Heritable and climatic sources of variation in juvenile tree growth in an Austrian common garden experiment of Central European Norway spruce populations

We leveraged publicly available data on juvenile tree height of 299 Central European Norway spruce populations grown in a common garden experiment across 24 diverse trial locations in Austria and weather data from the trial locations and population provenances to parse the heritable and climatic components of tree height variation. Principal component analysis of geospatial and weather variables demonstrated high interannual variation among trial environments, largely driven by differences in precipitation, and separation of population provenances based on altitude, temperature, and snowfall. Tree height was highly heritable and genetic variation for tree height was strongly associated with climatic relationships among population provenances. Modeling the covariance between populations and trial environments based on climatic data increased the heritable signal for tree height.

The mutationathon highlights the importance of reaching standardization in estimates of pedigree-based germline mutation rates

In the past decade, several studies have estimated the human per-generation germline mutation rate using large pedigrees. More recently, estimates for various non-human species have been published. However, methodological differences among studies in detecting germline mutations and estimating mutation rates make direct comparisons difficult. Here, we describe the many different steps involved in estimating pedigree-based mutation rates, including sampling, sequencing, mapping, variant calling, filtering, and how to appropriately account for false-positive and false-negative rates. For each step, we review the different methods and parameter choices that have been used in the recent literature. Additionally, we present the results from a 'Mutationathon', a competition organized among five research labs to compare germline mutation rate estimates for a single pedigree of rhesus macaques. We report almost a two-fold variation in the final estimated rate among groups using different post-alignment processing, calling, and filtering criteria and provide details into the sources of variation across studies. Though the difference among estimates is not statistically significant, this discrepancy emphasizes the need for standardized methods in mutation rate estimations and the difficulty in comparing rates from different studies. Finally, this work aims to provide guidelines for computational and statistical benchmarks for future studies interested in identifying germline mutations from pedigrees.

A comparative study of human glomerular basement membrane thickness using direct measurement and orthogonal intercept methods

Introduction Here we report estimates of glomerular basement membrane (GBM) thickness in the Brazilian population performed using direct (DM) and orthogonal interception methods (OIM), and comment on potential sources of variation among estimates made by different laboratories. Methodology A total of 38 patients, ranging from 3 to 78 years of age, 26 (68%) males and 12 (32%) females, were submitted to kidney biopsy procedures for renal disease diagnosis. Glomeruli were diagnosed with minor histological changes by conventional, immunofluorescence and electron microscopy. GBM thickness was estimated using both DM and OIM methods. Results Estimates of GBM thickness obtained using DM were higher than those obtained by OIM. However, the application of a correction for non-perpendicular membrane sectioning to DM estimates yielded similar results to those obtained under OIM. The estimated GMB thickness using DM after correction was 289 + 44 nm, versus 287 + 48 nm by OIM. No statistically significant differences were detected in GMB thickness, nor with respect to patient age or sex. Conclusions GBM thickness in the studied Brazilian population measured approximately 290 nm. The application of criteria for estimating the shortest distance between the endothelial and podocyte cell membranes with correction for non-perpendicular membrane sectioning can increase the accuracy of GBM thickness estimates using DM and OIM.

Partial Results Regarding the Genetic Determinism of Growth Process in a Native Horse Breed using Wither’s Height

Study of variability in domestic animal populations is the foundation of quantitative genetics. Based on statistical methods, the weights of the total phenotype variation that belong to its different fractions (causal components) are quantified: variation due to gene additive effect, variation due to allelic and non-allelic interactions, variation due to environment (general and special), variation due to genotype-environment interaction and possibly variation due to the association between genotype and environment. In this study, during 2017-2020, we used the method of analysis of variance with two sources of variation. The material was represented by 538 individuals from Hucul horse breed analyzed at 18, 30 and 42 months old). The heritability of character was 0.3402±0.1546 (18 months), 0.5549±0.2225 (30 months), 0.4506±0.1895 (42 months), suggest that this is a hereditary condition that follows a quantitative model of inheritance, where the influence of additive genetic factors is moderate to intense. We can conclude that, in this native breed and for this character, a significant share of the phenotypic value is due to the additive effect of genes.

Isolating salient variations of interest in single-cell transcriptomic data with contrastiveVI

Single-cell RNA sequencing (scRNA-seq) technologies enable a better understanding of previously unexplored biological diversity. Oftentimes, researchers are specifically interested in modeling the latent structures and variations enriched in one target scRNA-seq dataset as compared to another background dataset generated from sources of variation irrelevant to the task at hand. For example, we may wish to isolate factors of variation only present in measurements from patients with a given disease as opposed to those shared with data from healthy control subjects. Here we introduce Contrastive Variational Inference (contrastiveVI; https://github.com/suinleelab/contrastiveVI), a framework for end-to-end analysis of target scRNA-seq datasets that decomposes the variations into shared and target-specific factors of variation. On three target-background dataset pairs we demonstrate that contrastiveVI learns latent representations that recover known subgroups of target data points better than previous methods and finds differentially expressed genes that agree with known ground truths.

Keeping Lagocephalus sceleratus off the Table: Sources of Variation in the Quantity of TTX, TTX Analogues, and Risk of Tetrodotoxication

The invasion of the tetrodotoxin (TTX)-bearing silver-cheeked toadfish and potential poisoning due to its consumption (tetrodotoxication) threatens public safety in the Mediterranean Sea. In this study, TTX and TTX analogues of Lagocephalus sceleratus (Gmelin, 1789) were measured using liquid chromatography tandem mass spectrometry (LC-MS/MS) in fish collected off the island of Crete (Southern Mediterranean). We tested the synergistic effect of a suite of factors potentially affecting toxins’ levels and tetrodotoxication risk using general and generalized linear models, respectively. The type of tissue, geographic origin (Cretan Sea, Libyan Sea), sex, and fish maturity stage were significant predictors of toxin concentrations. Mean TTX was higher in gonads and lower in muscles, higher in the Libyan Sea and in female fish, and lower in juvenile (virgin) fish. The concentration of TTX was also significantly and positively correlated with the concentration of several TTX analogues (4-epiTTX, 4,9-anhydroTTX, 11-deoxyTTX, 5,11/6,11-dideoxyTTX, 5,6,11-trideoxyTTX, 11-norTTX-6-ol). The analysis showed that fish originating from the Libyan Sea had significantly higher probability to cause tetrodotoxication in case of consumption. The variability explained by the models developed in this study was relatively low, indicating that toxin levels are hard to predict and the consumption of L. sceleratus should therefore be avoided.

Heritage Tagalog Phonology and a Variationist Framework of Language Contact

Heritage language variation and change provides an opportunity to examine the interplay of contact-induced and language-internal effects while extending the variationist framework beyond monolingual speakers and majority languages. Using data from the Heritage Language Variation and Change in Toronto Project, we illustrate this with a case study of Tagalog (r), which varies between tap, trill, and approximant variants. Nearly 3000 tokens of (r)-containing words were extracted from a corpus of spontaneous speech of 23 heritage speakers in Toronto and 9 homeland speakers in Manila. Intergenerational and intergroup analyses were conducted using mixed-effects modeling. Results showed greater use of the approximant among second-generation (GEN2) heritage speakers and those that self-report using English more. In addition, the distributional patterns remain robust and the approximant appears in more contexts. We argue that these patterns reflect an interplay between internal and external processes of change. We situate these findings within a framework for distinguishing sources of variation in heritage languages: internal change, identity marking and transfer from the dominant language.

Nutraceutical profiles of apricots (Prunus armeniaca L.) as a source of fruit quality traits for breeding

Aim of study: In a social context of increasing concern about healthy diets, the development of new varieties with enhanced content in nutraceutical compounds is an important objective of the fruit breeding programs currently developed. In this sense, apricot is a fruit crop very appreciated by consumers worldwide due to its organoleptic characteristics, but also plays an important role in human nutrition due to its content of phytocompounds as sugars, organic acids, vitamins and polyphenols. Area of study: The identification of sources of variation for these traits could be useful for apricot breeding worldwide. Material and methods: New selections from the apricot breeding program carried out at the Instituto Valenciano de Investigaciones Agrarias (IVIA, Spain) and traditional varieties have been analysed aimed at identifying sources of genetic variation for fruit quality. For this purpose, sugar content, organic acids and ascorbic acid were studied during three crop years. Main results: Results revealed sucrose and glucose as the major sugars, malic and citric acid as the main organic acids, and diverse ascorbic acid content among the cultivars studied. Research highlights: Some accessions point as potential sources to increase fruit quality. In addition, the study showed that apricot peel is an excellent source of nutraceutical compounds. Moreover, this study opens up new possibilities to study the genetic control of these traits in apricot in the future.

Interaction Effects in Cross-Lagged Panel Models: SEM with Latent Interactions Applied to Work-Family Conflict, Job Satisfaction, and Gender

Researchers often combine longitudinal panel data analysis with tests of interactions (i.e., moderation). A popular example is the cross-lagged panel model (CLPM). However, interaction tests in CLPMs and related models require caution because stable (i.e., between-level, B) and dynamic (i.e., within-level, W) sources of variation are present in longitudinal data, which can conflate estimates of interaction effects. We address this by integrating literature on CLPMs, multilevel moderation, and latent interactions. Distinguishing stable B and dynamic W parts, we describe three types of interactions that are of interest to researchers: 1) purely dynamic or WxW; 2) cross-level or BxW; and 3) purely stable or BxB. We demonstrate estimating latent interaction effects in a CLPM using a Bayesian SEM in Mplus to apply relationships among work-family conflict and job satisfaction, using gender as a stable B variable. We support our approach via simulations, demonstrating that our proposed CLPM approach is superior to a traditional CLPMs that conflate B and W sources of variation. We describe higher-order nonlinearities as a possible extension, and we discuss limitations and future research directions.