Bayesian optimization for genomic selection: a method for discovering the best genotype among a large number of candidates

Key message

A new pre-breeding strategy based on an optimization algorithm is proposed and evaluated via simulations. This strategy can find superior genotypes with less phenotyping effort.

Abstract

Genomic prediction is a promising approach to search for superior genotypes among a large number of accessions in germplasm collections preserved in gene banks. When some accessions are phenotyped and genotyped, a prediction model can be built, and the genotypic values of the remaining accessions can be predicted from their marker genotypes. In this study, we focused on the application of genomic prediction to pre-breeding, and propose a novel strategy that would reduce the cost of phenotyping needed to discover better accessions. We regarded the exploration of superior genotypes with genomic prediction as an optimization problem, and introduced Bayesian optimization to solve it. Bayesian optimization, that samples unobserved inputs according to the expected improvement (EI) as a selection criterion, seemed to be beneficial in pre-breeding. The EI depends on the predicted distribution of genotypic values, whereas usual selection depends only on the point estimate. We simulated a search for the best genotype among candidate genotypes and showed that the EI-based strategy required fewer genotypes to identify the best genotype than the usual and random selection strategy. Therefore, Bayesian optimization can be useful for applying genomic prediction to pre-breeding and would reduce the number of phenotyped accessions needed to find the best accession among a large number of candidates.

     

Rabies among infrequently reported mammalian carnivores in the United States, 1960-2000

Most cases of rabies reported annually in the United States occur among three groups of carnivores--raccoons (Procyon lotor), skunks (Mephitis, Spilogale, and Putorius), foxes (Vulpes, Urocyon, and Alopex)--and among bats (numerous species). However, between 1960 and 2000, a total of 2,851 cases of rabies in 17 other carnivore taxa were reported to the Centers for Disease Control and Prevention, Atlanta, Georgia (USA), from 49 states, the District of Columbia, and Puerto Rico. Three species of these other carnivores (mongooses [Herpestes javanicus], coyotes [Canis latrans], and bobcats [Lynx rufus]) accounted for 92% (2,624/2,851) of the cases reported among other canivorous mammals (OCMs). Most OCMs demonstrated temporal or spatial variation in numbers of reported cases. Tests of specimens from OCMs infected in the United States identified variants of the rabies virus that corresponded with variants associated with the major terrestrial reservoirs within their respective regions of origin. Variants of the rabies virus in samples from mongooses in Puerto Rico could not be distinguished from those in samples from dogs in Puerto Rico by virus typing methods.     

Allocating HIV prevention funds in the United States: recommendations from an optimization model

The Centers for Disease Control and Prevention (CDC) had an annual budget of approximately $327 million to fund health departments and community-based organizations for core HIV testing and prevention programs domestically between 2001 and 2006. Annual HIV incidence has been relatively stable since the year 2000 and was estimated at 48,600 cases in 2006 and 48,100 in 2009. Using estimates on HIV incidence, prevalence, prevention program costs and benefits, and current spending, we created an HIV resource allocation model that can generate a mathematically optimal allocation of the Division of HIV/AIDS Prevention's extramural budget for HIV testing, and counseling and education programs. The model's data inputs and methods were reviewed by subject matter experts internal and external to the CDC via an extensive validation process. The model projects the HIV epidemic for the United States under different allocation strategies under a fixed budget. Our objective is to support national HIV prevention planning efforts and inform the decision-making process for HIV resource allocation. Model results can be summarized into three main recommendations. First, more funds should be allocated to testing and these should further target men who have sex with men and injecting drug users. Second, counseling and education interventions ought to provide a greater focus on HIV positive persons who are aware of their status. And lastly, interventions should target those at high risk for transmitting or acquiring HIV, rather than lower-risk members of the general population. The main conclusions of the HIV resource allocation model have played a role in the introduction of new programs and provide valuable guidance to target resources and improve the impact of HIV prevention efforts in the United States.     

The United States of the United Races: a rejoinder

I respond to a review by C. Matthew Snipp, revisiting how my book connects abolitionist leanings to acceptance of racial mixing in the Early Republic. I reiterate that, contrary to the reviewer's claims, the book does not suggest that the defence of interracial marriage has been a thriving social movement. I correct his reading of my chapter on the Civil War era, referring to both the variety of voices present, and the claims of reformers' opponents, who were the only ones who claimed racial mixing was an aim of the abolitionist movement. Lastly, I defend The United States of the United Races against Professor Snipp's characterization of it as a work anticipating a ‘post-racial’ ideal, embodied by racially mixed people, who would be the end point of the obsolescence of race as a relevant analytic tool.     

A hydrogeography of unregulated streams in the United States and an examination of scale-dependence in some hydrological descriptors

1. Relatively undisturbed streams in continental U.S.A. were classified according to variation in ten ecologically relevant hydrological characteristics. Measures of flow variability and predictability for average conditions, as well as for low- and high-flow extremes, were extracted from long-term (15–58-year) daily streamflow data for 806 streams. 2. Two groups of sites were analysed: all 806 sites and a subset of 420 ‘best’ sites. For each group, cluster analysis identified ten distinctive stream types, seven permanent and three intermittent. The geographical clustering exhibited by the stream types indicated regional differences in climatic and geological features. A bootstrapping technique applied to the permanent stream classes showed the majority of them were statistically robust. 3. The derived classification of U.S. streams based on ecologically relevant hydrological characteristics provides a comprehensive catalogue of small to mid-size streams that, according to ecological theory, may differ in major aspects of their ecological organization. The classification provides a basis for hypothesis generation and affords an objective framework for matching streams for purposes of comparative ecological investigations. 4. A subset of 118 streams from the ten classification groups was selected to determine whether certain hydrological variables often used by ecologists to make cross-system comparisons are sensitive to the temporal coarseness of the hydrological time series used to derive the variables. The three hydrological variables considered were streamflow predictability, streamflow variability and flood timing. 5. Streamflow predictability (using Colwell’s Index) was calculated at daily, weekly, monthly and seasonal time scales. Estimates of predictability showed either no change across time scales, a gradual and consistent increase across time scales, or a maximum value at the monthly time scale. Coefficient of variation of streamflow was calculated at daily, weekly, monthly, seasonal, and annual time steps. Daily values were always greatest for all streams. Some groups showed minimum variability at the monthly scale, others at the seasonal. Timing of daily peak flows could be detected with 50–90% accuracy across stream groups using coarser grain monthly and annual hydrographic data. 6. Inferences about hydrological similarity among streams across broad geographical scales can be sensitive to choice of time scale used in the hydrological characterization.     

Epidermophyton floccosum infection in a dog from the United States

Epidermophyton floccosum was isolated from a lesion of dermatophytosis on a dog with hyperadrenocorticism. This report is, to our knowledge, the first unequivocally documented case of canine infection in the United States.     

Chinese chestnut production in the United States: Practice,problems, and possible solutions

There are fewer than 162 ha of commercial Chinese chestnut orchards in the United States, with approximately half of these in the Southeast. Large numbers of Chinese chestnut seedlings are planted annually in the United States for home and game food production; however, knowledge about chestnut propagation, fertilization, pests, harvest, storage and marketing is not adequate. There is little commercial marketing of U.S.-grown Chinese chestnuts through roadside markets and local farmers’ markets as the supply is low and unpredictable. However, we yearly import 4.5 mill kg of European chestnuts to satisfy the U.S. market. Successful chestnut orchards will require vegetatively propagated selections, intensive management, mechanical harvesting, and control of insect and disease pests.     

Unexpected patterns of mitochondrial DNA variation among Native Americans from the southeastern United States

Mitochondrial DNA (mtDNA) haplogroups were determined by restriction fragment length polymorphism-typing for 66 individuals from four southeastern North American populations, and the HVS I portion of the mtDNA control region was sequenced in 48 of these individuals. Although populations from the same geographic region usually exhibit similar haplogroup frequency distributions (Lorenz and Smith [1996] Am. J. Phys. Anthropol. 101:307-323; Malhi et al. [2001] Hum. Biol. 73:17-55), those from the Southeast instead exhibit haplogroup frequency distributions that differ significantly from one another. Such divergent haplogroup frequency distributions are unexpected for the Muskogean-speaking southeastern populations, which share many sociocultural traits, speak closely related languages, and have experienced extensive admixture both with each other and with other eastern North American populations. Independent origins, genetic isolation from other Native American populations due to matrilocality, differential admixture, or a genetic bottleneck could be responsible for this heterogeneous distribution of haplogroup frequencies. Within a given haplogroup, however, the HVS I sequences from the four Muskogean-speaking populations appear relatively similar to one another, providing evidence for close relationships among them and for reduced diversity within haplogroups in the Southeast. Given additional archaeological, linguistic, and ethnographic evidence, these results suggest that a genetic bottleneck associated with the historical population decline is the most plausible explanation for such patterns of mtDNA variation.     

Compelling culture: The rhetoric of assimilation among Samoan migrants in the United States

Studies of assimilation tend to focus on whether or not members of a migrant group are adjusting to their new surroundings. This article inverts this focus, asking not how migrant groups adjust, but rather how migrant groups use the language of assimilation to explain generation gaps and other exigencies of migration. This inversion sheds light on the ways a migrant group's epistemological assumptions underlie their understandings of cultural identity, and shape how they might respond to dilemmas caused by migration. Building upon ethnographic fieldwork among Samoan migrants in the United States, the article explores how and why community workers use the rhetoric of assimilation to teach Samoan parents how to raise children in the US context.     

Spouse selection in Canada, 1921-78: an examination by age, sex and religion

This paper presents time series data on spouse selection in Canada for the period 1921-1978. Homogamous and endogamous trends are examined by age, sex, and religion. In the case of religious endogamy, most groups have shown decreasing proportions of marriages. There are also considerable differences in rates of endogamy among religious groups, and these differences have largely persisted over time. Until 1971, the proportions of brides marrying older and younger grooms decreased, while the proportion marrying the same age increased, after which these trends reversed. Younger males increasingly tended to select brides of their own age group until the 1960s, while older males have been increasingly heterogamous since World War II. While these changes in spouse selection have been examined with respect to changes in the unmarried population, the relation between the 2 trends is not clear, and it is difficult to account fully for the observed trends in spouse selection with respect to age.     

Hwabyung: The construction of a korean popular illness among korean elderly immigrant women in the United States

The cultural construction of Hwabyung, a Korean culture-bound syndrome, is explored among a sample of 20 elderly Korean immigrant women in the United States. Hwabyung results when distressed emotions associated with the specifically Korean way of perceiving and reacting to intolerable and tragic life situations cause bodily symptoms by interfering with the harmony of Ki (vital energy). Korean elderly immigrants report a broad range of symptoms associated with Hwabyung; they less frequently report the epigastric mass, which had been considered the cardinal symptom by cosmopolitan and traditional medical writers. Hwabyung is treated holistically with psychosocial support from family, spiritual comfort, home and popular remedies, traditional Korean medicine, and biomedical treatments. Hwabyung provides a way of conceptualizing and resolving emotional distress through somatization among Korean elderly immigrant women.     

Involuntary sterilization in the United States: a surgical solution

Although the eugenics movement in the United States flourished during the first quarter of the 20th Century, its roots lie in concerns over the cost of caring for "defective" persons, concerns that first became manifest in the 19th Century. The history of state-supported programs of involuntary sterilization indicates that this "surgical solution" persisted until the 1950s. A review of the archives of prominent eugenicists, the records of eugenic organizations, important legal cases, and state reports indicates that public support for the involuntary sterilization of insane and retarded persons was broad and sustained. During the early 1930s there was a dramatic increase in the number of sterilizations performed upon mildly retarded young women. This change in policy was a product of the Depression. Institutional officials were concerned that such women might bear children for whom they could not provide adequate parental care, and thus would put more demands on strained social services. There is little evidence to suggest that the excesses of the Nazi sterilization program (initiated in 1934) altered American programs. Data are presented here to show that a number of state-supported eugenic sterilization programs were quite active long after scientists had refuted the eugenic thesis.     

Seasonal sunshine and vitamin D: a possible explanation for differences in European and United States birth patterns

This study tests whether seasonal differences in the United States and European sunshine is associated with human birth patterns. Birth data are adjusted for 31-day months, leap years, and an annual percentage. Clear observations and birth indices are correlated for European and U.S. cities. With 2-month exposure to clearness, r-values are Chicago (0.63), Bismarck (0.81), Dallas (0.86), Thessaloniki (0.66), and Copenhagen (0.54) and, with 3-month exposure, Amsterdam (0.69). Peak clearness occurs during the autumn for the United States and spring/summer for Europe. Differences in clearness may explain birth pattern differences and reduced U.S. births in the 1930s. Although the effect of vitamin D is plausible, further research is required.     

Estimates of the number of mounted pteridophyte specimens in six major herbaria in the United States

A stratified-random sampling method was used to estimate the number of pteridophyte specimens in six of the largest herbaria in the United states (F, GH/A/NEBC, MO, NY, UC, US). The point estimate of the collection size and the 95% confidence intervals for each herbarium were found to be as follows: US 251,000 (±20,000); NY 201,000 (±20,000); MO 160,000 (±15,000); GH/A/NEBC 124,000 (±12,000); UC 119,000 (±9,000); F 97,000 (±10,000). It is hoped that these numbers will help assess the growth of these collections in the future.