On minimizing assignment errors and the trade-off between false positives and negatives in parentage analysis

Validation of the Turkish version of the Lewy body composite risk score

The Lewy Body Composite Risk Score (LBCRS) has been developed to increase the sensitivity and specificity of the diagnosis attributable to Lewy body pathology outside of specialty centers. We aimed to assess the validity and reliability of the Turkish version of the LBCRS in patients with dementia with Lewy Bodies (DLB) and investigate the discriminative power of the test in Turkish patients with Alzheimer's disease (AD) and DLB, and control group. The sample population (n = 512) comprised DLB (n = 113), DLB-Mild Cognitive Impairment (MCI)(n = 12), AD (n = 42), AD-MCI (n = 21), and control group (n = 324). A significant group difference was observed in the Turkish version of the LBCRS scores of the five groups (p < .001). The Cronbach's α value was 0.82 (95% CI: 0.799-0.868). The test-retest reliability score of the scale was r = 0.94 and p < .001. The subscales of the LBCRS (motor and nonmotor subdomains of the disease) were determined to explain 65.961% of the total variance with an eigenvalue >1. In patients with DLB, the cutoff score of ≥3 showed sensitivity (92%) and specificity (81%) (area under the curve [AUC] = 0.883, 95% CI: 0.815-0.951), p < .001) compared with the AD. Compared to the control group, the cutoff score of ≥3 showed a sensitivity of 98% and specificity of 97% (AUC = 0.994, 95% CI: 0.989-0.999, p < .001). The Turkish version of LBCRS permits accurate diagnosis of DLB with high sensitivity and specificity. Also, it can be useful to inform the caregivers regarding the course of the disease during the follow-up.

Maximum likelihood parentage assignment using quantitative genotypes

The cost of parentage assignment precludes its application in many selective breeding programmes and molecular ecology studies, and/or limits the circumstances or number of individuals to which it is applied. Pooling samples from more than one individual, and using appropriate genetic markers and algorithms to determine parental contributions to pools, is one means of reducing the cost of parentage assignment. This paper describes and validates a novel maximum likelihood (ML) parentage-assignment method, that can be used to accurately assign parentage to pooled samples of multiple individuals-previously published ML methods are applicable to samples of single individuals only-using low-density single nucleotide polymorphism (SNP) 'quantitative' (also referred to as 'continuous') genotype data. It is demonstrated with simulated data that, when applied to pools, this 'quantitative maximum likelihood' method assigns parentage with greater accuracy than established maximum likelihood parentage-assignment approaches, which rely on accurate discrete genotype calls; exclusion methods; and estimating parental contributions to pools by solving the weighted least squares problem. Quantitative maximum likelihood can be applied to pools generated using either a 'pooling-for-individual-parentage-assignment' approach, whereby each individual in a pool is tagged or traceable and from a known and mutually exclusive set of possible parents; or a 'pooling-by-phenotype' approach, whereby individuals of the same, or similar, phenotype/s are pooled. Although computationally intensive when applied to large pools, quantitative maximum likelihood has the potential to substantially reduce the cost of parentage assignment, even if applied to pools comprised of few individuals.

Minimum size limits and the reproductive value of numerous, young, mature female fish

Fisheries management relies on various catch and effort controls to preserve spawning stock biomass and maximize sustainable yields while limiting fishery impacts on marine ecosystems. These include species-specific minimum or maximum size limits to protect either small non-reproductive subadults, a portion of reproductively mature adults, or large highly fecund individuals. Protecting size classes of mature fish is expected to yield a viable source of larvae for replenishing populations and reduce the risk of recruitment overfishing, yet size-specific recruitment contributions have rarely been assessed empirically. Here, we apply genetic parentage analysis to measure the reproductive success of a size-structured population of a commercially important species of coral grouper (Plectropomus maculatus-Serranidae) in no-take marine reserves (NTMRs) in the Great Barrier Reef Marine Park, Australia. Although the per capita reproductive success of individual fish increases rapidly with body length, the numerous young mature female fish, below the minimum size limit (MSL) (38 cm total length), were responsible for generating disproportionately large contributions (36%) towards larval replenishment of both fished and reserve reefs. Our findings indicate that MSLs are an effective harvest control measure to safeguard a portion of the spawning stock biomass for coral grouper and supplement recruitment subsidies assured from NTMRs.

Development and validation of a RAD-Seq target-capture based genotyping assay for routine application in advanced black tiger shrimp (Penaeus monodon) breeding programs

Background

The development of genome-wide genotyping resources has provided terrestrial livestock and crop industries with the unique ability to accurately assess genomic relationships between individuals, uncover the genetic architecture of commercial traits, as well as identify superior individuals for selection based on their specific genetic profile. Utilising recent advancements in de-novo genome-wide genotyping technologies, it is now possible to provide aquaculture industries with these same important genotyping resources, even in the absence of existing genome assemblies. Here, we present the development of a genome-wide SNP assay for the Black Tiger shrimp (Penaeus monodon) through utilisation of a reduced-representation whole-genome genotyping approach (DArTseq).

Results

Based on a single reduced-representation library, 31,262 polymorphic SNPs were identified across 650 individuals obtained from Australian wild stocks and commercial aquaculture populations. After filtering to remove SNPs with low read depth, low MAF, low call rate, deviation from HWE, and non-Mendelian inheritance, 7542 high-quality SNPs were retained. From these, 4236 high-quality genome-wide loci were selected for baits-probe development and 4194 SNPs were included within a finalized target-capture genotype-by-sequence assay (DArTcap). This assay was designed for routine and cost effective commercial application in large scale breeding programs, and demonstrates higher confidence in genotype calls through increased call rate (from 80.2 ± 14.7 to 93.0% ± 3.5%), increased read depth (from 20.4 ± 15.6 to 80.0 ± 88.7), as well as a 3-fold reduction in cost over traditional genotype-by-sequencing approaches.

Conclusion

Importantly, this assay equips the P. monodon industry with the ability to simultaneously assign parentage of communally reared animals, undertake genomic relationship analysis, manage mate pairings between cryptic family lines, as well as undertake advance studies of genome and trait architecture. Critically this assay can be cost effectively applied as P. monodon breeding programs transition to undertaking genomic selection.

Microsatellite Mutation Rate in Atlantic Sturgeon (Acipenser oxyrinchus)

Understanding mutation rates can greatly extend the utility of population and conservation genetic analyses. Herein, we present an estimate of genome-wide microsatellite mutation rate in Atlantic sturgeon (Acipenser oxyrinchus) based on parent-offspring transmission patterns. We screened 307 individuals for parentage and mutation-rate analysis applying 43 variable markers. Out of 13228 allele transfers, 11 mutations were detected, producing a mutation rate of 8.3 × 10-4 per locus per generation (95% confidence interval: 1.48 × 10-3, 4.15 × 10-4). Single-step mutations predominated and there were trends toward mutations in loci with greater polymorphism and allele length. Two of the detected mutations were most probably cluster mutations, being identified in 12 and 28 sibs, respectively. Finally, we observed evidences of polyploidy based on the sporadic presence of 3 or 4 alleles per locus in the genotyped individuals, supporting previous reports of incomplete diploidization in Atlantic sturgeon.

Does sex-biased dispersal account for the lack of geographic and host-associated differentiation in introduced populations of an aphid parasitoid?

Host recognition and use in female parasitoids strongly relies on host fidelity, a plastic behavior which can significantly restrict the host preferences of parasitoids, thus reducing the gene flow between parasitoid populations attacking different insect hosts. However, the effect of migrant males on the genetic differentiation of populations has been frequently ignored in parasitoids, despite its known impact on gene flow between populations. Hence, we studied the extent of gene flow mediated by female and male parasitoids by assessing sibship relationships among parasitoids within and between populations, and its impact on geographic and host-associated differentiation in the aphid parasitoid Aphidius ervi. We report evidences of a high gene flow among parasitoid populations on different aphid hosts and geographic locations. The high gene flow among parasitoid populations was found to be largely male mediated, suggested by significant differences in the distribution of full-sib and paternal half-sib dyads of parasitoid populations.

Validation of microsatellite multiplexes for parentage analysis and species discrimination in two hybridizing species of coral reef fish (Plectropomus spp., Serranidae)

Microsatellites are often considered ideal markers to investigate ecological processes in animal populations. They are regularly used as genetic barcodes to identify species, individuals, and infer familial relationships. However, such applications are highly sensitive the number and diversity of microsatellite markers, which are also prone to error. Here, we propose a novel framework to assess the suitability of microsatellite datasets for parentage analysis and species discrimination in two closely related species of coral reef fish, Plectropomus leopardus and P. maculatus (Serranidae). Coral trout are important fisheries species throughout the Indo-Pacific region and have been shown to hybridize in parts of the Great Barrier Reef, Australia. We first describe the development of 25 microsatellite loci and their integration to three multiplex PCRs that co-amplify in both species. Using simulations, we demonstrate that the complete suite of markers provides appropriate power to discriminate between species, detect hybrid individuals, and resolve parent–offspring relationships in natural populations, with over 99.6% accuracy in parent–offspring assignments. The markers were also tested on seven additional species within the Plectropomus genus with polymorphism in 28–96% of loci. The multiplex PCRs developed here provide a reliable and cost-effective strategy to investigate evolutionary and ecological dynamics and will be broadly applicable in studies of wild populations and aquaculture brood stocks for these closely related fish species.