The Inbreeding Effective Population Number in Dioecious Populations

The inbreeding effective population number in a dioecious population with discrete, nonoverlapping generations is investigated for both autosomal and X-linked loci. The recursion relations for the probabilities of genic identity and the effective population numbers are analyzed and compared in two cases: (i) the offspring identified by sex in the calculation of the probability of common parentage and (ii) the offspring not so identified. Case i gives the correct evolution of the probabilities of identity, but case ii has been more widely studied and applied. A general symmetric framework that reduces the number of parameters is developed and used to examine a wide variety of models of panmixia and monogamy. Cases i and ii agree in many, but not all, models.     

Genome-Wide Estimates of Coancestry,Inbreeding and Effective Population Size in the Spanish Holstein Population

Estimates of effective population size in the Holstein cattle breed have usually been low despite the large number of animals that constitute this breed. Effective population size is inversely related to the rates at which coancestry and inbreeding increase and these rates have been high as a consequence of intense and accurate selection. Traditionally, coancestry and inbreeding coefficients have been calculated from pedigree data. However, the development of genome-wide single nucleotide polymorphisms has increased the interest of calculating these coefficients from molecular data in order to improve their accuracy. In this study, genomic estimates of coancestry, inbreeding and effective population size were obtained in the Spanish Holstein population and then compared with pedigree-based estimates. A total of 11,135 animals genotyped with the Illumina BovineSNP50 BeadChip were available for the study. After applying filtering criteria, the final genomic dataset included 36,693 autosomal SNPs and 10,569 animals. Pedigree data from those genotyped animals included 31,203 animals. These individuals represented only the last five generations in order to homogenise the amount of pedigree information across animals. Genomic estimates of coancestry and inbreeding were obtained from identity by descent segments (coancestry) or runs of homozygosity (inbreeding). The results indicate that the percentage of variance of pedigree-based coancestry estimates explained by genomic coancestry estimates was higher than that for inbreeding. Estimates of effective population size obtained from genome-wide and pedigree information were consistent and ranged from about 66 to 79. These low values emphasize the need of controlling the rate of increase of coancestry and inbreeding in Holstein selection programmes.     

Tests for a Disease-susceptibility Locus allowing for an Inbreeding Coefficient (F)

We begin by discussing the false positive test results that arise because of cryptic relatedness and population substructure when testing a disease susceptibility locus. We extend and evaluate the Hardy-Weinberg disequilibrium (HWD) method, allowing for an inbreeding coefficient (F) in a similar way that Devlin and Roeder (1999) allowed for inbreeding in a case-control study. Then we compare the HWD measure and the common direct measure of linkage disequilibrium, both when there is no population substructure (F = 0) and when there is population substructure (F not = 0), for a single marker. The HWD test statistic gives rise to false positives caused by population stratification. These false positives can be controlled by adjusting the test statistic for the amount of variance inflation caused by the inbreeding coefficient (F). The power loss for the HWD test that arises when controlling for population structure is much less than that which arises for the common direct measure of linkage disequilibrium. However, in the multiplicative model, the HWD test has virtually no power even when allowing for non-zero F.     

Severe Inbreeding and Small Effective Number of Breeders in a Formerly Abundant Marine Fish

In contrast to freshwater fish it is presumed that marine fish are unlikely to spawn with close relatives due to the dilution effect of large breeding populations and their propensity for movement and reproductive mixing. Inbreeding is therefore not typically a focal concern of marine fish management. We measured the effective number of breeders in 6 New York estuaries for winter flounder (Pseudopleuronectes americanus), a formerly abundant fish, using 11 microsatellite markers (6–56 alleles per locus). The effective number of breeders for 1–2 years was remarkably small, with point estimates ranging from 65–289 individuals. Excess homozygosity was detected at 10 loci in all bays (F_IS = 0.169–0.283) and individuals exhibited high average internal relatedness (IR; mean = 0.226). These both indicate that inbreeding is very common in all bays, after testing for and ruling out alternative explanations such as technical and sampling artifacts. This study demonstrates that even historically common marine fish can be prone to inbreeding, a factor that should be considered in fisheries management and conservation plans.     

DNA Polymorphism in a Subdivided Population: The Expected Number of Segregating Sites in the Two-Subpopulation Model

Using the two subpopulation model, the expected numbers of segregating sites in a number of DNA sequences randomly sampled from a subdivided population were examined for several types of population subdivisions. It is shown that, in the case where the pattern of migration is symmetrical such as the finite island model, the expected number of segregating sites is independent of the migration rate when two or three DNA sequences are randomly sampled from the same subpopulation, but depends on the migration rate when more than three DNA sequences are sampled. It is also shown that the population subdivision can increase the amount of DNA polymorphism even in a subpopulation in some cases.     

The Homozygosity Test after a Change in Population Size

The homozygosity of a population will be influenced by any recent change in the population size. The "homozygosity test" of the neutral mutation hypothesis might also be influenced by a population change. A computer simulation method is described that establishes the significance levels of observed homozygosities after a change in population size. Some numerical examples are given.     

Response to Selection and Inbreeding Depression in a Dynamic Population for Amount of Inbreeding

A method for predicting response to selection and inbreeding depression in a dynamic population for amount of inbreeding was derived and illustrated with an example of selection under full-sib mating.     

An Increase in the X-Linked Lethal Mutation Rate Associated with an Unstable Locus in DROSOPHILA MELANOGASTER

The behavior of an unstable allele of the singed-bristle locus on the X chromosome was studied in connection with the occurrence of lethal mutations on that same chromosome. The unstable allele, weak singed (sn^w), is under the control of the P-M system of hybrid dysgenesis and, in the M cytotype, mutates secondarily to extreme singed (sn^e) and to wild type (sn⁺) at high rates. Chromosomes whose sn^w allele had mutated in this fashion sustained lethal mutations at a rate of 3%; whereas, those whose sn^w allele had apparently remained unchanged, acquired lethals at a lower rate, 1.3%. The significant difference between these values indicates a statistical coincidence between the phenomena of sn^w instability and X-linked lethal mutation induction. This coincidence can be explained by postulating that mutations at the singed locus sometimes release a genetic element capable of reinserting elsewhere in the chromosome. Alternately, sn^w instability and lethal induction might be associated because they are the effects of a common cause, perhaps some mutation-inducing substance present in various amounts in the germ cells of dysgenic flies.—The lethals that occurred on chromosomes whose sn^w allele had mutated to sn^e mapped preferentially close to singed. The lethals on the sn^w and sn⁺ chromosomes did not show this concentration on the map. Cytological analysis of samples of all three types of lethal chromosomes indicated that, with one exception, there was no detectable breakage at the singed locus itself. The single instance of breakage at singed was not associated with any change in the singed phenotype. Thus, the instability of sn^w apparently does not involve detectable breakage of the singed locus, or if it does, this breakage is not a common event.     

Expected Linkage Disequilibrium for a Neutral Locus Linked to a Chromosomal Arrangement

The expected value of the squared linkage disequilibrium is derived for a neutral locus associated with a chromosomal arrangement that is maintained in the population by strong balancing selection. For a given value of recombination, the expected squared linkage disequilibrium is shown to decrease as the intensity of selection maintaining the arrangement increases. The transient behavior of the expected square linkage disequilibrium is also derived. This theory applies to loci that are closely linked to inversions in Drosophila species and to loci closely linked to the differential segments of the translocation complexes in ring-forming species of Oenothera. In both cases the strong linkage disequilibria that have been observed in natural populations can be explained by random drift.     

Inbreeding Depression and Inbreeding Avoidance in a Natural Population of Guppies (Poecilia reticulata)

Maintenance of genetic variation in the face of strong natural selection is a long‐standing problem in evolutionary biology. One of the most extreme examples of within‐population variation is the polymorphic, genetically determined color pattern of male Trinidad guppies (Poecilia reticulata). Female mating preference for rare or novel patterns has been implicated as a factor in maintaining this variation. The origin of this preference is not understood, although inbreeding avoidance has been proposed as a mechanism. Inbreeding avoidance is advantageous when populations exhibit inbreeding depression and the opportunity for mating between relatives exists. To determine whether these conditions are met in a natural guppy population, we assessed mating and reproductive patterns using polymorphic molecular markers. Females produced more offspring with less‐related males than with more‐related ones. In addition, females were more likely to have mated with less‐related males, but this trend was only marginally significant. Male heterozygosity was positively correlated with mating success and with the number of offspring sired, consistent with strong inbreeding depression for adult male fitness. These results provide substantial insight into mating patterns of a wild guppy population: strong inbreeding depression occurs, and individuals tend to avoid mating with relatives.     

Copy Number Variation at the APOL1 Locus

Two coding variants in the APOL1 gene (G1 and G2) explain most of the high rate of kidney disease in African Americans. APOL1-associated kidney disease risk inheritance follows an autosomal recessive pattern: The relative risk of kidney disease associated with inheritance of two high-risk variants is 7–30 fold, depending on the specific kidney phenotype. We wished to determine if the variability in phenotype might in part reflect structural differences in APOL1 gene. We analyzed sequence coverage from 1000 Genomes Project Phase 3 samples as well as exome sequencing data from African American kidney disease cases for copy number variation. 8 samples sequenced in the 1000 Genomes Project showed increased coverage over a ~100kb region that includes APOL2, APOL1 and part of MYH9, suggesting the presence of APOL1 copy number greater than 2. We reasoned that such duplications should be enriched in apparent G1 heterozygotes with kidney disease. Using a PCR-based assay, we observed the presence of this duplication in additional samples from apparent G0G1 or G0G2 individuals. The frequency of this APOL1 duplication was compared among cases (n = 123) and controls (n = 255) with apparent G0G1 heterozygosity. The presence of APOL1 duplication was observed in 4.06% of cases and 0.78% controls, preliminary evidence that this APOL1 duplication may alter susceptibility to kidney disease (p = 0.03). Taqman-based copy number assays confirmed the presence of 3 APOL1 copies in individuals positive for this specific duplication by PCR assay, but also identified a small number of individuals with additional APOL1 copies of presumably different structure. These observations motivate further studies to better assess the contribution of APOL1 copy number on kidney disease risk and on APOL1 function. Investigators and clinicians genotyping APOL1 should also consider whether the particular genotyping platform used is subject to technical errors when more than two copies of APOL1 are present.     

The Effective Production of Shikonin by Cultures with an Increased Cell Population

We have studied the efficient production of shikonin derivatives by suspension cultures of Lithospermum erythrorhizon with an increased cell population. The yield of shikonin derivatives was highest (800 mg/liter) when 2.8 g dry wt/liter of the cells was inoculated into the M-2 medium which we had developed for the production, but the excess inoculum lowered the yield.

We investigated suitable conditions for production with the increased cell population. The optimum amount of inoculum rose to 4.9 g dry wt/liter when the concentrations of all the components contained in the M-8 medium, which we developed for increasing the productivity by modification of the M-2 medium, were increased in proportion to the amount of inoculum, and consequently we could increase the yield of the shikonin derivatives from 1400 mg/liter to 1900 mg/liter. Moreover, the increased rate of oxygen supply in addition to the enrichment of the medium made it possible to produce 2300 mg/liter of the shikonin derivatives from a culture for which 5.6 g dry wt/liter of the cells was inoculated.     

Refined Linkage Disequilibrium and Physical Mapping of the Gene Locus for X-Linked Dystonia–Parkinsonism (DYT3)

X-linked dystonia-parkinsonism (XDP) is a recessive disorder characterized by generalized dystonia with some patients exhibiting parkinsonism. The disease gene, DYT3, is located between DXS453 (DXS993) and DXS559, and strongest linkage disequilibrium is found distal to DXS7117 and proximal to DXS559. We have isolated and analyzed four novel polymorphic markers between DXS7117 and DXS559 and, by haplotype analysis, have narrowed the candidate interval to <350 kb. A sequence-ready contig of 700 kb has been constructed spanning DXS7117 to DXS559 and is composed of 35 PACs, BACs, and cosmids. Nine genes and novel ESTs have been mapped into this contig, and mutations in the coding regions and intron-exon borders of two genes have been excluded as the cause of XDP. Several of the other genes and ESTs located within the contig code for proteins implicated in normal brain development and function and are candidates for DYT3.     

The Expected Number of Background Disease Events during Mass Immunization in China

It is critical to distinguish events that are temporarily associated with, but not caused by, vaccination from those caused by vaccination during mass immunization. We performed a literature search in China National Knowledge Infrastructure and Pubmed databases. The number of coincident events was calculated based on its incidence rate and periods after receipt of a dose of hypothesized vaccine. We included background incidences of Guillain-Barré syndrome, anaphylaxis, seizure, sudden adult death syndrome, sudden cardiac death, spontaneous abortion, and preterm labour or delivery. In a cohort of 10 million individuals, 7.71 cases of Guillain-Barré syndrome would be expected to occur within six weeks of vaccination as coincident background cases. Even for rare events, a large number of events can be expected in a short period because of the large population targeted for immunization. These findings may encourage health authorities to screen the safety of vaccines against unpredictable pathogens.     

Gene Copy Number Polymorphisms in an Arbuscular Mycorrhizal Fungal Population

Gene copy number polymorphism was studied in a population of the arbuscular mycorrhizal fungus Glomus intraradices by using a quantitative PCR approach on four different genomic regions. Variation in gene copy number was found for a pseudogene and for three ribosomal genes, providing conclusive evidence for a widespread occurrence of macromutational events in the population.     

The Effective Size of a Subdivided Population

This paper derives the long-term effective size, N(e), for a general model of population subdivision, allowing for differential deme fitness, variable emigration and immigration rates, extinction, colonization, and correlations across generations in these processes. We show that various long-term measures of N(e) are equivalent. The effective size of a metapopulation can be expressed in a variety of ways. At a demographic equilibrium, N(e) can be derived from the demography by combining information about the ultimate contribution of each deme to the future genetic make-up of the population and Wright's F(ST)'s. The effective size is given by N(e) = 1/(1 + var ( &))<(1 - f(STi))/N(i)n>, where n is the number of demes, &(i) is the eventual contribution of individuals in deme i to the whole population (scaled such that σ(i) &(i) = n), and < > denotes an average weighted by &(i)(2). This formula is applied to a catastrophic extinction model (where sites are either empty or at carrying capacity) and to a metapopulation model with explicit dynamics, where extinction is caused by demographic stochasticity and by chaos. Contrary to the expectation from the standard island model, the usual effect of population subdivision is to decrease the effective size relative to a panmictic population living on the same resource.