA and BABA, has seen considerable use. This statistic seeks to discern significant deviation from either a given species tree assumption, or from the balanced incomplete lineage sorting that could otherwise defy this species tree. However, while the D-statistic can successfully discriminate admixture from incomplete lineage sorting, it is not a simple matter to determine the directionality of admixture using only four-leaf tree models. As such, methods have been developed that use 5 leaves to evaluate admixture. Among these, the DFOIL method, which tests allelic patterns on the “symmetric” tree S = (((1,2),(3,4)),5), succeeds in finding admixture direction for many five-taxon examples. However, DFOIL does not make full use of all symmetry, nor can DFOIL function properly when ancient samples ...

Several methods have been proposed to test for introgression across genomes. One method tests for a genome-wide excess of shared derived alleles between taxa using Patterson's D statistic, but does not establish which loci show such an excess or whether the excess is due to introgression or ancestral population structure. Several recent studies have extended the use of D by applying the statistic to small genomic regions, rather than genome-wide. Here, we use simulations and whole genome data from Heliconius butterflies to investigate the behavior of D in small genomic regions. We find that D is unreliable in this situation as it gives inflated values when effective population size is low, causing D outliers to cluster in genomic regions of reduced diversity. As an alternative, we propose a related statistic f̂d, a modified version of a statistic originally developed to estimate the genome-wide fraction of admixture. f̂d is not subject to the same biases as D, and is better at identifying introgressed loci. Finally, we show that both D and f̂d outliers tend to cluster in regions of low absolute divergence (dXY), which can confound a recently proposed test for differentiating introgression from shared ancestral variation at individual loci.

When multiple speciation events occur rapidly in succession, discordant genealogies due to incomplete lineage sorting (ILS) can complicate the detection of introgression. A variety of methods, including the D-statistic (a.k.a. the "ABBA–BABA test"), have been proposed to infer introgression in the presence of ILS for a four-taxon clade. However, no integrated method exists to detect introgression using allelic patterns for more complex phylogenies. Here we explore the issues associated with previous systems of applying D-statistics to a larger tree topology, and propose new DFOIL tests as an integrated framework to infer both the taxa involved in and the direction of introgression for a symmetric five-taxon phylogeny. Using theory and simulations, we show that the DFOIL statistics correctly identify the introgression donor and recipient lineages, even at low rates of introgression. DFOIL is also shown to have extremely low false-positive rates. The DFOIL tests are computationally inexpensive to calculate and can easily be applied to phylogenomic data sets, both genome-wide and in windows of the genome. In addition, we explore both the principles and problems of introgression detection in even more complex phylogenies.

The evolutionary implications and frequency of hybridization and introgression are increasingly being recognized across the tree of life. To detect hybridization from multi-locus and genome-wide sequence data, a popular class of methods is based on summary statistics from subsets of 3 or 4 taxa. However, these methods often carry the assumption of a constant substitution rate across lineages and genes, which is commonly violated in many groups. In this work, we quantify the effects of rate variation on the D test (also known as ABBA-BABA test), the D3 test, and HyDe. All three tests are used widely across a range of taxonomic groups, in part because they are very fast to compute. We consider rate variation across species lineages, across genes, their lineage-by-gene interaction, and residual variation across gene-tree edges. We do so by simulating gene trees within species networks according to a birth-death-hybridization process so as to capture a range of realistic species phylogenies...

Phylogenetic relationships among recently diverged species are often difficult to resolve due to insufficient phylogenetic signal in available markers and/or conflict among gene trees. Here we explore the use of reduced-representation genome sequencing, specifically in the form of restriction-site associated DNA (RAD), for phylogenetic inference and the detection of ancestral hybridization in non-model organisms. As a case study, we investigate Pedicularis section Cyathophora, a systematically recalcitrant clade of flowering plants in the broomrape family (Orobanchaceae). Two methods of phylogenetic inference, maximum likelihood and Bayesian concordance, were applied to data sets that included as many as 40,000 RAD loci. Both methods yielded similar topologies that included two major clades: a "rex-thamnophila" clade, composed of two species and several subspecies with relatively low floral diversity, and geographically widespread distributions at lower elevations, and a "superba" clade, composed of three species characterized by relatively high floral diversity and isolated geographic distributions at higher elevations. Levels of molecular divergence between subspecies in the rex-thamnophila clade are similar to those between species in the superba clade. Using Patterson's D-statistic test, including a novel extension of the method that enables finer-grained resolution of introgression among multiple candidate taxa by removing the effect of their shared ancestry, we detect significant introgression among nearly all taxa in the rex-thamnophila clade, but not between clades or among taxa within the superba clade. These results suggest an important role for geographic isolation in the emergence of species barriers, by facilitating local adaptation and differentiation in the absence of homogenizing gene flow.

List of samples used with information about species, locality, date of collection, collector, and institution where collections are stored. (XLS 34 kb)

Introgression is now commonly reported in studies across the Tree of Life, aided by recent advancements in data collection and analysis. Nevertheless, researchers working with non‐model species lacking reference genomes may be stymied by a mismatch between available resources and methodological demands. In this study, we demonstrate a fast and simple approach for inferring introgression using RADseq data, and apply it to a case study involving spiny lizards (Sceloporus) from northeastern México. First, we find evidence for recurrent mtDNA introgression between the two focal species based on patterns of mito‐nuclear discordance. We then test for nuclear introgression by exhaustively applying the "five‐taxon" D‐statistic (DFOIL) to all relevant individuals sampled for RADseq data. In our case, this exhaustive approach (dubbed "ExDFOIL") entails testing up to ~250,000 unique four‐taxon combinations of individuals across species. To facilitate use of this ExDFOIL approach, we provide scripts for many relevant tasks, including the selection of appropriate four‐taxon combinations, execution of DFOIL tests in parallel, and visualization of introgression results in phylogenetic and geographic space. Using ExDFOIL, we find evidence for ancient introgression between the focal species. Furthermore, we reveal geographic variation in patterns of introgression that is consistent with patterns of mito‐nuclear discordance and with recurrent introgression. Overall, our study demonstrates that the combination of DFOIL and RADseq data can effectively detect introgression under a variety of sampling conditions (for individuals, populations, and loci). Importantly, we also find evidence that batch‐specific error and linkage in RADseq data may mislead inferences of introgression under certain conditions.

The CMS Program Statistics - Medicare Part D tables provide use and Part D drug costs by type of Part D plan (stand-alone prescription drug plan and Medicare Advantage prescription drug plan). For additional information on enrollment, providers, and Medicare use and payment, visit the CMS Program Statistics page. These data do not exist in a machine-readable format, so the view data and API options are not available. Please use the download function to access the data. Below is the list of tables: MDCR UTLZN D 1. Medicare Part D Utilization: Average Annual Prescription Drug Fills by Type of Plan, Low Income Subsidy (LIS) Eligibility, and Generic Dispensing Rate, Yearly Trend MDCR UTLZN D 2. Medicare Part D Utilization: Average Annual Gross Drug Costs Per Part D Enrollee, by Type of Plan, Low Income Subsidy (LIS) Eligibility, and Brand/Generic Drug Classification, Yearly Trend MDCR UTLZN D 3. Medicare Part D Utilization: Average Annual Gross Drug Costs Per Part D Enrollee, by Type of Plan, Low Income Subsidy (LIS) Eligibility, and Brand/Generic Drug Classification, Yearly Trend MDCR UTLZN D 4. Medicare Part D Utilization: Average Annual Prescription Drug Fills and Average Annual Gross Drug Cost Per Part D Enrollee, by Type of Plan and Demographic Characteristics MDCR UTLZN D 5. Medicare Part D Utilization: Average Annual Prescription Drug Fills and Average Annual Gross Drug Cost Per Part D Utilizer, by Type of Plan and Demographic Characteristics MDCR UTLZN D 6. Medicare Part D Utilization: Average Annual Prescription Drug Fills and Average Annual Gross Drug Cost Per Part D Enrollee, by Type of Plan, by Area of Residence MDCR UTLZN D 7. Medicare Part D Utilization: Average Annual Prescription Drug Fills and Average Annual Gross Drug Cost Per Part D Utilizer, by Type of Plan, by Area of Residence MDCR UTLZN D 8. Medicare Part D Utilization: Number of Part D Utilizers and Average Annual Prescription Drug Fills by Type of Part D Plan, Low Income Subsidy (LIS) Eligibility, and Part D Coverage Phase, Yearly Trend MDCR UTLZN D 9. Medicare Part D Utilization: Number of Part D Utilizers and Drug Costs by Type of Part D Plan, Low Income Subsidy (LIS) Eligibility, and Part D Coverage Phase, Yearly Trend MDCR UTLZN D 10. Medicare Part D Utilization: Number of Part D Utilizers, Average Annual Prescription Drug Events (Fills) and Average Annual Gross Drug Cost Per Part D Utilizer, by Part D Coverage Phase and Demographic Characteristics MDCR UTLZN D 11. Medicare Part D Utilization: Number of Part D Utilizers, Average Annual Prescription Drug Fills and Average Annual Gross Drug Cost Per Part D Utilizer, by Part D Coverage Phase and Area of Residence

Distribution of gene tree divergence times for all goose species. All distributions show a single peak, indicating gene flow during divergence. The divergence time of several gene trees was close to zero, suggesting low levels of recent gene flow between certain species. Final three figures represent the three subspecies of Brent Goose, which is depicted in the lower right panel. (ZIP 2715Â kb)

Despite being dominant elements of understory communities in the coniferous forests of western North America, phylogenetic relationships among bilberries (Vaccinium section Myrtillus) remain unresolved. Morphological delimitation among most western bilberry species is tenuous and traditionally employed molecular sources of phylogenetic information have yielded insufficient variability. Moreover, these species are hypothesized to have undergone extensive introgression. We used RADseq data analyzed under maximum likelihood species tree estimation to examine the influence of introgression on relationships among Vaccinium myrtillus, V. scoparium, and V. caespitosum. Additionally, we used these data to assess whether the populations of V. myrtillus disjunct between North America and Eurasia are monophyletic and should continue to be recognized as conspecific. Significant genome-wide introgression, as determined through D-statistic analyses, was detected between North American samples of V. myrtillus and V. caespitosum, and to a lesser extent, between V. myrtillus and V. scoparium. No significant D-values were detected between V. scoparium and V. caespitosum. Accessions of Vaccinium myrtillus from Eurasia and North America were recovered as non-monophyletic, prompting our proposed resurrection of V. oreophilum for North American material. The long-assumed sister species relationship between V. oreophilum and V. scoparium was not recovered in our analysis. Instead, V. oreophilum and V. caespitosum were inferred to be sister taxa. This study reveals considerable introgression detectable in the evolutionary history of western North American bilberries and demonstrates the utility of RADseq data to resolve species level relationships in groups that undergo reticulate evolution such as Vaccinium.

In 2024, 23.4 percent of Medicare's Part D beneficiaries were insured through United Healthcare. Part D covers prescription drugs and must be separately enrolled for beneficiaries in traditional Medicare plans in the United States. This statistic shows the distribution of Medicare Part D enrollment in 2024, by firm.

Statistical table of the number of cases by regions, age groups, and gender starting from 2003 (Disease name: Acute Viral Hepatitis D, Date type: Onset date, Case type: Confirmed case, Source of infection: Domestic, Imported)

Hydrographic and Impairment Statistics (HIS) is a National Park Service (NPS) Water Resources Division (WRD) project established to track certain goals created in response to the Government Performance and Results Act of 1993 (GPRA). One water resources management goal established by the Department of the Interior under GRPA requires NPS to track the percent of its managed surface waters that are meeting Clean Water Act (CWA) water quality standards. This goal requires an accurate inventory that spatially quantifies the surface water hydrography that each bureau manages and a procedure to determine and track which waterbodies are or are not meeting water quality standards as outlined by Section 303(d) of the CWA. This project helps meet this DOI GRPA goal by inventorying and monitoring in a geographic information system for the NPS: (1) CWA 303(d) quality impaired waters and causes; and (2) hydrographic statistics based on the United States Geological Survey (USGS) National Hydrography Dataset (NHD). Hydrographic and 303(d) impairment statistics were evaluated based on a combination of 1:24,000 (NHD) and finer scale data (frequently provided by state GIS layers).

The statistic shows 130 chemical companies with the highest research and development spending in 2009, by country. In the U.S., 40 chemical companies spent a total of 7,252 million euros on research and development in 2009.

N, number of sequences; S, number of SNPs (excluding insertion-deletions); π, nucleotide diversity estimated in DnaSP; θ, most probable estimate in LAMARC; θ(95%), 95% credible intervals; all π and θ are ×103; D, Tajima's D-statistic; D*, Fu and Li's D-statistic; F*, Fu and Li's F-statistic; FST and ΦCT, genetic differentiation between wild boars and domestic pigs; all FST and ΦCT are ×102;*, P

Young species complexes that are widespread across ecologically disparate regions offer important insights into the process of speciation because of their relevance to how local adaptation and gene flow influence diversification. We used mitochondrial DNA and up to 28,152 genome-wide SNPs from polytypic barking frogs (Craugastor augusti complex) to infer phylogenetic relationships and test for the signature of introgressive hybridization among diverging lineages. Our phylogenetic reconstructions suggest (1) a rapid Pliocene-Pleistocene radiation that produced at least nine distinct lineages and (2) that geographic features of the arid Central Mexican Plateau contributed to two independent northward expansions. Despite clear lineage differentiation (many private alleles and high between-lineage Fst scores), D-statistic tests, which differentiate introgression from ancestral polymorphism, allowed us to identify two putative instances of reticulate gene flow. Partitioned D-statistics provided evidence that these events occurred in the same direction between clades but at different points in time. After correcting for geographic distance, we found that lineages involved in hybrid gene flow interactions had higher levels of genetic variation than independently evolving lineages. These findings suggest that the nature of hybrid compatibility can be conserved over long periods of evolutionary time and that hybridization between diverging lineages may contribute to standing levels of genetic variation.

Background: Porous species boundaries can be a source of conflicting hypotheses, particularly when coupled with variable data and/or methodological approaches. Their impacts can often be magnified when non-model organisms with complex histories of reticulation are investigated. One such example is the genus Catostomus (Osteichthys, Catostomidae), a freshwater fish clade with conflicting morphological and mitochondrial phylogenies. The former is hypothesized as reflecting the presence of admixed genotypes within morphologically distinct lineages, whereas the latter is interpreted as the presence of distinct morphologies that emerged multiple times through convergent evolution. We tested these hypotheses using multiple methods, to including multispecies coalescent and concatenated approaches. Patterson's D-statistic was applied to resolve potential discord, examine introgression, and test the putative hybrid origin of two species. We also applied naïve binning to explore potential effects of concatenation. Results: We employed 14,007 loci generated from ddRAD sequencing of 184 individuals to derive the first highly supported nuclear phylogeny for Catostomus. Our phylogenomic analyses largely agreed with a morphological interpretation,with the exception of the placement of Xyrauchen texanus, which differs from both morphological and mitochondrial phylogenies. Additionally, our evaluation of the putative hybrid species C. columbianus revealed a lack introgression and instead matched the mitochondrial phylogeny. Furthermore, D-statistic tests clarified all discrepancies based solely on mitochondrial data, with agreement among topologies derived from concatenation and multispecies coalescent approaches. Extensive historic introgression was detected across six species-pairs. Potential endemism in the Virgin and Little Colorado Rivers was also apparent, and the former genus Pantosteus was derived as monophyletic, save for C. columbianus. Conclusions: Complex reticulated histories detected herein support the hypothesis that introgression was responsible for conflicts that occurred within the mitochondrial phylogeny, and explains discrepancies found between it and previous morphological phylogenies. Additionally, the hybrid origin of C. columbianus was refuted, but with the caveat that more fine-grain sampling is still needed. Our diverse phylogenomic approaches provided largely concordant results, with naïve binning useful in exploring the single conflict. Considerable diversity was found within Catostomus across southwestern North America, with two drainages [Virgin River (UT) and Little Colorado River (AZ)] reflecting unique composition.

Key Table Information.Table Title.Nonemployer Statistics by Demographics series (NES-D): Statistics for Employer and Nonemployer Firms by Industry and Ethnicity for the U.S., States, Metro Areas, Counties, and Places: 2022.Table ID.ABSNESD2022.AB00MYNESD01B.Survey/Program.Economic Surveys.Year.2022.Dataset.ECNSVY Nonemployer Statistics by Demographics Company Summary.Source.U.S. Census Bureau, 2022 Economic Surveys, Nonemployer Statistics by Demographics.Release Date.2025-05-08.Release Schedule.The Nonemployer Statistics by Demographics (NES-D) is released yearly, beginning in 2017..Sponsor.National Center for Science and Engineering Statistics, U.S. National Science Foundation.Table Universe.Data in this table combines estimates from the Annual Business Survey (employer firms) and the Nonemployer Statistics by Demographics (nonemployer firms).Includes U.S. firms with no paid employment or payroll, annual receipts of $1,000 or more ($1 or more in the construction industries) and filing Internal Revenue Service (IRS) tax forms for sole proprietorships (Form 1040, Schedule C), partnerships (Form 1065), or corporations (the Form 1120 series).Includes U.S. employer firms estimates of business ownership by sex, ethnicity, race, and veteran status from the 2023 Annual Business Survey (ABS) collection. The employer business dataset universe consists of employer firms that are in operation for at least some part of the reference year, are located in one of the 50 U.S. states, associated offshore areas, or the District of Columbia, have paid employees and annual receipts of $1,000 or more, and are classified in one of nineteen in-scope sectors defined by the 2022 North American Industry Classification System (NAICS), except for NAICS 111, 112, 482, 491, 521, 525, 813, 814, and 92 which are not covered.Data are also obtained from administrative records, the 2022 Economic Census, and other economic surveys. Note: For employer data only, the collection year is the year in which the data are collected. A reference year is the year that is referenced in the questions on the survey and in which the statistics are tabulated. For example, the 2023 ABS collection year produces statistics for the 2022 reference year. The "Year" column in the table is the reference year..Methodology.Data Items and Other Identifying Records.Total number of employer and nonemployer firmsTotal sales, value of shipments, or revenue of employer and nonemployer firms ($1,000)Number of nonemployer firmsSales, value of shipments, or revenue of nonemployer firms ($1,000)Number of employer firmsSales, value of shipments, or revenue of employer firms ($1,000)Number of employeesAnnual payroll ($1,000)These data are aggregated by the following demographic classifications of firm for:All firms Classifiable (firms classifiable by sex, ethnicity, race, and veteran status) Ethnicity Hispanic Equally Hispanic/non-Hispanic Non-Hispanic Unclassifiable (firms not classifiable by sex, ethnicity, race, and veteran status) Definitions can be found by clicking on the column header in the table or by accessing the Economic Census Glossary..Unit(s) of Observation.The reporting units for the NES-D and the ABS are companies or firms rather than establishments. A company or firm is comprised of one or more in-scope establishments that operate under the ownership or control of a single organization..Geography Coverage.The 2022 data are shown for the total of all sectors (00) and the 2- to 6-digit NAICS code levels for:United StatesStates and the District of ColumbiaIn addition, the total of all sectors (00) NAICS and the 2-digit NAICS code levels for:Metropolitan Statistical AreasMicropolitan Statistical AreasMetropolitan DivisionsCombined Statistical AreasCountiesEconomic PlacesFor information about geographies, see Geographies..Industry Coverage.The data are shown for the total of all sectors ("00"), and at the 2- through 6-digit NAICS code levels depending on geography. Sector "00" is not an official NAICS sector but is rather a way to indicate a total for multiple sectors. Note: Other programs outside of ABS may use sector 00 to indicate when multiple NAICS sectors are being displayed within the same table and/or dataset.The following are excluded from the total of all sectors:Crop and Animal Production (NAICS 111 and 112)Rail Transportation (NAICS 482)Postal Service (NAICS 491)Monetary Authorities-Central Bank (NAICS 521)Funds, Trusts, and Other Financial Vehicles (NAICS 525)Office of Notaries (NAICS 541120)Religious, Grantmaking, Civic, Professional, and Similar Organizations (NAICS 813)Private Households (NAICS 814)Public Administration (NAICS 92)For information about NAICS, see North American Industry Classification System..Sampling.NES-D nonemployer data are not conducted through sampling. Nonemployer Statistics (NES) data originate from statistical information obtained through business income tax records that the Internal Revenue Service (IRS) provides to the...