One’s trash is someone else’s treasure: sequence read archives from Lepidoptera genomes provide material for genome reconstruction of their endosymbionts

Background Maternally inherited bacterial symbionts are extremely widespread in insects. They owe their success to their ability to promote their own transmission through various manipulations of their hosts’ life-histories. Many symbionts however very often go undetected. Consequently, we have only a restricted idea of the true symbiont diversity in insects, which may hinder our understanding of even bigger questions in the field such as the evolution or establishment of symbiosis. Results In this study, we screened publicly available Lepidoptera genomic material for two of the most common insect endosymbionts, namely Wolbachia and Spiroplasma, in 1904 entries, encompassing 106 distinct species. We compared the performance of two screening software, Kraken2 and MetaPhlAn2, to identify the bacterial infections and using a baiting approach we reconstruct endosymbiont genome assemblies. Of the 106 species screened, 20 (19%) and nine (8.5%) were found to be infected with either Wolbachia or Spiroplasma, respectively. Construction of partial symbiotic genomes and phylogenetic analyses suggested the Wolbachia strains from the supergroup B were the most prevalent type of symbionts, while Spiroplasma infections were scarce in the Lepidoptera species screened here. Conclusions Our results indicate that many of the host-symbiont associations remain largely unexplored, with the majority of associations we identify never being recorded before. This highlights the usefulness of public databases to explore the hidden diversity of symbiotic entities, allowing the development of hypotheses regarding host-symbiont associations. The ever-expanding genomic databases provide a diverse databank from which one can characterize and explore the true diversity of symbiotic entities.Peer reviewe

One’s trash is someone else’s treasure: sequence read archives from Lepidoptera genomes provide material for genome reconstruction of their endosymbionts

Background Maternally inherited bacterial symbionts are extremely widespread in insects. They owe their success to their ability to promote their own transmission through various manipulations of their hosts’ life-histories. Many symbionts however very often go undetected. Consequently, we have only a restricted idea of the true symbiont diversity in insects, which may hinder our understanding of even bigger questions in the field such as the evolution or establishment of symbiosis. Results In this study, we screened publicly available Lepidoptera genomic material for two of the most common insect endosymbionts, namely Wolbachia and Spiroplasma, in 1904 entries, encompassing 106 distinct species. We compared the performance of two screening software, Kraken2 and MetaPhlAn2, to identify the bacterial infections and using a baiting approach we reconstruct endosymbiont genome assemblies. Of the 106 species screened, 20 (19%) and nine (8.5%) were found to be infected with either Wolbachia or Spiroplasma, respectively. Construction of partial symbiotic genomes and phylogenetic analyses suggested the Wolbachia strains from the supergroup B were the most prevalent type of symbionts, while Spiroplasma infections were scarce in the Lepidoptera species screened here. Conclusions Our results indicate that many of the host-symbiont associations remain largely unexplored, with the majority of associations we identify never being recorded before. This highlights the usefulness of public databases to explore the hidden diversity of symbiotic entities, allowing the development of hypotheses regarding host-symbiont associations. The ever-expanding genomic databases provide a diverse databank from which one can characterize and explore the true diversity of symbiotic entities.Peer reviewe

Soldiers and Bureaucrats in Late Roman Britain: interpreting the imperial occupation through the medium of the crossbow brooch

The crossbow brooch is a type of material culture which has been associated by scholars with the soldiers and bureaucrats of the late Roman state. Building upon previous research, this thesis examines the distribution of a sample of 350 crossbow brooches discovered throughout the landscape of the former diocese of Roman Britain. By utilising typological schemes which locate these particular objects within a chronology ranging from the third to the early fifth centuries; this thesis argues that the regional distributions of the crossbow brooch throughout Britain can be considered as the consequences of long-term developments relating to when and where imperial servants were posted rather than a late fourth-century phenomenon per se. Furthermore, by employing various discursive approaches to data analysis this thesis discusses how the crossbow brooch was constructed, considered and discussed within late Roman society. In particular, the rhetorical and political utilities of the crossbow brooch are explored to contemplate its roles in localised identity work within various social practices which allowed contextually dependent subject positions to be claimed. It is argued that the crossbow brooch was associated with a particular discourse relating to the concepts of gender and service that acquired the status of ‘truth.’ Thus, while this brooch type could have signified a potential multiplicity of contextually dependent meanings within society, this ‘truth’ was an important discourse in structuring power relations and one that had permeated society to reach its widest influence during the mid-late fourth century. Consequently, when the networks supplying this material culture failed c. AD 400, the construction of new discursive ‘truths’ and subsequent power relationships would have been required in Britain as the empire’s occupation disintegrated

Exploring bycatch diversity of organisms in whole genome sequencing of Erebidae moths (Lepidoptera)

Models estimate that up to 80% of all butterfly and moth species host vertically transmitted endosymbiotic microorganisms, which can affect the host fitness, metabolism, reproduction, population dynamics, and genetic diversity, among others. The supporting empirical data are however currently highly biased towards the generally more colourful butterflies, and include less information about moths. Additionally, studies of symbiotic partners of Lepidoptera predominantly focus on the common bacterium Wolbachia pipientis, while infections by other inherited microbial partners have more rarely been investigated. Here, we mine the whole genome sequence data of 47 species of Erebidae moths, with the aims to both inform on the diversity of symbionts potentially associated with this Lepidoptera group, and discuss the potential of metagenomic approaches to inform on host associated microbiome diversity. Based on the result of Kraken2 and MetaPhlAn2 analyses, we found clear evidence of the presence of Wolbachia in four species. Our result also suggests the presence of three other bacterial symbionts (Burkholderia spp., Sodalis spp. and Arsenophonus spp.) in three other moth species. Additionally, we recovered genomic material from bracovirus in about half of our samples. The detection of the latter, usually found in mutualistic association to braconid parasitoid wasps, may inform on host-parasite interactions that take place in the natural habitat of the Erebidae moths, suggesting either contamination with material from species of the host community network, or horizontal transfer of members of the microbiome between interacting species.Peer reviewe

Novel Approach to the Energy Analysis of Mine Cooling Strategies

The extraction of minerals and coal at increasing depth, employing higher-powered, mechanized machinery to increase production levels imposes an increased burden on the ability to maintain an acceptable mine climate. Any deterioration in the mine climate within working zones may adversely affect the health and safety of the workforce. The combination of the optimal design of the mine system layout, together with the selective application of suitable ventilation and cooling systems, may be used to control the climate within working zones. The adoption of mechanical cooling within mines is an expensive process in terms of both capital and operating costs. Therefore, as mechanized mining takes place at increased depth, the need to maintain or improve the mine climate becomes more expensive. Consequently, to decrease overhead costs, reduce energy consumption and meet current and future environmental obligations, it is essential to provide the mine operator with a method with which to determine the most cost effective and efficient mine cooling system. To perform this analysis it is necessary to have a good understanding of the energy balances governing both the operation and utilization of a cooling system. This paper introduces the application of a novel approach to energy analysis of mine cooling systems, with a combination of the concepts of exergy and composite curves. These methods are used extensively throughout chemical and process industries to increase energy efficiency and reduce capital and operating costs. An outline of the methods employed in the application of these techniques to the energy analysis of a mining cooling system is presented

Museomics of a rare taxon: placing Whalleyanidae in the Lepidoptera Tree of Life

https://doi.org/10.1111/syen.12503Museomics is a valuable approach that utilizes the diverse biobanks that are natural history museums. The ability to sequence genomes from old specimens has expanded not only the variety of interesting taxa available to study but also the scope of questions that can be investigated in order to further knowledge about biodiversity. Here, we present whole genome sequencing results from the enigmatic genus Whalleyana (comprising two species - occurring in drier biomes of Madagascar - previously placed in a monotypic superfamily, Whalleyanoidea), as well as from certain species of the families Callidulidae and Hyblaeidae (Calliduloidea and Hyblaeoidea, respectively). Library preparation was carried out on four museum specimens and one existing DNA extract and sequenced with Illumina short reads. De novo assembly resulted in highly fragmented genomes with the N50 ranging from 317 to 2078 bp. Mining of a manually curated gene set of 331 genes from these draft genomes had an overall gene recovery rate of 64-90%. Phylogenetic analysis places Whalleyana as sister to Callidulidae and Hyblaea as sister to Pyraloidea. Since the former sister-group relationship turns out to be also supported by ten morphological synapomorphies, we propose to formally assign the Whalleyanidae to the superfamily Calliduloidea. These results highlight the usefulness of not only museum specimens but also existing DNA extracts, for whole genome sequencing and gene mining for phylogenomic studies.Peer reviewe

Divergent Gene Expression Following Duplication of Meiotic Genes in the Stick Insect Clitarchus hookeri

evab060Some animal groups, such as stick insects (Phasmatodea), have repeatedly evolved alternative reproductive strategies, including parthenogenesis. Genomic studies have found modification of the genes underlying meiosis exists in some of these animals. Here we examine the evolution of copy number, evolutionary rate, and gene expression in candidate meiotic genes of the New Zealand geographic parthenogenetic stick insect Clitarchus hookeri. We characterized 101 genes from a de novo transcriptome assembly from female and male gonads that have homology with meiotic genes from other arthropods. For each gene we determined copy number, the pattern of gene duplication relative to other arthropod orthologs, and the potential for meiosis-specific expression. There are five genes duplicated in C hookers; including one also duplicated in the stick insect Timema cristinae, that are not or are uncommonly duplicated in other arthropods. These included two sister chromatid cohesion associated genes (SA2 and SCC2), a recombination gene (HOPI), an RNA-silencing gene (AGO2) and a cell-cycle regulation gene (WEE1). Interestingly, WEE1 and SA2 are also duplicated in the cyclical parthenogenetic aphid Acyrthosiphon pisum and Daphnia duplex, respectively, indicating possible roles in the evolution of reproductive mode. Three of these genes (SA2, SCC2, and WEE1) have one copy displaying gonad-specific expression. All genes, with the exception of WEE1, have significantly different nonsynonymous/synonymous ratios between the gene duplicates, indicative of a shift in evolutionary constraints following duplication. These results suggest that stick insects may have evolved genes with novel functions in gamete production by gene duplication.Peer reviewe

High genetic connectivity among large populations of Pteronotus gymnonotus in bat caves in Brazil and its implications for conservation

Bat caves in the Neotropical region harbor exceptional bat populations (> 100,000 individuals). These populations play a wider role in ecological interactions, are vulnerable due to their restriction to caves, and have a disproportionate conservation value. Current knowledge of bat caves in Brazil is still small. However, systematic monitoring of some bat caves in northeastern Brazil shows that they experience strong population fluctuations over short periods of time, suggesting large-scale movements between roosts and a much broader use of the landscape than previously considered. Spatio-temporal reproductive connectivity between distant populations would change our understanding of the use of roosts among bat species in Brazil, and important gaps in knowledge of long-distance bat movements in the country would be filled. Here, we used ddRADseq data to analyze the genetic structure of Pteronotus gymnonotus across nine bat caves over 700 km. Our results indicate the lack of a clear geographic structure with gene flow among all the caves analyzed, suggesting that P. gymnonotus uses a network of bat caves geographically segregated hundreds of kilometers apart. Facing strong anthropogenic impacts and an underrepresentation of caves in conservation action plans worldwide, the genetic connectivity demonstrated here confirms that bat caves are priority sites for bat and speleological conservation in Brazil and elsewhere. Moreover, our results demonstrate a warning call: the applied aspects of the environmental licensing process of the mining sector and its impact must be reviewed, not only in Brazil, but wherever this licensing process affects caves having exceptional bat populations.Peer reviewe

The (non) accuracy of mitochondrial genomes for family-level phylogenetics in Erebidae (Lepidoptera)

The use of molecular data to study the evolutionary history of organisms has revolutionized the field of systematics. Now with the appearance of high throughput sequencing (HTS) technologies, more and more genetic sequence data are available. One of the important sources of genetic data for phylogenetic analyses has been mitochondrial DNA. The limitations of mitochondrial DNA for the study of phylogenetic relationships have been thoroughly explored in the age of single locus phylogenetic studies. Now with the appearance of genomic scale data, increasing number of mitochondrial genomes are available, leading to an increasing number of mitophylogenomic studies. Here, we assemble 47 mitochondrial genomes using whole genome Illumina short reads from representatives of the family Erebidae (Lepidoptera), in order to evaluate the accuracy of mitochondrial genome application in resolving deep phylogenetic relationships. We find that mitogenomes are inadequate for resolving subfamily-level relationships in Erebidae, but given good taxon sampling, we see its potential in resolving lower level phylogenetic relationships.Peer reviewe