The evolution of termite immunity

Alongside sexual reproduction and multicellularity, eusociality is considered one of the major transitions in evolution (Szathmary and Smith 1995). Eusociality has evolved most often among the insects, particularly the Hymenoptera (the ants, bees and wasps) and termites. The hallmark of social evolution in insects is the appearance of permanently sterile castes, which is reflected by reproductive division of labour. A notable feature of insect societies is the emergence of sophisticated immune adaptations at the individual and group level to control the spread of disease. However, the evolution of termite immunity remains poorly understood. In particular, information regarding molecular evolution of the canonical immune pathways, and how innate and induced immunity were shaped by the evolution of a sterile caste system, remain major gaps in knowledge. A comparative approach in the study of the evolution of termite immunity requires robust knowledge of the immune system of the nearest non-social insect lineages: the cockroaches. To this end, the immunity of a cockroach, Blatta orientalis, was explored in Chapter I. Using de novo transcriptomes, a full repertoire of immune gene members was identified. Interestingly, expansions of immune gene families of receptors, including GNBP, PGRP and hemolymph LPS-binding protein (LPSBP) were identified. After immune challenging cockroaches with a mixture of heat-killed microbes (Bacillus thuringiensis, Pseudomonas entomophila, Saccharomyces cerevisiae), I was able to record a broad induced response in canonical immune pathways, pointing to the presence of effective and potentially long-lasting protection against infection, which is a key trait for organisms that thrive in a rich antigenic environment. In the first part of Chapter II, I examined the evolution of immunity in termites by first reconstructing a termite phylogeny with 19 newly sequenced transcriptomes and 16 available genomic datasets. As a result, we confirmed termites as the sister group to the Cryptocercus, a subsocial cockroach genus, and located their most recent common ancestor (MRCA) to the lower Jurassic. An evolutionary analysis of immune related gene families was then performed based on 18 of the newly sequenced transcriptomes. A family of antimicrobial peptide, Drosomycin, was found to be lost in the ancestor to the subsocial wood roaches and all termites. A further analysis of two other classic effectors, catalase and thioredoxin peroxidase, revealed a rapid contraction of related genes in the ancestor to all eusocial termite species. In addition, a family of receptors, C-type lectins (CTLs), showed contraction in the MRCA of Cryptocercus and termites as well as in the root of the Termitidae. In addition, these contracted gene families underwent a subsequent re-expansion in some individual higher termite lineages. These results suggest a substantial re-modelling of the termite immune system during the evolution of eusociality. This qualitative analysis focusing on major shifts in termite immunity was followed in the second part of Chapter II by a quantitative analysis of individual immunity across different castes of a representative lower termite, Neotermes castaneus. Gene expression changes were then compared with a subsocial wood roach, Cryptocercus meridianus, and the solitary cockroach, B. orientalis. Interestingly, I found evidence for higher investment into innate immunity in the reproductive termite caste as compared to sterile soldier caste members or false-workers. Furthermore, the induced immune response elicited in soldiers, but particularly in the reproductive caste mimicked the induced immune responses of C. meridianus and B. orientalis more closely than the response of false-workers. Additionally, the induced response to the same experimental immune challenge was remarkably similar between the subsocial C. meridianus and the solitary B. orientalis. From these results, I argue that the evolution of division of labor in termites was linked to the evolution of a fundamental change in individual immune defence between the sterile and non-sterile castes. In Chapter III, I expand on the role of the sterile caste in eusociality and immunity by examining the function of soldiers in social immunity in the Darwin termite, Mastotermes darwiniensis. In this chapter, M. darwiniensis soldiers are shown to contribute significantly to the social immunity of the colony by increasing the survival of groups of workers, probably via the secretion of potent orally-derived antimicrobial substances. In a comprehensive proteomic analysis, I demonstrate that M. darwiniensis soldier oral secretions possess a rich array of immune related proteins and enzymes involved in the biosynthesis of cytotoxins such as benzoquinone. These findings shed new light on termite societies, indicating that termites are likely to have evolved a sterile soldier caste with important functions not only in colony defence but also in social immunity. In this thesis I reveal how the termite immune system evolved during the transition to eusociality. I have established a robust foundation for the study of molecular immunity in termites and contributed new insights into the evolution of immunity in social animals in general. As the contraction and re-expansion of receptors and effectors in termites indicates, the function of a number of immune gene families should be examined in much greater detail. Furthermore, it will be particularly interesting to explore the individual immune (as well as general) responses of termite in a wider social context, particularly given the observed immune differences that were detected between the termite castes. Comparisons with immune adaptations in the Hymenoptera and other social animals would also be highly beneficial to understand commonalities and differences during this key evolutionary transition

MC-SpEx: Towards Effective Speaker Extraction with Multi-Scale Interfusion and Conditional Speaker Modulation

The previous SpEx+ has yielded outstanding performance in speaker extraction and attracted much attention. However, it still encounters inadequate utilization of multi-scale information and speaker embedding. To this end, this paper proposes a new effective speaker extraction system with multi-scale interfusion and conditional speaker modulation (ConSM), which is called MC-SpEx. First of all, we design the weight-share multi-scale fusers (ScaleFusers) for efficiently leveraging multi-scale information as well as ensuring consistency of the model's feature space. Then, to consider different scale information while generating masks, the multi-scale interactive mask generator (ScaleInterMG) is presented. Moreover, we introduce ConSM module to fully exploit speaker embedding in the speech extractor. Experimental results on the Libri2Mix dataset demonstrate the effectiveness of our improvements and the state-of-the-art performance of our proposed MC-SpEx.Comment: Accepted by InterSpeech 202

Comparative analysis of adipokinetic hormones and their receptors in Blattodea reveals novel patterns of gene evolution

Adipokinetic hormone (AKH) is a neuropeptide produced in the insect corpora cardiaca that plays an essential role in mobilising carbohydrates and lipids from the fat body to the haemolymph. AKH acts by binding to a rhodopsin-like G protein-coupled receptor (GPCR), the adipokinetic hormone receptor (AKHR). In this study, we tackle AKH ligand and receptor gene evolution as well as the evolutionary origins of AKH gene paralogues from the order Blattodea (termites and cockroaches). Phylogenetic analyses of AKH precursor sequences point to an ancient AKH gene duplication event in the common ancestor of Blaberoidea, yielding a new group of putative decapeptides. In total, 16 different AKH peptides from 90 species were obtained. Two octapeptides and seven putatively novel decapeptides are predicted for the first time. AKH receptor sequences from 18 species, spanning solitary cockroaches and subsocial wood roaches as well as lower and higher termites, were subsequently acquired using classical molecular methods and in silico approaches employing transcriptomic data. Aligned AKHR open reading frames revealed 7 highly conserved transmembrane regions, a typical arrangement for GPCRs. Phylogenetic analyses based on AKHR sequences support accepted relationships among termite, subsocial (Cryptocercus spp.) and solitary cockroach lineages to a large extent, while putative post-translational modification sites do not greatly differ between solitary and subsocial roaches and social termites. Our study provides important information not only for AKH and AKHR functional research but also for further analyses interested in their development as potential candidates for biorational pest control agents against invasive termites and cockroaches

KQA Pro: A Large-Scale Dataset with Interpretable Programs and Accurate SPARQLs for Complex Question Answering over Knowledge Base

Complex question answering over knowledge base (Complex KBQA) is challenging because it requires various compositional reasoning capabilities, such as multi-hop inference, attribute comparison, set operation, and etc. Existing benchmarks have some shortcomings that limit the development of Complex KBQA: 1) they only provide QA pairs without explicit reasoning processes; 2) questions are either generated by templates, leading to poor diversity, or on a small scale. To this end, we introduce KQA Pro, a large-scale dataset for Complex KBQA. We define a compositional and highly-interpretable formal format, named Program, to represent the reasoning process of complex questions. We propose compositional strategies to generate questions, corresponding SPARQLs, and Programs with a small number of templates, and then paraphrase the generated questions to natural language questions (NLQ) by crowdsourcing, giving rise to around 120K diverse instances. SPARQL and Program depict two complementary solutions to answer complex questions, which can benefit a large spectrum of QA methods. Besides the QA task, KQA Pro can also serves for the semantic parsing task. As far as we know, it is currently the largest corpus of NLQ-to-SPARQL and NLQ-to-Program. We conduct extensive experiments to evaluate whether machines can learn to answer our complex questions in different cases, that is, with only QA supervision or with intermediate SPARQL/Program supervision. We find that state-of-the-art KBQA methods learnt from only QA pairs perform very poor on our dataset, implying our questions are more challenging than previous datasets. However, pretrained models learnt from our NLQ-to-SPARQL and NLQ-to-Program annotations surprisingly achieve about 90\% answering accuracy, which is even close to the human expert performance..

TEA-PSE 3.0: Tencent-Ethereal-Audio-Lab Personalized Speech Enhancement System For ICASSP 2023 DNS Challenge

This paper introduces the Unbeatable Team's submission to the ICASSP 2023 Deep Noise Suppression (DNS) Challenge. We expand our previous work, TEA-PSE, to its upgraded version -- TEA-PSE 3.0. Specifically, TEA-PSE 3.0 incorporates a residual LSTM after squeezed temporal convolution network (S-TCN) to enhance sequence modeling capabilities. Additionally, the local-global representation (LGR) structure is introduced to boost speaker information extraction, and multi-STFT resolution loss is used to effectively capture the time-frequency characteristics of the speech signals. Moreover, retraining methods are employed based on the freeze training strategy to fine-tune the system. According to the official results, TEA-PSE 3.0 ranks 1st in both ICASSP 2023 DNS-Challenge track 1 and track 2.Comment: Accepted by ICASSP 202

A phylogenomic analysis of Marek's disease virus reveals independent paths to virulence in Eurasia and North America

Virulence determines the impact a pathogen has on the fitness of its host, yet current understanding of the evolutionary origins and causes of virulence of many pathogens is surprisingly incomplete. Here, we explore the evolution of Marek's disease virus (MDV), a herpesvirus commonly afflicting chickens and rarely other avian species. The history of MDV in the 20th century represents an important case study in the evolution of virulence. The severity of MDV infection in chickens has been rising steadily since the adoption of intensive farming techniques and vaccination programs in the 1950s and 1970s, respectively. It has remained uncertain, however, which of these factors is causally more responsible for the observed increase in virulence of circulating viruses. We conducted a phylogenomic study to understand the evolution of MDV in the context of dramatic changes to poultry farming and disease control. Our analysis reveals evidence of geographical structuring of MDV strains, with reconstructions supporting the emergence of virulent viruses independently in North America and Eurasia. Of note, the emergence of virulent viruses appears to coincide approximately with the introduction of comprehensive vaccination on both continents. The time-dated phylogeny also indicated that MDV has a mean evolutionary rate of ~1.6 × 10−5 substitutions per site per year. An examination of gene-linked mutations did not identify a strong association between mutational variation and virulence phenotypes, indicating that MDV may evolve readily and rapidly under strong selective pressures and that multiple genotypic pathways may underlie virulence adaptation in MDV