Seasonality and competition select for variable germination behavior in perennials

The common occurrence of within-population variation in germination behavior and associated traits such as seed size has long fascinated evolutionary ecologists. In annuals, unpredictable environments are known to select for bet-hedging strategies causing variation in dormancy duration and germination strategies. Variation in germination timing and associated traits is also commonly observed in perennials, and often tracks gradients of environmental predictability. Although bet-hedging is thought to occur less frequently in long-lived organisms, these observations suggest a role of bet-hedging strategies in perennials occupying unpredictable environments. We use complementary numerical and evolutionary simulation models of within- and among-individual variation in germination behavior in seasonal environments to show how bet-hedging interacts with density dependence, life-history traits, and priority effects due to competitive differences among germination strategies. We reveal substantial scope for bet-hedging to produce variation in germination behavior in long-lived plants, when "false starts" to the growing season results in either competitive advantages or increased mortality risk for alternative germination strategies. Additionally, we find that two distinct germination strategies can evolve and coexist through negative frequency-dependent selection. These models extend insights from bet-hedging theory to perennials and explore how competitive communities may be affected by ongoing changes in climate and seasonality patterns.

Estimating Pan evolutionary history from nucleotide site patterns

Introgression appears increasingly ubiquitous in the evolutionary history of various taxa, including humans. However, accurately estimating introgression is difficult, particularly when 1) there are many parameters, 2) multiple models fit the data well, and 3) parameters are not simultaneously estimated. Here, we use the software Legofit to investigate the evolutionary history of bonobos (Pan paniscus) and chimpanzees (P. troglodytes) using whole genome sequences. This approach 1) ignores within-population variation, reducing the number of parameters requiring estimation, 2) allows for model selection, and 3) simultaneously estimates all parameters. We tabulated site patterns from the autosomes of 71 bonobos and chimpanzees representing all five extant Pan lineages. We then compared previously proposed demographic models and estimated parameters using a deterministic approach. We further considered sex bias in Pan evolutionary history by analyzing the site patterns from the X chromosome. Introgression from bonobos into the ancestor of eastern and central chimpanzees and from western into eastern chimpanzees best explained the autosomal site patterns. This second event was substantial with an estimated 0.21 admixture proportion. Estimates of effective population size and most divergence dates are consistent with previous findings; however, we observe a deeper divergence within chimpanzees at 987 ka. Finally, we identify male-biased reproduction in Pan evolutionary history and suggest that western to eastern chimpanzee introgression was driven by western males mating with eastern females.

Trait variation between and within Andes and coastal mountain ranges in the iconic South American tree Araucaria araucana in Chile

As global commitments to restoration are underway, science is needed to support capacity to achieve meaningful gains for ecosystems and human communities. In Chile, identification and generation of appropriate plant material is a barrier to achieving major restoration goals under the Paris Climate Agreement. Understanding genetic differentiation among plant populations is needed to maximize restoration success. For Araucaria araucana, a highly threatened iconic South American tree, this information is greatly needed to guide restoration and conservation efforts because this species occurs across a strong climate gradient. We grew seedlings from 12 populations of A. araucana across its range in Chile in a common garden to assess regional (coastal versus Andes mountain ranges) and population variation in key plant traits and relate this variation to environmental variables. We demonstrate that A. araucana is differentiated within regions and populations across its range in Chile by a suite of traits, particularly branch number and length (showing plant architectural differences) and needle width (showing leaf investment differences). We show that this variation is at least partly explained by climate and soil variables, with the most variation explained by differences between regions in temperature annual range. Thus, we recommend that restoration efforts focus on conserving genetic variation among and within regions and their populations and preventing the translocations of genotypes between coastal and Andes populations.

Multimodal bioinformatic analyses of the neurodegenerative disease-associated TECPR2 gene reveal its diverse roles

BackgroundLoss of tectonin β-propeller repeat-containing 2 (TECPR2) function has been implicated in an array of neurodegenerative disorders, yet its physiological function remains largely unknown. Understanding TECPR2 function is essential for developing much needed precision therapeutics for TECPR2-related diseases.MethodsWe leveraged considerable amounts of functional data to obtain a comprehensive perspective of the role of TECPR2 in health and disease. We integrated expression patterns, population variation, phylogenetic profiling, protein-protein interactions and regulatory network data for a minimally biased multimodal functional analysis. Genes and proteins linked to TECPR2 via multiple lines of evidence were subject to functional enrichment analyses to identify molecular mechanisms involving TECPR2.ResultsTECPR2 was found to be part of a tight neurodevelopmental gene expression programme that includes KIF1A, ATXN1, TOM1L2 and FA2H, all implicated in neurological diseases. Functional enrichment analyses of TECPR2-related genes converged on a role in late autophagy and ribosomal processes. Large-scale population variation data demonstrated that this role is non-redundant.ConclusionsTECPR2 might serve as an indicator for the energy balance between protein synthesis and autophagy, and a marker for diseases associated with their imbalance, such as Alzheimer’s disease and Huntington’s disease. Specifically, we speculate that TECPR2 plays an important role as a proteostasis regulator during synaptogenesis, highlighting its importance in developing neurons. By advancing our understanding of TECPR2 function, this work provides an essential stepping stone towards the development of precision diagnostics and targeted treatment options for TECPR2-related disorders.

Socioecology of the Australian Tree Skink (Egernia striolata)

There is great diversity in social behavior across the animal kingdom. Understanding the factors responsible for this diversity can help inform theory about how sociality evolves and is maintained. The Australian Tree Skink (Egernia striolata) exhibits inter- and intra-population variability in sociality and is therefore a good system for informing models of social evolution. Here, we conducted a multi-year study of a Tree Skink population to describe intra-population variation in the social organization and mating system of this species. Skinks aggregated in small groups of 2–5 individuals, and these aggregations were typically associated with shared shelter sites (crevices and hollows within rocks and trees). Aggregations were typically made up of one or more adult females and, often, one male and/or juvenile(s). Social network and spatial overlap analyses showed that social associations were strongly biased toward kin. Tree skinks also exhibited high site fidelity regardless of age or sex. There were high levels of genetic monogamy observed with most females (87%) and males (68%) only breeding with a single partner. Our results indicate that Tree Skinks reside in small family groups and are monogamous, which corresponds with existing research across populations. Similar to previous work, our study area consisted of discrete habitat patches (i.e., rock outcrops, trees, or both), which likely limits offspring dispersal and promotes social tolerance between parents and their offspring. Our study clearly demonstrates that there is intra-population variability in Tree Skink social behavior, but it also provides evidence that there is a high degree of inter-population consistency in sociality across their geographic range. We also highlight promising possible avenues for future research, specifically discussing the importance of studying the nature and extent of Tree Skink parental care and quantifying the fitness outcomes of kin-based sociality in this species, which are topics that will further our understanding of the mechanisms underlying variation in vertebrate social behavior.

Population variation in Y-chromosome microdeletion and its role in the evaluation of male infertility management: a systematic review

Background: Infertility has been a significantly growing problem worldwide, affecting approximately 10-15% of couples within reproductive age. Among the many causes of male infertility, Y-chromosome microdeletion is considered one of the most frequent genetic causes. Thus, this systematic review was constructed to determine the prevalence of Y-chromosome microdeletion and the population variations in the different types of Y-chromosome microdeletions. Methods: We searched the PubMed, Scielo, and Science Direct databases to obtain articles that addressed the frequency of Y-chromosome microdeletion and male infertility. We identified 14 articles that originated from China, India, Iran, Brazil, Indonesia, North America, South Korea, and Slovakia, and the vital information collected included the year of publication, authors, number of patients with different types of Y-chromosome microdeletions, and the proportion of microdeletion in the major affected sub-regions of the Y-chromosome. Results: In this review, we attempted to highlight the variation in the frequency of Y-chromosome microdeletion in different geographical populations. The highest and lowest frequencies of Y-chromosome microdeletion were found in Indonesian (23.94%) and Slovakian (3.5%) populations, respectively. Conclusion: In conclusion, Y-chromosome microdeletion was undeniably found to be one of the leading genetic causes of male infertility. Azoospermic factor c (AZFc) microdeletion was the most frequent type of Y-chromosome microdeletion, typically presenting in patients with various clinical manifestations that ranged from oligozoospermia to azoospermia and exhibiting the highest chance for sperm retrieval. This review will undoubtedly help clinicians in providing a more accurate consultation to their patients and determining the success rates of assisted reproductive technology.

Health Behaviors in the LGB+ Population: Variation Across Adulthood

Health behaviors, which predict physical and mental health, are patterned by social factors, with some groups engaging in more health-enhancing behaviors than others. LGB+ people face more economic and social barriers to participation in healthy behaviors, along with the stress of discrimination that could lead to unhealthy behaviors to cope. Although some studies have examined variation in health behaviors by sexual identity, they focus almost exclusively on adolescents and young adults. However, such differences may decline across adulthood, as stress related to sexual identity declines with age among LGB+ individuals. Addressing this issue, we use data from the National Health Interview Survey (2016-2018) to examine differences by sexual identity in substance use, weight-related behaviors, healthcare utilization, and sleep. We compare the patterns across three age groups – young, middle-aged, and older adults. Results for each health behavior reveal that differences by sexual identity are indeed greatest among young adults. The magnitude is smaller in middle age, and no significant differences by sexual minority status are observed at older ages.

Genetic Diversity and Population Structure of Dendrobium Nobile in Southwest of China Based On Genotyping-by-Sequencing

Dendrobium nobile Lindl. is one of the most important Orchid plants worldwide. The genotype-by-sequencing (GBS) method has now been widely used to access genetic diversity because of its high-throughput and cost-effective in molecular markers. The goal of this study was to employ the GBS technique for diversity evaluation of D. nobile and determine genetic differences between populations. A total of 129 accessions of D. nobile collected originally between 2019 and 2020 from 10 imitation-wild cultivated populations growing in Sichuan, Guizhou and Yunnan of southwestern China were sequenced, a total of 135G clean reads and a total of 836,786 SNPs of high quality data was yielded and were used for final analysis of genetic diversity and population structure. The quality value 20(Q20) ≥ 92.61%, the quality value 30(Q30) ≥ 82.38%. The GC contents distributed between 37.58% and 38.82%. It was also found that more transitions than transversions, and the ratio of transition/transversion varied from 1.804 to 1.911. By the methods of STRUCTURE, the most appropriate number was found to be k=3, all accessions of D. nobile were classified into three groups, excepts for 14 accessions belonging to admixed group. Phylogenetic tree and principal component analysis (PCA) were consistent with the result. The first two principal components explained a total of 23.25% of the variation by PCA. The genetic diversity of ML population showed the lower genetic diversity as indicated by the effective number of alleles (Ne) = 1.287, polymorphism information content (PIC) = 0.141, and Shannon's information index (I) = 0.205, while WT population showed slightly higher genetic diversity by the Ne =1.512, PIC =0.256, and I =0.360. ML population and other nine populations (FB, FM, FX, LJ, SJ, SP, WL, WT and XM) were the most divergent between them respectively owing to all pairwise Fst values above 0.25, while FM population and FX population were considered identical because the pairwise Fst value was 0.0 between the two populations. Correlation analysis showed that highly significant correlation was observed between genetic distance and actual geographical distance (r = 0.854, P < 0.0001), indicating that the genetic differentiation of the 10 D.nobile populations conformed to the geographical isolation model. Analysis of molecular variance (AMOVA) revealed that the genetic variation was greater within populations (87.8%) than among populations (12.2%). This confirmed that intra-population variation was the main source of genetic variation in 10 D. nobile populations. The results also showed that Nm = 1.799 > 1, indicating that there was gene exchange between different populations. Analysis of unweighted pair-group method with arithmetic mean (UPGMA) suggested that the 10 populations were classified into three groups (Group I, Group II and Group III), Group III could be further divided into two subgroups (Group IIIa and Group IIIb). The results will not only provide valuable information for the level of genetic diversity of D.nobile growing in southwestern of China but also help for formulation of strategies for resource protection and utilization. Moreover, GBS appears as an efficient tool to detect intra-population variation.

The effects of weak selection on neutral diversity at linked sites

The effects of selection on variability at linked sites have an important influence on levels and patterns of within-population variation across the genome. Most theoretical models of these effects have assumed that selection is sufficiently strong that allele frequency changes at the loci concerned are largely deterministic. These models have led to the conclusion that directional selection for new selectively favorable mutations, or against recurrent deleterious mutations, reduces nucleotide site diversity at linked neutral sites. Recent work has shown, however, that fixations of weakly selected mutations, accompanied by significant stochastic changes in allele frequencies, can sometimes cause higher diversity at linked sites when compared with the effects of fixations of neutral mutations. The present paper extends this work by deriving approximate expressions for the mean times to loss and fixation of mutations subject to selection, and analysing the conditions under which selection increases rather than reduces these times. Simulations are used to examine the relations between diversity at a neutral site and the fixation and loss times of mutations at a linked site subject to selection. It is shown that the long-term level of neutral diversity can be increased over the equilibrium expectation in the absence of selection by recurrent fixations and losses of linked, weakly selected dominant or partially dominant favorable mutations, and by linked recessive or partially recessive deleterious mutations. The results are used to examine the conditions under which associative overdominance, as opposed to background selection, is likely to operate.

A Complete Pedigree-Based Graph Workflow for Rare Candidate Variant Analysis

Methods that use a linear genome reference for genome sequencing data analysis are reference biased. In the field of clinical genetics for rare diseases, a resulting reduction in genotyping accuracy in some regions has likely prevented the resolution of some cases. Pangenome graphs embed population variation into a reference structure. While pangenome graphs have helped to reduce reference mapping bias, further performance improvements are possible. We introduce VG-Pedigree, a pedigree-aware workflow based on the pangenome-mapping tool of Giraffe (Sirén et al. 2021) and the variant-calling tool DeepTrio (Kolesnikov et al. 2021) using a specially-trained model for Giraffe-based alignments. We demonstrate mapping and variant calling improvements in both single-nucleotide variants (SNVs) and insertion and deletion (INDEL) variants over those produced by alignments created using BWA MEM to a linear-reference and Giraffe mapping to a pangenome graph containing data from the 1000 Genomes Project. We have also adapted and upgraded the deleterious-variant (DV) detecting methods and programs of Gu et al. into a streamlined workflow (Gu et al. 2019). We used these workflows in combination to detect small lists of candidate DVs among 15 family quartets and quintets of the Undiagnosed Diseases Program (UDP). All candidate DVs that were previously diagnosed using the mendelian models covered by the previously published Gu et al. methods were recapitulated by these workflows. The results of these experiments indicate a slightly greater absolute count of DVs are detected in the proband population than in their matched unaffected siblings.