A general approach to single-nucleotide polymorphism discovery

Computational Analysis of Single Nucleotide Polymorphisms in Human HIC1 Gene

Background A putative tumor suppressor gene called HIC1 (hypermethylated in cancer) is situated at 17p13.3, a locus where the allelic loss occurs often in human malignancies, including breast cancer. Hypermethylated in cancer 1 protein is a protein that in humans is encoded by the HIC1 gene and it's a Homo sapiens (Human). This gene functions as a growth regulatory and tumor repressor gene. The molecular function of HIC1 gene includes DNA-binding transcription factor activity, sequence-specific DNA binding, DNA binding, histone deacetylase binding, protein binding, metal ion binding, nucleic acid binding, DNA-binding transcription repressor activity, RNA polymerase II-specific, DNA-binding transcription factor activity, RNA polymerase II-specific. The biological process of HIC1 gene includes multicellular organism development, negative regulation of Wnt signaling pathway, positive regulation of DNA damage response, signal transduction by p53 class mediator regulation of transcription, DNA-templated, negative regulation of transcription by RNA polymerase II, Wnt signaling pathway, transcription, DNA-templated, intrinsic apoptotic signaling pathway in response to DNA damage, cellular response to DNA damage stimulus. The study aimed to predict the stability and structure of the protein that will arise from single nucleotide polymorphisms (SNPs) in the human HIC1 gene. Methodology To investigate the possible negative effects associated with these SNPs, bioinformatic analysis is typically essential. The following tools were employed for forecasting harmful SNPs: scale-invariant feature transform (SIFT), Protein Analysis Through Evolutionary Relationships (PANTHER), nonsynonymous SNP by Protein Variation Effect Analyzer (PROVEAN), and nonsynonymous SNP by Single Nucleotide Polymorphism Annotation Platform (SNAP). Results The present study identified a total of 36 SNPs using the SIFT approach, which were shown to have functional significance. Twenty-six were determined to be tolerable, whereas 10 were shown to be detrimental. Out of 20 SNPs, seven (P370A, P646S, R654P, A476T, S400S, D666N, D7V) SNPs were predicted as "Possibly damaging" and seven (L9F, G468R, G490R, L482R, S12W, G489D, S12P) were identified as "probably benign", and six (R725G, G620S, A56V, E463D, D394N, L338V) were identified as "probably damaging" according to the predictions made by PANTHER tools. The majority of the pixels on the strip were red, indicating that the gene changes may have dangerous consequences. These results highlight the need for more research to fully comprehend how these mutations affect the hic1 protein's function, which is essential for the emergence of different types of cancer. Conclusion The current research has provided us with essential information about how SNPs might be used as a diagnostic marker for cancer, given that SNPs may be candidates for cellular changes caused by mutations linked to cancer.

Comparative Genomic Analysis of Bacterial Data in BV-BRC: An Example Exploring Antimicrobial Resistance

As genomic and related data continue to expand, research biologists are often hampered by the computational hurdles required to analyze their data. The National Institute of Allergy and Infectious Diseases (NIAID) established the Bioinformatics Resource Centers (BRC) to assist researchers with their analysis of genome sequence and other omics-related data. Recently, the PAThosystems Resource Integration Center (PATRIC), the Influenza Research Database (IRD), and the Virus Pathogen Database and Analysis Resource (ViPR) BRCs merged to form the Bacterial and Viral Bioinformatics Resource Center (BV-BRC) at https://www.bv-brc.org/ . The combined BV-BRC leverages the functionality of the original resources for bacterial and viral research communities with a unified data model, enhanced web-based visualization and analysis tools, and bioinformatics services. Here we demonstrate how antimicrobial resistance data can be analyzed in the new resource.

A large-scale comparative genomics study reveals niche-driven and within-sample intra-species functional diversification in Lacticaseibacillus rhamnosus

Lacticaseibacillus rhamnosus (L. rhamnosus) is widely recognized as a probiotic species, and it exists in a variety of environments including host gut and dairy products. This work aimed at conducting a large-scale comparative genomics analysis of 384 L. rhamnosus genomes (257 whole-sequence or metagenomic-assembled genomes from gut-associated isolates [122 and 135 retrieved from the UHGG and NCBI databases, respectively] and 127 genomes from dairy isolates [34 from the NCBI database; 93 isolated from a cheese sample and sequenced here]). Our results showed that L. rhamnosus had a large and open pan-genome (15,253 pan-genes identified from all 384 genomes; 15,028 pan-genes if the 93 cheese-originated isolates were excluded). The core-gene phylogenetic tree constructed from the 384 L. rhamnosus genomes comprised five phylogenetic branches, with a random distribution of dairy and gut-associated isolates/genomes across the tree. No significant difference was identified in the overall profile of metabolism-related genes between dairy and gut-associated genomes; however, notably, the gut-associated strains/isolates contained more genes coding for specific metabolic pathways and carbohydrate-active enzymes, e.g., lacto-N-biosidase (EC 3.2.1.140; GT20) and lacto-N-biose phosphorylase/galacto-N-biose phosphorylase (EC 2.4.1.211; GH112). Further, we found that there was obvious intra-species diversification of the 93 cheese-originated L. rhamnosus isolates, forming three clades (Clades A, B, and C) in the reconstructed core-gene phylogenetic tree. There were numerous single nucleotide variations (over 10,000) across the three clades. Moreover, significant differences were observed in the content of metabolism-related genes across clades (p < 0.05, Adonis test), characterized by the enrichment in glycoside hydrolases in Clade C and the possession of unique metabolic pathways in each clade. These results implicated genomics/functional diversification of L. rhamnosus in a single food matrix and niche-driven adaptive evolution of isolates from dairy and host gut-associated origins. Our study shed insights into the selection of candidate strains for food industry applications.

Preimplantation genetic testing for Aicardi-Goutières syndrome induced by novel compound heterozygous mutations of TREX1: an unaffected live birth

BACKGROUND

Aicardi-Goutières syndrome (AGS) is a rare, autosomal recessive, hereditary neurodegenerative disorder. It is characterized mainly by early onset progressive encephalopathy, concomitant with an increase in interferon-α levels in the cerebrospinal fluid. Preimplantation genetic testing (PGT) is a procedure that could be used to choose unaffected embryos for transfer after analysis of biopsied cells, which prevents at-risk couples from facing the risk of pregnancy termination.

METHODS

Trio-based whole exome sequencing, karyotyping and chromosomal microarray analysis were used to determine the pathogenic mutations for the family. To block the inheritance of the disease, multiple annealing and looping-based amplification cycles was used for whole genome amplification of the biopsied trophectoderm cells. Sanger sequencing and next-generation sequencing (NGS)-based single nucleotide polymorphism (SNP) haplotyping were used to detect the state of the gene mutations. Copy number variation (CNV) analysis was also carried out to prevent embryonic chromosomal abnormalities. Prenatal diagnosis was preformed to verify the PGT outcomes.

RESULTS

A novel compound heterozygous mutation in TREX1 gene was found in the proband causing AGS. A total of 3 blastocysts formed after intracytoplasmic sperm injection were biopsied. After genetic analyses, an embryo harbored a heterozygous mutation in TREX1 and without CNV was transferred. A healthy baby was born at 38th weeks and prenatal diagnosis results confirmed the accuracy of PGT.

CONCLUSIONS

In this study, we identified two novel pathogenic mutations in TREX1, which has not been previously reported. Our study extends the mutation spectrum of TREX1 gene and contributes to the molecular diagnosis as well as genetic counseling for AGS. Our results demonstrated that combining NGS-based SNP haplotyping for PGT-M with invasive prenatal diagnosis is an effective approach to block the transmission of AGS and could be applied to prevent other monogenic diseases.

Automatic extraction of ranked SNP-phenotype associations from text using a BERT-LSTM-based method

Extraction of associations of singular nucleotide polymorphism (SNP) and phenotypes from biomedical literature is a vital task in BioNLP. Recently, some methods have been developed to extract mutation-diseases affiliations. However, no accessible method of extracting associations of SNP-phenotype from content considers their degree of certainty. In this paper, several machine learning methods were developed to extract ranked SNP-phenotype associations from biomedical abstracts and then were compared to each other. In addition, shallow machine learning methods, including random forest, logistic regression, and decision tree and two kernel-based methods like subtree and local context, a rule-based and a deep CNN-LSTM-based and two BERT-based methods were developed in this study to extract associations. Furthermore, the experiments indicated that although the used linguist features could be employed to implement a superior association extraction method outperforming the kernel-based counterparts, the used deep learning and BERT-based methods exhibited the best performance. However, the used PubMedBERT-LSTM outperformed the other developed methods among the used methods. Moreover, similar experiments were conducted to estimate the degree of certainty of the extracted association, which can be used to assess the strength of the reported association. The experiments revealed that our proposed PubMedBERT-CNN-LSTM method outperformed the sophisticated methods on the task.

Bioinformatics approaches and big data analytics opportunities in improving fisheries and aquaculture

Aquaculture has witnessed an excellent growth rate during the last two decades and offers huge potential to provide nutritional as well as livelihood security. Genomic research has contributed significantly toward the development of beneficial technologies for aquaculture. The existing high throughput technologies like next-generation technologies generate oceanic data which requires extensive analysis using appropriate tools. Bioinformatics is a rapidly evolving science that involves integrating gene based information and computational technology to produce new knowledge for the benefit of aquaculture. Bioinformatics provides new opportunities as well as challenges for information and data processing in new generation aquaculture. Rapid technical advancements have opened up a world of possibilities for using current genomics to improve aquaculture performance. Understanding the genes that govern economically relevant characteristics, necessitates a significant amount of additional research. The various dimensions of data sources includes next-generation DNA sequencing, protein sequencing, RNA sequencing gene expression profiles, metabolic pathways, molecular markers, and so on. Appropriate bioinformatics tools are developed to mine the biologically relevant and commercially useful results. The purpose of this scoping review is to present various arms of diverse bioinformatics tools with special emphasis on practical translation to the aquaculture industry.

A protein enzyme-free strategy for fluorescence detection of single nucleotide polymorphisms using asymmetric MNAzymes

To establish protein enzyme-free and simple approach for sensitive detection of single nucleotide polymorphisms (SNPs), the nucleic acid amplification reactions were developed to reduce the dependence on protein enzymes (polymerase, endonuclease, ligase). These methods, while enabling highly amplified analysis for the short sequences, cannot be generalized to long genomic sequences. Herein, we develop a protein enzyme-free and general SNPs assay based on asymmetric MNAzyme probes. The multi-arm probe (MNAzyme-9_M-13) with two asymmetric recognition arms, containing a short (9 nt) and a long (13 nt) arm, is designed to detect EGFR T790 M mutation (MT). Owing to the excellent selectivity of short recognition arm, MNAzyme-9_M-13 probe can efficiently avoid interferences from wild-type target (WT) and various single-base mutations. Through a one-pot mixing, MNAzyme-9_M-13 probe enables the sensitive detection of MT, without protein enzyme or multi-step operation. The calculated detection limit for MT is 0.59 nM and 0.83%. Moreover, this asymmetric MNAzyme strategy can be applied for SNPs detection in long genomic sequences as well as short microRNAs (miRNAs) only by changing the low-cost unlabeled recognition arms. Therefore, along with simple operation, low-cost, protein enzyme-free and strong versatility, our asymmetric MNAzyme strategy provides a novel solution for SNPs detection and genes analysis.

An automated system for interrogating the evolution of microbial endosymbiosis

Inter-kingdom endosymbiotic interactions between bacteria and eukaryotic cells are critical to human health and disease. However, the molecular mechanisms that drive the emergence of endosymbiosis remain obscure. Here, we describe the development of a microfluidic system, named SEER (S̲ystem for the E̲volution of E̲ndosymbiotic R̲elationships), that automates the evolutionary selection of bacteria with enhanced intracellular survival and persistence within host cells, hallmarks of endosymbiosis. Using this system, we show that a laboratory strain of Escherichia coli that initially possessed limited abilities to survive within host cells, when subjected to SEER selection, rapidly evolved to display a 55-fold enhancement in intracellular survival. Notably, molecular dissection of the evolved strains revealed that a single-point mutation in a flexible loop of CpxR, a gene regulator that controls bacterial stress responses, substantially contributed to this intracellular survival. Taken together, these results establish SEER as the first microfluidic system for investigating the evolution of endosymbiosis, show the importance of CpxR in endosymbiosis, and set the stage for evolving bespoke inter-kingdom endosymbiotic systems with novel or emergent properties.

In Silico Mining and Characterization of High-Quality SNP/Indels in Some Agro-Economically Important Species Belonging to the Family Euphorbiaceae

(1) Background: To assess the genetic makeup among the agro-economically important members of Euphorbiaceae, the present study was conducted to identify and characterize high-quality single-nucleotide polymorphism (SNP) markers and their comparative distribution in exonic and intronic regions from the publicly available expressed sequence tags (ESTs). (2) Methods: Quality sequences obtained after pre-processing by an EG assembler were assembled into contigs using the CAP3 program at 95% identity; the mining of SNP was performed by QualitySNP; GENSCAN (standalone) was used for detecting the distribution of SNPs in the exonic and intronic regions. (3) Results: A total of 25,432 potential SNPs (pSNP) and 14,351 high-quality SNPs (qSNP), including 2276 indels, were detected from 260,479 EST sequences. The ratio of quality SNP to potential SNP ranged from 0.22 to 0.75. A higher frequency of transitions and transversions was observed more in the exonic than the intronic region, while indels were present more in the intronic region. C↔T (transition) was the most dominant nucleotide substitution, while in transversion, A↔T was the dominant nucleotide substitution, and in indel, A/- was dominant. (4) Conclusions: Detected SNP markers may be useful for linkage mapping; marker-assisted breeding; studying genetic diversity; mapping important phenotypic traits, such as adaptation or oil production; or disease resistance by targeting and screening mutations in important genes.

Genetic landscape of indolent and aggressive Kaposi sarcomas

BACKGROUND

Kaposi sarcoma (KS) is a rare skin tumour caused by herpesvirus 8 infection and characterized by either indolence or an aggressive course necessitating systemic therapies. The genetic basis of this difference remains unknown.

OBJECTIVES

To explore the tumour mutational burden in indolent and aggressive KS.

METHODS

We performed whole-exome sequencing on a cohort of 21 KS patients. We compared genetic landscape including tumor mutational burden between the two forms of indolent and agressive KS.

RESULTS

Aggressive KS tumours had a significantly higher TMB and a larger cumulative number of deleterious mutations than indolent KS tumours. In addition, all aggressive tumours had at least three deleterious mutations, whereas most indolent tumours harboured only one or no predicted deleterious mutations. Deleterious mutations listed in the Cancer Gene Census were detected exclusively in patients with aggressive disease. An analysis of somatic copy-number alterations (SCNA) revealed a tendency towards higher number of alterations in aggressive KS.

CONCLUSIONS

These data suggest that SCNA alterations and an increase in mutational burden promote aggressive KS and that it might be more appropriate to consider indolent KS as an opportunistic skin disease rather than a cancer.

Variation in fine-scale recombination rate in temperature-evolved Drosophila melanogaster populations in response to selection

Meiotic recombination plays a critical evolutionary role in maintaining fitness in response to selective pressures due to changing environments. Variation in recombination rate has been observed amongst and between species and populations and within genomes across numerous taxa. Studies have demonstrated a link between changes in recombination rate and selection, but the extent to which fine-scale recombination rate varies between evolved populations during the evolutionary period in response to selection is under active research. Here, we utilize a set of 3 temperature-evolved Drosophila melanogaster populations that were shown to have diverged in several phenotypes, including recombination rate, based on the temperature regime in which they evolved. Using whole-genome sequencing data from these populations, we generated linkage disequilibrium-based fine-scale recombination maps for each population. With these maps, we compare recombination rates and patterns among the 3 populations and show that they have diverged at fine scales but are conserved at broader scales. We further demonstrate a correlation between recombination rates and genomic variation in the 3 populations. Lastly, we show variation in localized regions of enhanced recombination rates, termed warm spots, between the populations with these warm spots and associated genes overlapping areas previously shown to have diverged in the 3 populations due to selection. These data support the existence of recombination modifiers in these populations which are subject to selection during evolutionary change.

Digital Droplet Loop-Mediated Isothermal Amplification Featuring a Molecular Beacon Assay, 3D Printed Droplet Generation, and Smartphone Imaging for Sequence-Specific DNA Detection

Nucleic acid detection is widely used in the amplification and quantitation of nucleic acids from biological samples. While polymerase chain reaction (PCR) enjoys great popularity, expensive thermal cyclers are required for precise temperature control. Loop-mediated isothermal amplification (LAMP) enables highly sensitive, rapid, and low-cost amplification of nucleic acids at constant temperatures. LAMP detection often relies on double-stranded DNA-binding dyes or metal indicators that lack sequence selectivity. Molecular beacons (MBs) are hairpin-shaped oligonucleotide probes whose sequence specificity in LAMP provides the capability of differentiating between single-nucleotide polymorphisms (SNPs). Digital droplet LAMP (ddLAMP) enables a large number of independent LAMP reactions to be performed and provides quantification of target DNA sequences. However, a major challenge with ddLAMP is the requirement of expensive droplet generators to form homogeneous microdroplets. In this study, we demonstrate for the first time that a three-dimensional (3D) printed droplet generation platform can be coupled to a LAMP assay featuring MBs as sequence-specific probes. The low-cost 3D printed droplet generator system was designed, and its customizability was demonstrated in the formation of monodisperse ddLAMP assay-in-oil microdroplets. Additionally, a smartphone-based imaging system is demonstrated to increase accessibility for point-of-care applications. The MB-ddLAMP assay is shown to discriminate between two SNPs at various amplification temperatures to afford a useful platform for sequence-specific, sensitive, and accurate DNA quantification. This work expands the utility of MBs to ddLAMP for quantitative studies in the detection of SNPs and exploits the customizability of 3D printing technologies to optimize the homogeneity, size, and volume of oil-in-water microdroplets.

Patterns and distribution of de novo mutations in multiplex Middle Eastern families

While de novo mutations (DNMs) are key to genetic diversity, they are also responsible for a high number of rare disorders. To date, no study has systematically examined the rate and distribution of DNMs in multiplex families in highly consanguineous populations. Leveraging WGS profiles of 645 individuals in 146 families, we implemented a combinatorial approach using 3 complementary tools for DNM discovery in 353 unique trio combinations. We found a total of 27,168 DNMs (median: 70 single-nucleotide and 6 insertion-deletions per individual). Phasing revealed around 80% of DNMs were paternal in origin. Notably, using whole-genome methylation data of spermatogonial stem cells, these DNMs were significantly more likely to occur at highly methylated CpGs (OR: 2.03; p value = 6.62 × 10⁻¹¹). We then examined the effects of consanguinity and ethnicity on DNMs, and found that consanguinity does not seem to correlate with DNM rate, and special attention has to be considered while measuring such a correlation. Additionally, we found that Middle-Eastern families with Arab ancestry had fewer DNMs than African families, although not significant (p value = 0.16). Finally, for families with diseased probands, we examined the difference in DNM counts and putative impact across affected and unaffected siblings, but did not find significant differences between disease groups, likely owing to the enrichment for recessive disorders in this part of the world, or the small sample size per clinical condition. This study serves as a reference for DNM discovery in multiplex families from the globally under-represented populations of the Middle-East.

Evaluation of ApaI and FokI polymorphism of VDR gene and functional characterization in patients with fibromyalgia

Abstract Introduction: Fibromyalgia (FM) is a syndrome of unknown origin characterized by several symptoms, and although its pathogenesis has not been completely elucidated, it seems to be related to inflammatory path-ways and neurochemical changes in the brain. Objective: To evaluate the association between BsmI, ApaI and FokI polymorphisms of the vitamin D receptor (VDR) gene, their polymorphisms, and clinical variables in women with and without FM. Methods: This is a case-control study composed of a group of 53 women with FM and another with 40 women without the disease. The McGill Pain Questionnaire, Fibromyalgia Impact Questionnaire, Pain Visual Analogue Scale and the sit-up test were applied. Real-time PCR was performed to analyze the ApaI and FokI polymorphism. Results: There was a statistical association between race, comorbidity and FM, where 78.4% of the individuals were white and had FM (p < 0.002) and 96.1% had some comorbidity (p < 0.001). Seventy-six point five percent (76.5%) of patients with FM underperformed in the sit-up test (p < 0.001). There was also an association between the genotypic and allele frequencies of the VDR and FM gene Apal and FokI polymorphisms (p < 0.001). In the VDR gene ApaI polymorphism, the CC genotype exhibited a higher frequency in women with FM, the C allele for the Apal polymorphism was 3.33 times more likely, and the FokI polymorphism was 10.9 times more likely to develop FM (p < 0,0001). Conclusion: Women with C allele for ApaI polymorphism are 3.33 times more likely to have FM (95%CI = 1.58-7.02; p = 0.0024), and in FokI polymorphism, the prevalence of T allele is 10.9 times greater (95% CI = 4.76-25.38; p < 0.0001). No significant associations were found in relation to BsmI polymorphism and frequency alleles (p = 0.062 and p = 0.078, respectively).

IL1RL1 single nucleotide polymorphisms are associated with asthma in the Iranian population

Asthma is a chronic and multifactorial disease which is known to result from environmental and genetic factors. Interleukin 1 receptor-like 1 (IL1RL1) is a receptor, which promotes inflammatory responses after binding to its ligand IL-33. Several studies have shown that IL1RL1 gene polymorphisms are related to susceptibility or protection to asthma. The objective of this study was to evaluate the association between two IL1RL1 single nucleotide polymorphisms (rs10208293 and rs1041973) and the risk of asthma in the Iranian population. We performed genotyping of the IL1RL1 SNPs in 126 adult asthmatics and 300 healthy controls using TaqMan genotyping assay. Moreover, total serum IgE level, eosinophil count, and skin prick test were accomplished. The results indicated that the AA genotype of rs10208293 was positively associated with asthma susceptibility (p=0.028). We did not find any association between rs1041973 and asthma. Overall, our findings indicate that rs10208293 has a positive association with asthma in the Iranian population.

Genomics of Recombination Rate Variation in Temperature-Evolved Drosophila melanogaster Populations

Meiotic recombination is a critical process that ensures proper segregation of chromosome homologs through DNA double-strand break repair mechanisms. Rates of recombination are highly variable among various taxa, within species, and within genomes with far-reaching evolutionary and genomic consequences. The genetic basis of recombination rate variation is therefore crucial in the study of evolutionary biology but remains poorly understood. In this study, we took advantage of a set of experimental temperature-evolved populations of Drosophila melanogaster with heritable differences in recombination rates depending on the temperature regime in which they evolved. We performed whole-genome sequencing and identified several chromosomal regions that appear to be divergent depending on temperature regime. In addition, we identify a set of single-nucleotide polymorphisms and associated genes with significant differences in allele frequency when the different temperature populations are compared. Further refinement of these gene candidates emphasizing those expressed in the ovary and associated with DNA binding reveals numerous potential candidate genes such as Hr38, EcR, and mamo responsible for observed differences in recombination rates in these experimental evolution lines thus providing insight into the genetic basis of recombination rate variation.

Accuracy and reproducibility of somatic point mutation calling in clinical-type targeted sequencing data

Background

Treating cancer depends in part on identifying the mutations driving each patient’s disease. Many clinical laboratories are adopting high-throughput sequencing for assaying patients’ tumours, applying targeted panels to formalin-fixed paraffin-embedded tumour tissues to detect clinically-relevant mutations. While there have been some benchmarking and best practices studies of this scenario, much variant calling work focuses on whole-genome or whole-exome studies, with fresh or fresh-frozen tissue. Thus, definitive guidance on best choices for sequencing platforms, sequencing strategies, and variant calling for clinical variant detection is still being developed.

Methods

Because ground truth for clinical specimens is rarely known, we used the well-characterized Coriell cell lines GM12878 and GM12877 to generate data. We prepared samples to mimic as closely as possible clinical biopsies, including formalin fixation and paraffin embedding. We evaluated two well-known targeted sequencing panels, Illumina’s TruSight 170 hybrid-capture panel and the amplification-based Oncomine Focus panel. Sequencing was performed on an Illumina NextSeq500 and an Ion Torrent PGM respectively. We performed multiple replicates of each assay, to test reproducibility. Finally, we applied four different freely-available somatic single-nucleotide variant (SNV) callers to the data, along with the vendor-recommended callers for each sequencing platform.

Results

We did not observe major differences in variant calling success within the regions that each panel covers, but there were substantial differences between callers. All had high sensitivity for true SNVs, but numerous and non-overlapping false positives. Overriding certain default parameters to make them consistent between callers substantially reduced discrepancies, but still resulted in high false positive rates. Intersecting results from multiple replicates or from different variant callers eliminated most false positives, while maintaining sensitivity.

Conclusions

Reproducibility and accuracy of targeted clinical sequencing results depend less on sequencing platform and panel than on variability between replicates and downstream bioinformatics. Differences in variant callers’ default parameters are a greater influence on algorithm disagreement than other differences between the algorithms. Contrary to typical clinical practice, we recommend employing multiple variant calling pipelines and/or analyzing replicate samples, as this greatly decreases false positive calls.

Analysis with biological nanopore: On-pore, off-pore strategies and application in biological fluids

Inspired from ion channels in biology, nanopores have been developed as promising analytical tools. In principle, nanopores provide crucial information from the observation and analysis of ionic current modulations caused by the interaction between target analytes and fluidic pores. In this respect, the biological, chemical and physical parameters of the nanopore regime need to be well-understood and regulated for intermolecular interaction. Because of well-defined molecular structures, biological nanopores consequently are of a focal point, allowing precise interaction analysis at single-molecule level. In this overview, two analytical strategies are summarized and discussed accordingly, upon the challenges arising in case-dependent analysis using biological nanopores. One kind of strategies relies on modification, functionalization and engineering on nanopore confined interface to improve molecular recognition sites (on-pore strategies); The other kind of highlighted strategies concerns to measurement of various chemistry/biochemistry based interactions triggered by employed molecular agents or probes (off-pore strategies). In particularly, a few recent paradigms using these strategies for practical application of accurate analysis of biomarkers in biological fluids are illustrated. To end, the challenging and future outlook of using analytical tools by means of biological nanopores are depicted.

Genomic profiling of bacterial and fungal communities and their predictive functionality during pulque fermentation by whole-genome shotgun sequencing

Pulque is a culturally important 4,000-year-old traditional Mexican fermented drink. Pulque is produced by adding fresh aguamiel (agave sap) to mature pulque, resulting in a mixture of microbial communities and chemical compositions. We performed shotgun metagenomic sequencing of five stages of pulque fermentation to characterize organismal and functional diversity. We identified 6 genera (Acinetobacter, Lactobacillus, Lactococcus, Leuconostoc, Saccharomyces and Zymomonas) and 10 species (Acinetobacter boissieri, Acinetobacter nectaris, Lactobacillus sanfranciscensis, Lactococcus lactis, Lactococcus piscium, Lactococcus plantarum, Leuconostoc citreum, Leuconostoc gelidum, Zymomonas mobilis and Saccharomyces cerevisiae) that were present ≥ 1% in at least one stage of pulque fermentation. The abundance of genera and species changed during fermentation and was associated with a decrease in sucrose and increases in ethanol and lactic acid, suggesting that resource competition shapes organismal diversity. We also predicted functional profiles, based on organismal gene content, for each fermentation stage and identified an abundance of genes associated with the biosynthesis of folate, an essential B-vitamin. Additionally, we investigated the evolutionary relationships of S. cerevisiae and Z. mobilis, two of the major microbial species found in pulque. For S. cerevisiae, we used a metagenomics assembly approach to identify S. cerevisiae scaffolds from pulque, and performed phylogenetic analysis of these sequences along with a collection of 158 S. cerevisiae strains. This analysis suggests that S. cerevisiae from pulque is most closely related to Asian strains isolated from sake and bioethanol. Lastly, we isolated and sequenced the whole-genomes of three strains of Z. mobilis from pulque and compared their relationship to seven previously sequenced isolates. Our results suggest pulque strains may represent a distinct lineage of Z. mobilis.

Discovery of tandem and interspersed segmental duplications using high-throughput sequencing

MOTIVATION

Several algorithms have been developed that use high-throughput sequencing technology to characterize structural variations (SVs). Most of the existing approaches focus on detecting relatively simple types of SVs such as insertions, deletions and short inversions. In fact, complex SVs are of crucial importance and several have been associated with genomic disorders. To better understand the contribution of complex SVs to human disease, we need new algorithms to accurately discover and genotype such variants. Additionally, due to similar sequencing signatures, inverted duplications or gene conversion events that include inverted segmental duplications are often characterized as simple inversions, likewise, duplications and gene conversions in direct orientation may be called as simple deletions. Therefore, there is still a need for accurate algorithms to fully characterize complex SVs and thus improve calling accuracy of more simple variants.

RESULTS

We developed novel algorithms to accurately characterize tandem, direct and inverted interspersed segmental duplications using short read whole genome sequencing datasets. We integrated these methods to our TARDIS tool, which is now capable of detecting various types of SVs using multiple sequence signatures such as read pair, read depth and split read. We evaluated the prediction performance of our algorithms through several experiments using both simulated and real datasets. In the simulation experiments, using a 30× coverage TARDIS achieved 96% sensitivity with only 4% false discovery rate. For experiments that involve real data, we used two haploid genomes (CHM1 and CHM13) and one human genome (NA12878) from the Illumina Platinum Genomes set. Comparison of our results with orthogonal PacBio call sets from the same genomes revealed higher accuracy for TARDIS than state-of-the-art methods. Furthermore, we showed a surprisingly low false discovery rate of our approach for discovery of tandem, direct and inverted interspersed segmental duplications prediction on CHM1 (<5% for the top 50 predictions).

AVAILABILITY AND IMPLEMENTATION

TARDIS source code is available at https://github.com/BilkentCompGen/tardis, and a corresponding Docker image is available at https://hub.docker.com/r/alkanlab/tardis/.

SUPPLEMENTARY INFORMATION

Supplementary data are available at Bioinformatics online.

Comprehensive Molecular Characterization Identifies Distinct Genomic and Immune Hallmarks of Renal Medullary Carcinoma

Renal medullary carcinoma (RMC) is a highly lethal malignancy that mainly afflicts young individuals of African descent and is resistant to all targeted agents used to treat other renal cell carcinomas. Comprehensive genomic and transcriptomic profiling of untreated primary RMC tissues was performed to elucidate the molecular landscape of these tumors. We found that RMC was characterized by high replication stress and an abundance of focal copy-number alterations associated with activation of the stimulator of the cyclic GMP-AMP synthase interferon genes (cGAS-STING) innate immune pathway. Replication stress conferred a therapeutic vulnerability to drugs targeting DNA-damage repair pathways. Elucidation of these previously unknown RMC hallmarks paves the way to new clinical trials for this rare but highly lethal malignancy.

A versatile single-molecule counting-based platform by generation of fluorescent silver nanoclusters for sensitive detection of multiple nucleic acids

The good photostability and strong brightness of individual DNA-templated silver nanoclusters (DNA-AgNCs) have been confirmed by single-molecule imaging in this work and DNA-AgNCs as a new class of outstanding fluorophores are applied in the construction of single-molecule counting-based probes for the first time. Based on the fluorescent AgNC-generating molecular beacons (AgNC-MBs), we present a versatile method for simultaneous analysis of multiple nucleic acids. Distinct from previous designs in which a AgNC stabilizing sequence is incorporated into the stem of a hairpin DNA to form the AgNC-MB, we prepared a nicked MB in which the AgNC stabilizing sequence is hybridized with the longer stem of a single-stranded DNA (ssDNA) with a stem-loop structure. Our proposed AgNC-MB is activated by probe-target hybridization then releasing the AgNC stabilizing sequence via a toehold-mediated strand displacement reaction, the versatility of which has been greatly improved because bases in the target-binding region are not involved in the formation of DNA-AgNCs. As a proof of concept, the simultaneous detection of two breast cancer-related MicroRNAs (miR-21 and let-7a miRNA) has been achieved with total internal reflection fluorescence (TIRF)-based imaging and the detection sensitivity of our method has been demonstrated to be improved by at least two orders of magnitude compared with conventional AgNC-MBs. Furthermore, in the single-nucleotide mutation identification assay, the simultaneous detection strategy introduces a competitive reaction between the two probe-target hybridizations, resulting in the excellent discrimination ability of the AgNC-MB sensing platform and the mutant-type targets can be successfully detected at low abundance. The new AgNC-MB sensing platform demonstrated potential to make AgNCs an attractive alternative to conventional organic dyes for single-molecule studies.

PLANET-SNP pipeline: PLants based ANnotation and Establishment of True SNP pipeline

Acute prediction of SNPs (Single Nucleotide Polymorphisms) from high throughput sequencing data is a challenging problem, having potential to explore possible variation within plants species. For the extraction of profitable information from bulk of data, machine learning (ML) could lead to development of accurate model based on the learning of prior information. We performed state of art, in-depth learning on six different plant species. Comparative evaluation of five different algorithms showed that Random Forest substantially outperformed in selection of potential SNPs, with markedly improved prediction accuracy via 10-fold cross validation technique and integrated in system known as PLANET-SNP. We present the accurate method to extract the potential SNPs with user specific customizable parameters. It will facilitate the identification of efficient and functional SNPs in most easy and intuitive way. PLANET-SNP pipeline is very flexible in terms of data input and output formats. PLANET-SNP Pipeline is available at http://www.ncgd.nbri.res.in/PLANET-SNP-Pipeline.aspx.

Life history consequences of developing in anthropogenic noise

When environments change rapidly, adaptive phenotypic plasticity can ameliorate negative effects of environmental change on survival and reproduction. Recent evidence suggests, however, that plastic responses to human-induced environmental change are often maladaptive or insufficient to overcome novel selection pressures. Anthropogenic noise is a ubiquitous and expanding disturbance with demonstrated effects on fitness-related traits of animals like stress responses, foraging, vigilance, and pairing success. Elucidating the lifetime fitness effects of noise has been challenging because longer-lived vertebrate systems are typically studied in this context. Here, we follow noise-stressed invertebrates throughout their lives, assessing a comprehensive suite of life history traits, and ultimately, lifetime number of surviving offspring. We reared field crickets, Teleogryllus oceanicus, in masking traffic noise, traffic noise from which we removed frequencies that spectrally overlap with the crickets' mate location song and peak hearing (nonmasking), or silence. We found that exposure to masking noise delayed maturity and reduced adult lifespan; crickets exposed to masking noise spent 23% more time in juvenile stages and 13% less time as reproductive adults than those exposed to no traffic noise. Chronic lifetime exposure to noise, however, did not affect lifetime reproductive output (number of eggs or surviving offspring), perhaps because mating provided females a substantial longevity benefit. Nevertheless, these results are concerning as they highlight multiple ways in which traffic noise may reduce invertebrate fitness. We encourage researchers to consider effects of anthropogenic disturbance on growth, survival, and reproductive traits simultaneously because changes in these traits may amplify or nullify one another.

Evolution of age at primiparity in pinnipeds in the absence of the quality-quantity trade-off in reproduction

Age at primiparity (AP) is a key life history trait which is crucial to the evolution of life history strategies. This trait is particularly interesting in pinnipeds (walrus, eared seals, and true seals), which are monotocous animals. Thus, the commonly observed trade-off between offspring quality and quantity does not apply to this taxon. Therefore, comparative studies on the evolution of AP might shed light on other important evolutionary correlates when litter size is fixed. Using phylogenetic generalized least squares analyses, we found a strong negative and robust correlation between relative birth mass (mean pup birth mass as a proportion of mean adult female mass) and AP. Rather than trading-off an early start of reproduction with light relative offspring mass, this result suggests that pinnipeds exhibit either faster (i.e., higher relative offspring mass leading to shorter lactation length, and thus shorter interbirth interval) or slower life histories and that an early AP and a heavy relative offspring mass co-evolved into a comparatively fast life history strategy. On the other hand, AP was positively related to lactation length: A later start of reproduction was associated with a longer lactation length. Consequently, variation in AP in pinnipeds seems to be affected by an interplay between costs and benefits of early reproduction mediated by relative investment into the single offspring via relative birth mass and lactation length.

Male-mediated prenatal loss: Functions and mechanisms

Sexually selected infanticide has been the subject of intense empirical and theoretical study for decades; a related phenomenon, male-mediated prenatal loss, has received much less attention in evolutionary studies. Male-mediated prenatal loss occurs when inseminated or pregnant females terminate reproductive effort following exposure to a nonsire male, either through implantation failure or pregnancy termination. Male-mediated prenatal loss encompasses two sub-phenomena: sexually selected feticide and the Bruce effect. In this review, we provide a framework that explains the relationship between feticide and the Bruce effect and describes what is known about the proximate and ultimate mechanisms involved in each. Using a simple model, we demonstrate that male-mediated prenatal loss can provide greater reproductive benefits to males than infanticide. We therefore suggest that, compared to infanticide, male-mediated prenatal loss may be more prevalent in mammalian species and may have played a greater role in their social evolution than has previously been documented.

Age at mating and male quality influence female patterns of reproductive investment and survival

The trade-off between the allocation of resources toward somatic maintenance or reproduction is one of the fundamentals of life history theory and predicts that females invest in offspring at the expense of their longevity or vice versa. Mate quality may also affect life history trade-offs through mechanisms of sexual conflict; however, few studies have examined the interaction between mate quality and age at first mating in reproductive decisions. Using house crickets (Acheta domesticus), this study examines how survival and reproductive trade-offs change based on females' age at first reproduction and exposure to males of varying size. Females were exposed to either a large (presumably high-quality) or small male at an early (young), middle (intermediate), or advanced (old) age, and longevity and reproductive investment were subsequently tracked. Females mated at a young age had the largest number of eggs but the shortest total lifespans while females mated at older ages produced fewer eggs but had longer total lifespans. The trade-off between age at first mating and eggs laid appears to be mediated through higher egg-laying rates and shorter postmating lifespans in females mated later in life. Exposure to small males resulted in shorter lifespans and higher egg-laying rates for all females indicating that male manipulation of females, presumably through spermatophore contents, varies with male size in this species. Together, these data strongly support a trade-off between age at first reproduction and lifespan and support the role of sexual conflict in shaping patterns of reproduction.

Live fast, don't die young: Survival-reproduction trade-offs in long-lived income breeders

Trade-offs between survival and reproduction are at the core of life-history theory, and essential to understanding the evolution of reproductive tactics as well as population dynamics and stability. Factors influencing these trade-offs are multiple and often addressed in isolation. Further problems arise as reproductive states and survival in wild populations are estimated based on imperfect and potentially biased observation processes, which might lead to flawed conclusions. In this study, we aimed at elucidating trade-offs between current reproduction (both pregnancy and lactation), survival and future reproduction, including the specific costs of first reproduction, in long-lived, income breeding small mammals, an under-studied group. We developed a novel statistical framework that encapsulates the breeding life cycle of females, and accounts for incomplete information on female pregnancy and lactation and imperfect and biased recapture rates. We applied this framework to longitudinal data on two sympatric, closely related bat species (Myotis daubentonii and M. nattereri). We revealed the existence of several, to our knowledge previously unknown, trends in survival and breeding of these closely related, sympatric species and detected remarkable differences in their age and costs of first reproduction, as well as their survival-reproduction trade-offs. Our results indicate that species with this type of life history exhibit a mixture of patterns expected for long-lived and short-lived animals, and between income and capital breeders. Thus, we call for more studies to be conducted in similar study systems, increasing our ability to fully understand the evolutionary origin and fitness effects of trade-offs and senescence.

Plant size influences abundance of floral visitors and biomass allocation for the cushion plant Thylacospermum caespitosum under an extreme alpine environment

Variation in size may influence the abundance of visitors and reproductive allocation for cushion plants in the extreme alpine environments. To assess effects of plant size on the abundance of main visitors and reproductive allocation in Thylacospermum caespitosum populations at two altitudes, the abundance of the visitors, visiting frequency, total number of flowers, number of fruits, number of unseeded flowers, and reproductive allocation were investigated during the period of reproductive growth. Concurrently, the effects of plant size on the visitors' contributions to fruit setting rate were assessed by a bagging experiment. Our results showed that flies (Musca domestica and Dasyphora asiatica) were the main pollinating insects of T. caespitosum, and they could obvious facilitate (p < 0.05) the fruit setting rate of this cushion plant. Seed set and floral visitation were significantly influenced (p < 0.001) by plant size. Moreover, the reproductive allocation and fruit setting rate of T. caespitosum was influenced (p < 0.001) by plant size. More biomass was allocated to reproduction in plants of greater diameter. There is an increase in reproductive success (increases of fruit number with increase in plant size) in relation to plant size. In conclusion, the extent of M. domestica and D. asiatica to facilitate the fruit setting rate mainly depended on the size of T. caespitosum. Size-dependent reproductive allocation occurred in T. caespitosum and was the chief factor affecting the contribution of flies to fruit setting rate. These traits reflect reproductive fitness of T. caespitosum related to plant size in extreme alpine environments.

Reproductive fitness consequences of progenesis: Sex-specific pay-offs in safe and risky environments

Progenesis is considered to have an important role in evolution because it allows the retention of both a larval body size and shape in an adult morphology. However, the cost caused by the adoption of a progenetic process in both males and females remains to be explored to explain the success of progenesis and particularly its biased prevalence across the sexes and environments. Here, through an experimental approach, we used a facultative progenetic species, the palmate newt (Lissotriton helveticus) that can either mature at a small size and retain gills or mature after metamorphosis, to test three hypotheses for sex-specific pay-offs of progenesis in safe versus risky habitats. Goldfish were used because they caused a higher decline in progenetic than metamorphic newts. We determined that progenetic newts have a lower reproductive fitness than metamorphic newts. We also found that, when compared to metamorphs, progenetic males have lower reproductive activity than progenetic females and that predatory risk affects more progenetic than metamorphic newts. By identifying ultimate causes of the female-biased sex ratios found in nature, these results support the male escape hypothesis, that is the higher metamorphosis rate of progenetic males. They also highlight that although progenesis is advantageous in advancing the age at first reproduction, it also brings an immediate fitness cost and this, particularly, in hostile predatory environments. This means that whereas some environmental constraints could favour facultative progenesis, some others, such as predation, can ultimately counter-select progenesis. Altogether, these results improve our understanding of how developmental processes can affect the sexes differently and how species invasions can impair the success of alternative developmental phenotypes.

Stage- and thermal-specific genetic architecture for preadult viability in natural populations of Drosophila melanogaster

Studying the processes affecting variation for preadult viability is essential to understand the evolutionary trajectories followed by natural populations. This task requires focusing on the complex nature of the phenotype-genotype relationship by taking into account usually neglected aspects of the phenotype and recognizing the modularity between different ontogenetic stages. Here, we describe phenotypic variability for viability during the larval and pupal stages in lines derived from three natural populations of Drosophila melanogaster, as well as the variability for phenotypic plasticity and canalization at two different rearing temperatures. The results indicate that the three populations present significant phenotypic differences for preadult viability. Furthermore, distinct aspects of the phenotype (means, plasticity, canalization, plasticity of canalization) are affected by different genetic bases underlying changes in viability in a stage- and environment-specific manner. These findings explain the generalized maintenance of genetic variability for this fitness trait.

The influence of early-life allocation to antlers on male performance during adulthood: Evidence from contrasted populations of a large herbivore

To secure mating opportunities, males often develop and maintain conspicuous traits that are involved in intrasexual and/or intersexual competition. While current models of sexual selection rely on the assumption that producing such traits is costly, quantifying the cost of allocating to secondary sexual traits remains challenging. According to the principle of allocation, high energy allocation to growth or sexual traits in males should lead to reduced energy allocation to the maintenance of cellular and physiological functions, potentially causing them to age faster, with impaired survival. We evaluated the short-term and delayed consequences of energy allocation to antlers early in life in two contrasted populations of roe deer, Capreolus capreolus. Although most males mate successfully for the first time in their fourth year, antlers are grown annually from the first year of life onwards. We tested the prediction that a high level of allocation to antler growth during the first two years of life should lead to lower body mass, antler size and survival during the early and late prime stages, as well as to reduced longevity overall. Growing and carrying long antlers during the first years of life was not associated with any detectable cost in the late prime stage. The positive association between antler growth in early life and adult body mass instead supports that fawn antler acts as an honest signal of phenotypic quality in roe deer. For a given body mass, yearling males growing longer antlers displayed impaired performance during their late prime. We also found a trend for a short-term survival cost of allocation to relative antler length during the second year of life. Yearling males that grow long antlers relative to their mass might display a fast life-history tactic. We argue that differential allocation to secondary sexual traits generates a diversity of individual trajectories that should impact population dynamics.

Offspring mass variation in tree swallows: A case of bet‐hedging?

The evolution of reproductive strategies is affected by the ability of organisms to deal with future environmental conditions. When environments are temporally unpredictable, however, it is difficult to anticipate optimal offspring phenotype. Diversification of offspring phenotypes, a strategy called diversified bet‐hedging, may allow parents to maximize their fitness by reducing between‐year variation in reproductive success. The link between diversification of offspring phenotypes and individual reproductive success, however, has rarely been documented empirically. We used an eight‐year dataset (1215 broods, 870 females) on individually marked tree swallows (Tachycineta bicolor) to assess whether intra‐brood mass variation was compatible with a diversified bet‐hedging strategy. Intra‐brood mass variation was weakly, but significantly repeatable within females, suggesting consistent individual differences. Greater intra‐brood mass variation, however, was not associated with reduced between‐year variation in reproductive success or increased female reproductive success. Moreover, contrary to diversified bet‐hedging expectations, fledging success of large broods was greater when hatchlings had similar rather than variable masses. Our results suggest that intra‐brood mass variation may not result from diversified bet‐hedging, but rather from complex interactions between environmental, brood, and maternal characteristics.

Males from populations with higher competitive mating success produce sons with lower fitness

Female mate choice can result in direct benefits to the female or indirect benefits through her offspring. Females can increase their fitness by mating with males whose genes encode increased survivorship and reproductive output. Alternatively, male investment in enhanced mating success may come at the cost of reduced investment in offspring fitness. Here, we measure male mating success in a mating arena that allows for male-male, male-female and female-female interactions in Drosophila melanogaster. We then use isofemale line population measurements to correlate male mating success with sperm competitive ability, the number of offspring produced and the indirect benefits of the number of offspring produced by daughters and sons. We find that males from populations that gain more copulations do not increase female fitness through increased offspring production, nor do these males fare better in sperm competition. Instead, we find that these populations have a reduced reproductive output of sons, indicating a potential reproductive trade-off between male mating success and offspring quality.

Adaptation to developmental diet influences the response to selection on age at reproduction in the fruit fly

Experimental evolution (EE) is a powerful tool for addressing how environmental factors influence life-history evolution. While in nature different selection pressures experienced across the lifespan shape life histories, EE studies typically apply selection pressures one at a time. Here, we assess the consequences of adaptation to three different developmental diets in combination with classical selection for early or late reproduction in the fruit fly Drosophila melanogaster. We find that the response to each selection pressure is similar to that observed when they are applied independently, but the overall magnitude of the response depends on the selection regime experienced in the other life stage. For example, adaptation to increased age at reproduction increased lifespan across all diets; however, the extent of the increase was dependent on the dietary selection regime. Similarly, adaptation to a lower calorie developmental diet led to faster development and decreased adult weight, but the magnitude of the response was dependent on the age-at-reproduction selection regime. Given that multiple selection pressures are prevalent in nature, our findings suggest that trade-offs should be considered not only among traits within an organism, but also among adaptive responses to different-sometimes conflicting-selection pressures, including across life stages.

Hormonal pleiotropy and the evolution of allocation trade-offs

Recent empirical evidence suggests that trade-off relationships can evolve, challenging the classical image of their high entrenchment. For energy reliant traits, this relationship should depend on the endocrine system that regulates resource allocation. Here, we model changes in this system by mutating the expression and conformation of its constitutive hormones and receptors. We show that the shape of trade-offs can indeed evolve in this model through the combined action of genetic drift and selection, such that their evolutionarily expected curvature and length depend on context. In particular, the shape of a trade-off should depend on the cost associated with resource storage, itself depending on the traded resource and on the ecological context. Despite this convergence at the phenotypic level, we show that a variety of physiological mechanisms may evolve in similar simulations, suggesting redundancy at the genetic level. This model should provide a useful framework to interpret and unify the overly complex observations of evolutionary endocrinology and evolutionary ecology.

Size-mediated priority and temperature effects on intra-cohort competition and cannibalism in a damselfly

A shift in the relative arrival of offspring, for example a shift in hatching time, can affect competition at the intraspecific level through size-mediated priority effects, where the larger individuals gain more resources. These priority effects are likely to be affected by climate warming and the rate of intraspecific predation, that is cannibalism. In a laboratory experiment, we examined size-mediated priority effects in larvae of the univoltine damselfly, Lestes sponsa, at two different temperatures (21 and 23°C). We created three size groups of larvae by manipulating hatching time: early hatched with a large size (extra-advanced), intermediate hatched with an intermediate size (advanced) and late hatched with a small size (non-advanced). Thereafter, we reared the larvae from these groups in non-mixed and mixed groups of 12 larvae. We found strong priority and temperature effects. First, extra-advanced larvae most often had higher survival, growth and development rates than non-advanced larvae in mixed groups, compared to groups that consisted of only extra-advanced larvae. Second, temperature increased growth and development rates and cannibalism. However, the strength of priority effects did not differ between the two experimental temperatures, because there was no statistical interaction between temperature and treatments. That is, the mixed and non-mixed groups of non-advanced, advanced and extra-advanced larvae showed the same relative change in life-history traits across the two temperatures. Non-advanced and advanced larvae had similar or higher growth rate and mass in mixed groups compared to non-mixed groups, suggesting that predation from advanced larvae in the mixed group released resources for the non-advanced and advanced larvae that survived despite cannibalism risk. Thus, a thinning effect occurred due to cannibalism caused by priority effects. The results suggest that a shift in the relative arrival of offspring can cause temperature-dependent priority effects, mediated through cannibalism, growth and development, which may change the size distribution and abundance of emerging aquatic insects.

Estimating age-dependent survival when juveniles resemble females: Invasive ring-necked parakeets as an example

Many species only show sexual dimorphism at the age of maturity, such that juveniles typically resemble females. Under these circumstances, estimating accurate age-specific demographic parameters is challenging. Here, we propose a multievent model parameterization able to estimate age-dependent survival using capture-recapture data with uncertainty in age and sex assignment of individuals. We illustrate this modeling approach with capture-recapture data from the ring-necked parakeet Psittacula krameri. We analyzed capture, recapture, and resighting data (439 recaptures/resightings) of 156 ring-necked parakeets tagged with neck collars in Barcelona city from 2003 to 2016 to estimate the juvenile and adult survival rate. Our models successfully estimated the survival probabilities of the different age classes considered. Survival probability was similar between adults (0.83, 95% CI = 0.77-0.87) and juveniles during their second (0.79, 95% CI = 0.58-0.87) and third winter (0.83, 95% CI = 0.65-0.88). The youngest juveniles (1st winter) showed a slightly lower survival (0.57, 95% CI = 0.37-0.79). Among adults, females showed a slightly higher survival than males (0.87, 95% CI = 0.78-0.93; and 0.80, 95% CI = 0.73-0.86, respectively). These high survival figures predict high population persistence in this species and urge management policies. The analysis also stresses the usefulness of multievent models to estimate juvenile survival when age cannot be fully ascertained.

A Guide to Next Generation Sequence Analysis of Leishmania Genomes

Next generation sequencing (NGS) technology transformed Leishmania genome studies and became an indispensable tool for Leishmania researchers. Recent Leishmania genomics analyses facilitated the discovery of various genetic diversities including single nucleotide polymorphisms (SNPs), copy number variations (CNVs), somy variations, and structural variations in detail and provided valuable insights into the complexity of the genome and gene regulation. Many aspects of Leishmania NGS analyses are similar to those of related pathogens like trypanosomes. However, the analyses of Leishmania genomes face a unique challenge because of the presence of frequent aneuploidy. This makes characterization and interpretation of read depth and somy a key part of Leishmania NGS analyses because read depth affects the accuracy of detection of all genetic variations. However, there are no general guidelines on how to explore and interpret the impact of aneuploidy, and this has made it difficult for biologists and bioinformaticians, especially for beginners, to perform their own analyses and interpret results across different analyses. In this guide we discuss a wide range of topics essential for Leishmania NGS analyses, ranging from how to set up a computational environment for genome analyses, to how to characterize genetic variations among Leishmania samples, and we will particularly focus on chromosomal copy number variation and its impact on genome analyses.

Maternal size and body condition predict the amount of post-fertilization maternal provisioning in matrotrophic fish

Maternal effects often provide a mechanism for adaptive transgenerational phenotypic plasticity. The maternal phenotype can profoundly influence the potential for such environmentally induced adjustments of the offspring phenotype, causing correlations between offspring and maternal traits. Here, we study potential effects of the maternal phenotype on offspring provisioning prior to and during gestation in the matrotrophic live-bearing fish species Poeciliopsis retropinna. Specifically, we examine how maternal traits such as body fat, lean mass, and length relate to pre- (i.e., allocation to the egg prior to fertilization) and post-fertilization (i.e., allocation to the embryo during pregnancy) maternal provisioning and how this ultimately affects offspring size and body composition at birth. We show that pre- and post-fertilization maternal provisioning is associated with maternal length and body fat, but not with maternal lean mass. Maternal length is proportionally associated with egg mass at fertilization and offspring mass at birth, notably without changing the ratio of pre- to post-fertilization maternal provisioning. This ratio, referred to as the matrotrophy index (MI), is often used to quantify the level of matrotrophy. By contrast, the proportion of maternal body fat is positively associated with post-fertilization, but not pre-fertilization, maternal provisioning and consequently is strongly positively correlated with the MI. We furthermore found that the composition of embryos changes throughout pregnancy. Females invest first in embryo lean mass, and then allocate fat reserves to embryos very late in pregnancy. We argue that this delay in fat allocation may be adaptive, because it delays an unnecessary high reproductive burden to the mother during earlier stages of pregnancy, potentially leading to a more slender body shape and improved locomotor performance. In conclusion, our study suggests that (a) offspring size at birth is a plastic trait that is predicted by both maternal length and body fat, and (b) the MI is a plastic trait that is predicted solely by the proportion of maternal body fat. It herewith provides new insights into the potential maternal causes and consequences of embryo provisioning during pregnancy in matrotrophic live-bearing species.

Sunning themselves in heaps, knots, and snarls: The extraordinary abundance and demography of island watersnakes

Snakes represent a sizable fraction of vertebrate biodiversity, but until recently, data on their demography have been sparse. Consequently, generalizations regarding patterns of variation are weak and the potential for population projections is limited. We address this information gap through an analysis of spatial and temporal variation in demography (population size, annual survival, and realized population growth) of the Lake Erie Watersnake, Nerodia sipedon insularum, and a review of snake survival more generally. Our study spans a period during which the Lake Erie Watersnake was listed as threatened under the U.S. Endangered Species Act, recovered, and was delisted. We collected capture-mark-recapture data at 14 study sites over 20 years, accruing 20,000 captures of 13,800 individually marked adults. Lake Erie Watersnakes achieve extraordinary abundance, averaging 520 adults per km of shoreline (ca. 260 adult per ha) at our study sites (range = 160-1,600 adults per km; ca. 80-800 adults per ha) and surpassing population recovery and postdelisting monitoring criteria. Annual survival averages 0.68 among adult females and 0.76 among adult males, varies among sites, and is positively correlated with body size among study sites. Temporal process variance in annual survival is low, averaging 0.0011 or less than 4% of total variance; thus, stochasticity in annual survival may be of minor significance to snake extinction risk. Estimates of realized population growth indicate that population size has been stable or increasing over the course of our study. More generally, snake annual survival overlaps broadly across continents, climate zones, families, subfamilies, reproductive modes, body size categories, maturation categories, and parity categories. Differences in survival in relation to size, parity, and maturation are in the directions predicted by life history theory but are of small magnitude with much variation around median values. Overall, annual survival appears to be quite plastic, varying with food availability, habitat quality, and other ecological variables.

Oxidative damage and antioxidant defense are assay and tissue-dependent both in captive and wild-caught bank voles (Myodes glareolus) before and after reproduction

Reproduction is costly and life-history theory predicts that current parental investment will result in lower survival or decreased future reproduction. The physiological mechanisms mediating the link between reproduction and survival are still under debate and elevated oxidative damage during reproduction has been proposed as a plausible candidate. Previous studies of oxidative stress during reproduction in animals under natural conditions have been restricted to analyses of blood. Herein, we measured the level of oxidative damage to lipids (tiobarbituric-acid-reactive substances) and proteins (carbonyls) in the liver, kidneys, heart and skeletal muscles in free-living bank vole females from spring and autumn generations, before and after reproduction. Antioxidant defense in the liver and kidneys was also determined. We expected oxidative damage to tissues and hypothesized that the damage would be more uniform between tissues in wild animals compared to those breeding under laboratory conditions. Considering all combinations of markers/tissues/generations, oxidative damage in females did not differ before and after reproduction in 12 comparisons, was lower after reproduction in three comparisons, and was higher after breeding in one comparison. The total glutathione was significantly increased after reproduction only in the liver of the autumn generation and there was no change in catalase activity. Our results confirm-for the first time in the field-previous observations from laboratory studies that there is no simple link between oxidative stress and reproduction and that patterns depend on the tissue and marker being studied. Overall, however, our study does not support the hypothesis that the cost of reproduction in bank voles is mediated by oxidative stress in these tissues.