Phylogenomics recovers multiple origins of portable case making in caddisflies (Insecta: Trichoptera), nature's underwater architects.

Caddisflies (Trichoptera) are among the most diverse groups of freshwater animals with more than 16 000 described species. They play a fundamental role in freshwater ecology and environmental engineering in streams, rivers and lakes. Because of this, they are frequently used as indicator organisms in biomonitoring programmes. Despite their importance, key questions concerning the evolutionary history of caddisflies, such as the timing and origin of larval case making, remain unanswered owing to the lack of a well-resolved phylogeny. Here, we estimated a phylogenetic tree using a combination of transcriptomes and targeted enrichment data for 207 species, representing 48 of 52 extant families and 174 genera. We calibrated and dated the tree with 33 carefully selected fossils. The first caddisflies originated approximately 295 million years ago in the Permian, and major suborders began to diversify in the Triassic. Furthermore, we show that portable case making evolved in three separate lineages, and shifts in diversification occurred in concert with key evolutionary innovations beyond case making.

Effects of migration rates and vaccination on the spread of yellow fever in Latin American communities.

Objective: To assess how relevant the flow of people between communities is, compared to vaccination and type of vector, on the spread and potential outbreaks of yellow fever in a disease-free host community. Methods: Using a SEIRV-SEI model for humans and vectors, we applied numerical simulations to the scenarios: (1) migration from an endemic community to a disease-free host community, comparing the performance of Haemagogus janthinomys and Aedes aegypti as vectors; (2) migration through a transit community located on a migratory route, where the disease is endemic, to a disease-free one; and (3) effects of different vaccination rates in the host community, considering the vaccination of migrants upon arrival. Results: Results show no remarkable differences between scenarios 1 and 2. The type of vector and vaccination coverage in the host community are more relevant for the occurrence of outbreaks than migration rates, with H. janthinomys being more effective than A. aegypti. Conclusions: With vaccination being more determinant for a potential outbreak than migration rates, vaccinating migrants on arrival may be one of the most effective measures against yellow fever. Furthermore, H. janthinomys is a more competent vector than A. aegypti at similar densities, but the presence of A. aegypti is a warning to maintain vaccination above recommended levels.

Effects of migration rates and vaccination on the spread of yellow fever in Latin American communities

[ABSTRACT]. Objective. To assess how relevant the flow of people between communities is, compared to vaccination and type of vector, on the spread and potential outbreaks of yellow fever in a disease-free host community. Methods. Using a SEIRV-SEI model for humans and vectors, we applied numerical simulations to the scenarios: (1) migration from an endemic community to a disease-free host community, comparing the performance of Haemagogus janthinomys and Aedes aegypti as vectors; (2) migration through a transit community located on a migratory route, where the disease is endemic, to a disease-free one; and (3) effects of different vaccination rates in the host community, considering the vaccination of migrants upon arrival. Results. Results show no remarkable differences between scenarios 1 and 2. The type of vector and vaccination coverage in the host community are more relevant for the occurrence of outbreaks than migration rates, with H. janthinomys being more effective than A. aegypti. Conclusions. With vaccination being more determinant for a potential outbreak than migration rates, vac- cinating migrants on arrival may be one of the most effective measures against yellow fever. Furthermore, H. janthinomys is a more competent vector than A. aegypti at similar densities, but the presence of A. aegypti is a warning to maintain vaccination above recommended levels.

[RESUMEN]. Objetivo. Evaluar la importancia del flujo de personas entre comunidades, en comparación con la vacunación y el tipo de vector, para la propagación y los posibles brotes de fiebre amarilla en una comunidad de acogida libre de la enfermedad. Métodos. Con el empleo de un modelo SEIRV—SEI para personas y vectores, aplicamos simulaciones numéricas a las siguientes situaciones hipotéticas: 1) migración desde una comunidad con endemicidad a una comunidad de acogida libre de la enfermedad, en la que se compararon los resultados producidos por Haemagogus janthinomys y Aedes aegypti como vectores; 2) migración a través de una comunidad de tránsito situada en una ruta migratoria, donde la enfermedad es endémica, hacia otra comunidad libre de la enfermedad; y 3) efectos de tasas de vacunación diferentes en la comunidad de acogida, tomando en consideración la vacunación de las personas migrantes a su llegada. Resultados. Los resultados no muestran diferencias notables entre las situaciones 1 y 2. En cuanto a la aparición de brotes, tanto la cobertura vacunal en la comunidad de acogida como el tipo de vector tienen más importancia que las tasas de migración; y H. janthinomys muestra mayor eficacia que A. aegypti. Conclusiones. Dado que, para determinar la aparición de un posible brote, la vacunación tiene mayor importancia que las tasas de migración, la vacunación de las personas migrantes a su llegada puede ser una de las medidas más eficaces contra la fiebre amarilla. Además, a densidades similares, H. janthinomys es un vector más competente que A. aegypti, por lo que la presencia de A. aegypti constituye una señal de alerta para mantener la vacunación por encima de los niveles recomendados.

[RESUMO]. Objetivo. Avaliar a relevância do fluxo de pessoas entre comunidades em comparação com a vacinação e tipo de vetor para a propagação e potenciais surtos de febre amarela em uma comunidade de destino livre da doença. Métodos. Usando um modelo SEIRV-SEI para humanos e vetores, foram aplicadas simulações numéricas aos seguintes cenários: (1) migração de uma comunidade endêmica para uma comunidade de destino livre da doença, comparando o desempenho de Haemagogus janthinomys e de Aedes aegypti como vetores; (2) migração através de uma comunidade de trânsito localizada em uma rota migratória, onde a doença é endêmica, para uma comunidade de destino livre da doença; e (3) efeitos de diferentes taxas de vacinação na comunidade de destino, considerando-se a vacinação dos migrantes ao chegarem. Resultados. Os resultados não revelaram diferenças marcantes entre os cenários 1 e 2. O tipo de vetor e a cobertura vacinal na comunidade de destino são mais relevantes para a ocorrência de surtos do que as taxas de migração; o vetor H. janthinomys é mais efetivo do que A. aegypti. Conclusões. Na medida em que a vacinação é mais determinante para um potencial surto que as taxas de migração, a vacinação de migrantes na chegada pode ser uma das medidas mais efetivas contra a febre amarela. Além disso, o H. janthinomys é um vetor mais competente do que o A. aegypti em densidades similares, mas a presença de A. aegypti é um alerta para manter a vacinação acima dos níveis recomendados.

Espalhamento da febre amarela no contexto da crise migratória na América Latina: um estudo de modelagem matemática de múltiplos cenários / Spread of yellow fever in the context of the Latin American migration crisis: a mathematical modelling study of multiple scenarios

INTRODUÇÃO: As doenças infecciosas desconhecem fronteiras e, com a crise climática, a disseminação de doenças sensíveis ao clima tende a aumentar em frequência, intensidade e expansão geográfica. Isso preocupa as organizações humanitárias pois as crises humanitárias são alteradas e entrelaçadas pelos padrões climáticos, cujas interações podem ser imprevisíveis. Com a pandemia da Covid19 agravou-se a estigmatização dos migrantes como meros vetores de doenças, negligenciando as circunstâncias determinantes para propagação de doenças perante a migração. MÉTODOS: A tese é composta por três manuscritos nos quais são aplicados modelos epidêmicos compartimentais: (i) modelo SEIRV-SEI para humanos e vetores aplicado à migração unidirecional de uma comunidade endêmica para uma comunidade hospedeira livre de doença; (ii) SEIRV-SEI para humanos e vetores aplicado a três diferentes populações acopladas - caravanas, comunidade endêmica e comunidade livre de doença, avaliando os efeitos da vacinação em comunidades endêmicas e em caravanas; (iii) o modelo SEIR-SEI para humanos, macacos e vetores onde o tempo gasto para atravessar a floresta é uma medida de exposição. RESULTADOS: O primeiro artigo mostra que o tipo de vetor e a cobertura vacinal nas comunidades hospedeiras são mais relevantes para a ocorrência de surtos do que as taxas de migração. O segundo estudo demonstra que quando as comunidades endêmicas são fonte de migração, a imunidade do rebanho é determinante, mas a vacinação de caravanas é de longe a intervenção mais significativa para proteger comunidades do risco de introdução da FA. Por fim, os resultados mostram que poderia haver mais de 23 mil casos humanos se ocorrer um surto de FA no Gap de Darién, e 19.000 deles deixariam a floresta ainda infectados. O número de mortes está fortemente relacionado ao tempo para atravessar a floresta. CONCLUSÃO: A prevenção de surtos de doenças infecciosas sensíveis ao clima no contexto da migração deve ser um esforço conjunto de interesse comum. Estabelecer corredores de migração oficiais e seguros onde seja possível vacinar os migrantes pode contribuir significativamente para o controle de doenças. Os migrantes são infinitamente mais vulneráveis a infecções, enquanto os responsáveis pela disseminação de doenças infecciosas sensíveis ao clima são a falta de vacinação consistente e as mudanças climáticas. Somente um esforço coletivo deliberado e consistente de vacinação pode garantir a migração segura como direito humano e para adaptação climática.

INTRODUCTION: Infectious diseases do not recognize borders, and with the climate crisis, the spread of climate-sensitive diseases is expected to increase in frequency, intensity, and geographic expansion. This poses a serious concern for humanitarian organizations as weather patterns can alter and intertwine humanitarian crises, leading to unpredictable interactions. Furthermore, with the ongoing Covid19 pandemic, migrants have been stigmatized as mere carriers of diseases, ignoring the underlying circumstances that lead to the spread of diseases during migration. METHODS: The thesis consists of three manuscripts that use compartmental epidemic models. The first manuscript uses a SEIRV-SEI model to study one-way migration from an endemic community to a disease-free host community. The second manuscript uses a SEIRV-SEI model to study three coupled human populations: caravans, resident endemic communities, and a disease-free community to assess the effects of vaccination in endemic communities and caravans. The third manuscript uses a SEIR-SEI model to study humans, monkeys, and vectors, where the time taken to cross the Darién forest is a measure of exposure to the Yellow Fever virus. RESULTS: The first manuscript shows that the type of vector and vaccination coverage in host communities are more relevant for the occurrence of outbreaks than migration rates. The second manuscript demonstrates that vaccinating caravans is the most significant intervention to protect disease-free communities from the risk of Yellow Fever introduction. The third manuscript shows that over 23,000 human cases may occur if an outbreak occurs in the Darién Gap, with 19,000 leaving the forest still infected. The number of deaths is strongly related to the time taken to cross the forest. CONCLUSION: Preventing outbreaks of climate-sensitive infectious diseases during migration must be a collective effort. Establishing official and safe migration corridors where migrants can be vaccinated can significantly contribute to controlling diseases such as Yellow Fever. Migrants are particularly vulnerable to infections, and the spread of climate-sensitive infectious diseases is linked to the lack of consistent vaccination in a changing climate. Only a collective and consistent vaccination effort can guarantee safe migration as a human right and serve as a climate adaptation measure.

Effects of migration rates and vaccination on the spread of yellow fever in Latin American communities / Efectos de las tasas de migración y de la vacunación en la propagación de la fiebre amarilla en comunidades de América Latina / Efeitos das taxas de migração e vacinação na propagação da febre amarela em comunidades latino-americanas

ABSTRACT Objective. To assess how relevant the flow of people between communities is, compared to vaccination and type of vector, on the spread and potential outbreaks of yellow fever in a disease-free host community. Methods. Using a SEIRV-SEI model for humans and vectors, we applied numerical simulations to the scenarios: (1) migration from an endemic community to a disease-free host community, comparing the performance of Haemagogus janthinomys and Aedes aegypti as vectors; (2) migration through a transit community located on a migratory route, where the disease is endemic, to a disease-free one; and (3) effects of different vaccination rates in the host community, considering the vaccination of migrants upon arrival. Results. Results show no remarkable differences between scenarios 1 and 2. The type of vector and vaccination coverage in the host community are more relevant for the occurrence of outbreaks than migration rates, with H. janthinomys being more effective than A. aegypti. Conclusions. With vaccination being more determinant for a potential outbreak than migration rates, vaccinating migrants on arrival may be one of the most effective measures against yellow fever. Furthermore, H. janthinomys is a more competent vector than A. aegypti at similar densities, but the presence of A. aegypti is a warning to maintain vaccination above recommended levels.

RESUMEN Objetivo. Evaluar la importancia del flujo de personas entre comunidades, en comparación con la vacunación y el tipo de vector, para la propagación y los posibles brotes de fiebre amarilla en una comunidad de acogida libre de la enfermedad. Métodos. Con el empleo de un modelo SEIRV—SEI para personas y vectores, aplicamos simulaciones numéricas a las siguientes situaciones hipotéticas: 1) migración desde una comunidad con endemicidad a una comunidad de acogida libre de la enfermedad, en la que se compararon los resultados producidos por Haemagogus janthinomys y Aedes aegypti como vectores; 2) migración a través de una comunidad de tránsito situada en una ruta migratoria, donde la enfermedad es endémica, hacia otra comunidad libre de la enfermedad; y 3) efectos de tasas de vacunación diferentes en la comunidad de acogida, tomando en consideración la vacunación de las personas migrantes a su llegada. Resultados. Los resultados no muestran diferencias notables entre las situaciones 1 y 2. En cuanto a la aparición de brotes, tanto la cobertura vacunal en la comunidad de acogida como el tipo de vector tienen más importancia que las tasas de migración; y H. janthinomys muestra mayor eficacia que A. aegypti. Conclusiones. Dado que, para determinar la aparición de un posible brote, la vacunación tiene mayor importancia que las tasas de migración, la vacunación de las personas migrantes a su llegada puede ser una de las medidas más eficaces contra la fiebre amarilla. Además, a densidades similares, H. janthinomys es un vector más competente que A. aegypti, por lo que la presencia de A. aegypti constituye una señal de alerta para mantener la vacunación por encima de los niveles recomendados.

RESUMO Objetivo. Avaliar a relevância do fluxo de pessoas entre comunidades em comparação com a vacinação e tipo de vetor para a propagação e potenciais surtos de febre amarela em uma comunidade de destino livre da doença. Métodos. Usando um modelo SEIRV-SEI para humanos e vetores, foram aplicadas simulações numéricas aos seguintes cenários: (1) migração de uma comunidade endêmica para uma comunidade de destino livre da doença, comparando o desempenho de Haemagogus janthinomys e de Aedes aegypti como vetores; (2) migração através de uma comunidade de trânsito localizada em uma rota migratória, onde a doença é endêmica, para uma comunidade de destino livre da doença; e (3) efeitos de diferentes taxas de vacinação na comunidade de destino, considerando-se a vacinação dos migrantes ao chegarem. Resultados. Os resultados não revelaram diferenças marcantes entre os cenários 1 e 2. O tipo de vetor e a cobertura vacinal na comunidade de destino são mais relevantes para a ocorrência de surtos do que as taxas de migração; o vetor H. janthinomys é mais efetivo do que A. aegypti. Conclusões. Na medida em que a vacinação é mais determinante para um potencial surto que as taxas de migração, a vacinação de migrantes na chegada pode ser uma das medidas mais efetivas contra a febre amarela. Além disso, o H. janthinomys é um vetor mais competente do que o A. aegypti em densidades similares, mas a presença de A. aegypti é um alerta para manter a vacinação acima dos níveis recomendados.

Family dinner: Transcriptional plasticity of five Noctuidae (Lepidoptera) feeding on three host plant species.

Polyphagous insects often show specialization in feeding on different host plants in terms of survival and growth and, therefore, can be considered minor or major pests of particular hosts. Whether polyphagous insects employ a common transcriptional response to cope with defenses from diverse host plants is under-studied. We focused on patterns of transcriptional plasticity in polyphagous moths (Noctuidae), of which many species are notorious pests, in relation to herbivore performance on different host plants. We compared the transcriptional plasticity of five polyphagous moth species feeding and developing on three different host plant species. Using a comparative phylogenetic framework, we evaluated if successful herbivory, as measured by larval performance, is determined by a shared or lineage-specific transcriptional response. The upregulated transcriptional activity, or gene expression pattern, of larvae feeding on the different host plants and artificial control diet was highly plastic and moth species-specific. Specialization, defined as high herbivore success for specific host plants, was not generally linked to a lower number of induced genes. Moths that were more distantly related and showing high herbivore success for certain host plants showed shared expression of multiple homologous genes, indicating convergence. We further observed specific transcriptional responses within phylogenetic lineages. These expression patterns for specific host plant species are likely caused by shared evolutionary histories, for example, symplesiomorphic patterns, and could therefore not be associated with herbivore success alone. Multiple gene families, with roles in plant digestion and detoxification, were widely expressed in response to host plant feeding but again showed highly moth species-specific. Consequently, high herbivore success for specific host plants is also driven by species-specific transcriptional plasticity. Thus, potential pest moths display a complex and species-specific transcriptional plasticity.

Expanding the Menu: Are Polyphagy and Gene Family Expansions Linked across Lepidoptera?

Evolutionary expansions and contractions of gene families are often correlated with key innovations and/or ecological characteristics. In butterflies and moths (Lepidoptera), expansions of gene families involved in detoxification of plant specialized metabolites are hypothesized to facilitate a polyphagous feeding style. However, analyses supporting this hypothesis are mostly based on a limited number of lepidopteran species. We applied a phylogenomics approach, using 37 lepidopteran genomes, to analyze if gene family evolution (gene gain and loss) is associated with the evolution of polyphagy. Specifically, we compared gene counts and evolutionary gene gain and loss rates of gene families involved in adaptations with plant feeding. We correlated gene evolution to host plant family range (phylogenetic diversity) and specialized metabolite content of plant families (functional metabolite diversity). We found a higher rate for gene loss than gene gain in Lepidoptera, a potential consequence of genomic rearrangements and deletions after (potentially small-scale) duplication events. Gene family expansions and contractions varied across lepidopteran families, and were associated to host plant use and specialization levels. Within the family Noctuidae, a higher expansion rate for gene families involved in detoxification can be related to the large number of polyphagous species. However, gene family expansions are observed in both polyphagous and monophagous lepidopteran species and thus seem to be species-specific in the taxa sampled. Nevertheless, a significant positive correlation of gene counts of the carboxyl- and choline esterase and glutathione-S-transferase detoxification gene families with the level of polyphagy was identified across Lepidoptera.

Reinstatement of Athis miastagma (Dyar, 1925) (Lepidoptera: Castniidae) as a valid species inhabiting the Pacific slope of Central Mexico.

Mexico is the Mesoamerican country with the highest number of Castniidae species (12), most of which are found in the dry regions of the country. Among these, Athis hechtiae (Dyar, 1910) was considered a species widely distributed in Mexico after Athis miastagma (Dyar, 1925) was synonymized with A. hechtiae over two decades ago. A genetic and morphological study, as well as details of the natural history of various populations of these two taxa have led us to restore Athis miastagma as a valid species (stat. rest.), increasing the number of castniids recorded in Mexico to 13.

Genome and transcriptome analysis of the beet armyworm Spodoptera exigua reveals targets for pest control.

The genus Spodoptera (Lepidoptera: Noctuidae) includes some of the most infamous insect pests of cultivated plants including Spodoptera frugiperda, Spodoptera litura, and Spodoptera exigua. To effectively develop targeted pest control strategies for diverse Spodoptera species, genomic resources are highly desired. To this aim, we provide the genome assembly and developmental transcriptome comprising all major life stages of S. exigua, the beet armyworm. Spodoptera exigua is a polyphagous herbivore that can feed on > 130 host plants, including several economically important crops. The 419 Mb beet armyworm genome was sequenced from a female S. exigua pupa. Using a hybrid genome sequencing approach (Nanopore long-read data and Illumina short read), a high-quality genome assembly was achieved (N50 = 1.1 Mb). An official gene set (18,477 transcripts) was generated by automatic annotation and by using transcriptomic RNA-seq datasets of 18 S. exigua samples as supporting evidence. In-depth analyses of developmental stage-specific expression combined with gene tree analyses of identified homologous genes across Lepidoptera genomes revealed four potential genes of interest (three of them Spodoptera-specific) upregulated during first- and third-instar larval stages for targeted pest-outbreak management. The beet armyworm genome sequence and developmental transcriptome covering all major developmental stages provide critical insights into the biology of this devastating polyphagous insect pest species worldwide. In addition, comparative genomic analyses across Lepidoptera significantly advance our knowledge to further control other invasive Spodoptera species and reveals potential lineage-specific target genes for pest control strategies.

Great chemistry between us: The link between plant chemical defenses and butterfly evolution.

Plants constantly cope with insect herbivory, which is thought to be the evolutionary driver for the immense diversity of plant chemical defenses. Herbivorous insects are in turn restricted in host choice by the presence of plant chemical defense barriers. In this study, we analyzed whether butterfly host-plant patterns are determined by the presence of shared plant chemical defenses rather than by shared plant evolutionary history. Using correlation and phylogenetic statistics, we assessed the impact of host-plant chemical defense traits on shaping northwestern European butterfly assemblages at a macroevolutionary scale. Shared chemical defenses between plant families showed stronger correlation with overlap in butterfly assemblages than phylogenetic relatedness, providing evidence that chemical defenses may determine the assemblage of butterflies per plant family rather than shared evolutionary history. Although global congruence between butterflies and host-plant families was detected across the studied herbivory interactions, cophylogenetic statistics showed varying levels of congruence between butterflies and host chemical defense traits. We attribute this to the existence of multiple antiherbivore traits across plant families and the diversity of insect herbivory associations per plant family. Our results highlight the importance of plant chemical defenses in community ecology through their influence on insect assemblages.

Comparative transcriptomics of ice-crawlers demonstrates cold specialization constrains niche evolution in a relict lineage.

Key changes in ecological niche space are often critical to understanding how lineages diversify during adaptive radiations. However, the converse, or understanding why some lineages are depauperate and relictual, is more challenging, as many factors may constrain niche evolution. In the case of the insect order Grylloblattodea, highly conserved thermal breadth is assumed to be closely tied to their relictual status, but has not been formerly tested. Here, we investigate whether evolutionary constraints in the physiological tolerance of temperature can help explain relictualism in this lineage. Using a comparative transcriptomics approach, we investigate gene expression following acute heat and cold stress across members of Grylloblattodea and their sister group, Mantophasmatodea. We additionally examine patterns of protein evolution, to identify candidate genes of positive selection. We demonstrate that cold specialization in Grylloblattodea has been accompanied by the loss of the inducible heat shock response under both acute heat and cold stress. Additionally, there is widespread evidence of selection on protein-coding genes consistent with evolutionary constraints due to cold specialization. This includes positive selection on genes involved in trehalose transport, metabolic function, mitochondrial function, oxygen reduction, oxidative stress, and protein synthesis. These patterns of molecular adaptation suggest that Grylloblattodea have undergone evolutionary trade-offs to survive in cold habitats and should be considered highly vulnerable to climate change. Finally, our transcriptomic data provide a robust backbone phylogeny for generic relationships within Grylloblattodea and Mantophasmatodea. Major phylogenetic splits in each group relate to arid conditions driving biogeographical patterns, with support for a sister-group relationship between North American Grylloblatta and Altai-Sayan Grylloblattella, and a range disjunction in Namibia splitting major clades within Mantophasmatodea.

Author Correction: Phylogenomic analysis sheds light on the evolutionary pathways towards acoustic communication in Orthoptera.

An amendment to this paper has been published and can be accessed via a link at the top of the paper.

Phylogenomic analysis sheds light on the evolutionary pathways towards acoustic communication in Orthoptera.

Acoustic communication is enabled by the evolution of specialised hearing and sound producing organs. In this study, we performed a large-scale macroevolutionary study to understand how both hearing and sound production evolved and affected diversification in the insect order Orthoptera, which includes many familiar singing insects, such as crickets, katydids, and grasshoppers. Using phylogenomic data, we firmly establish phylogenetic relationships among the major lineages and divergence time estimates within Orthoptera, as well as the lineage-specific and dynamic patterns of evolution for hearing and sound producing organs. In the suborder Ensifera, we infer that forewing-based stridulation and tibial tympanal ears co-evolved, but in the suborder Caelifera, abdominal tympanal ears first evolved in a non-sexual context, and later co-opted for sexual signalling when sound producing organs evolved. However, we find little evidence that the evolution of hearing and sound producing organs increased diversification rates in those lineages with known acoustic communication.

An influential meal: host plant dependent transcriptional variation in the beet armyworm, Spodoptera exigua (Lepidoptera: Noctuidae).

BACKGROUND: To understand the genetic mechanisms of insect herbivory, the transcriptional response of insects feeding on different host plant species has to be studied. Here, we generated gene expression data of the generalist herbivore Spodoptera exigua (Hübner) feeding on three selected host plant species and a control (artificial diet). The host plant species used in this study -cabbage (Brassica oleracea), maize (Zea mays) and tobacco (Nicotiana tabacum)- are members of different plant families that each employ specific defence mechanisms and toxins. RESULTS: Spodoptera exigua larvae had a higher growth rate, indicator for herbivore success, when feeding on Z. mays compared to larvae feeding on B. oleracea or N. tabacum. Larvae feeding on the different host plant species showed divergent transcriptional responses. We identified shared and unique gene expression patterns dependent of the host plant species the larvae fed on. Unique gene expression patterns, containing uniquely upregulated transcripts including specific detoxification genes, were found for larvae feeding on either B. oleracea or N. tabacum. No diet-specific gene cluster was identified for larvae feeding on the host for which larvae showed optimal herbivore success, Z. mays, or artificial diet. In contrast, for larvae feeding on hosts for which they showed low herbivore success, specific diet-dependent gene clusters were identified. Functional annotation of these clusters indicates that S. exigua larvae deploy particular host plant-specific genes for digestion and detoxification. CONCLUSIONS: The lack of a host plant-specific gene activity for larvae feeding on Z. mays and the artificial diet suggest a general and non-specific gene activity for host plants with optimal herbivore success. Whereas the finding of specific gene clusters containing particular digestion and detoxifying genes expressed in larvae feeding on B. oleracea and N. tabacum, with low herbivore success, imply a host plant-specific gene activity for larvae feeding on host plants with suboptimal herbivore success. This observation leads to the conclusion that a polyphagous herbivore is able to feed on a large variation of host plants due to the flexibility and diversity of genes involved in digestion and detoxification that are deployed in response to particular host plant species.

An integrative phylogenomic approach illuminates the evolutionary history of cockroaches and termites (Blattodea).

Phylogenetic relationships among subgroups of cockroaches and termites are still matters of debate. Their divergence times and major phenotypic transitions during evolution are also not yet settled. We addressed these points by combining the first nuclear phylogenomic study of termites and cockroaches with a thorough approach to divergence time analysis, identification of endosymbionts, and reconstruction of ancestral morphological traits and behaviour. Analyses of the phylogenetic relationships within Blattodea robustly confirm previously uncertain hypotheses such as the sister-group relationship between Blaberoidea and remaining Blattodea, and Lamproblatta being the closest relative to the social and wood-feeding Cryptocercus and termites. Consequently, we propose new names for various clades in Blattodea: Cryptocercus + termites = Tutricablattae; Lamproblattidae + Tutricablattae = Kittrickea; and Blattoidea + Corydioidea = Solumblattodea. Our inferred divergence times contradict previous studies by showing that most subgroups of Blattodea evolved in the Cretaceous, reducing the gap between molecular estimates of divergence times and the fossil record. On a phenotypic level, the blattodean ground-plan is for egg packages to be laid directly in a hole while other forms of oviposition, including ovovivipary and vivipary, arose later. Finally, other changes in egg care strategy may have allowed for the adaptation of nest building and other novelties.

Evolutionary history of Polyneoptera and its implications for our understanding of early winged insects.

Polyneoptera represents one of the major lineages of winged insects, comprising around 40,000 extant species in 10 traditional orders, including grasshoppers, roaches, and stoneflies. Many important aspects of polyneopteran evolution, such as their phylogenetic relationships, changes in their external appearance, their habitat preferences, and social behavior, are unresolved and are a major enigma in entomology. These ambiguities also have direct consequences for our understanding of the evolution of winged insects in general; for example, with respect to the ancestral habitats of adults and juveniles. We addressed these issues with a large-scale phylogenomic analysis and used the reconstructed phylogenetic relationships to trace the evolution of 112 characters associated with the external appearance and the lifestyle of winged insects. Our inferences suggest that the last common ancestors of Polyneoptera and of the winged insects were terrestrial throughout their lives, implying that wings did not evolve in an aquatic environment. The appearance of the first polyneopteran insect was mainly characterized by ancestral traits such as long segmented abdominal appendages and biting mouthparts held below the head capsule. This ancestor lived in association with the ground, which led to various specializations including hardened forewings and unique tarsal attachment structures. However, within Polyneoptera, several groups switched separately to a life on plants. In contrast to a previous hypothesis, we found that social behavior was not part of the polyneopteran ground plan. In other traits, such as the biting mouthparts, Polyneoptera shows a high degree of evolutionary conservatism unique among the major lineages of winged insects.

Reanalyzing the Palaeoptera problem - The origin of insect flight remains obscure.

The phylogenetic relationships of the winged insect lineages - mayflies (Ephemeroptera), damselflies and dragonflies (Odonata), and all other winged insects (Neoptera) - are still controversial with three hypotheses supported by different datasets: Palaeoptera, Metapterygota and Chiastomyaria. Here, we reanalyze available phylogenomic data with a focus on detecting confounding and alternative signal. In this context, we provide a framework to quantitatively evaluate and assess incongruent molecular phylogenetic signal inherent in phylogenomic datasets. Despite overall support for the Palaeoptera hypothesis, we also found considerable signal for Chiastomyaria, which is not easily detectable by standardized tree inference approaches. Analyses of the accumulation of signal across gene partitions showed that signal accumulates gradually. However, even in case signal only slightly supported one over the other hypothesis, topologies inferred from large datasets switch from statistically strongly supported Palaeoptera to strongly supported Chiastomyaria. From a morphological point of view, Palaeoptera currently appears to be the best-supported hypothesis; however, recent analyses were restricted to head characters. Phylogenetic approaches covering all organ systems including analyses of potential functional or developmental convergence are still pending so that the Palaeoptera problem has to be considered an open question in insect systematics.

Comparative transcriptomics reveal developmental turning points during embryogenesis of a hemimetabolous insect, the damselfly Ischnura elegans.

Identifying transcriptional changes during embryogenesis is of crucial importance for unravelling evolutionary, molecular and cellular mechanisms that underpin patterning and morphogenesis. However, comparative studies focusing on early/embryonic stages during insect development are limited to a few taxa. Drosophila melanogaster is the paradigm for insect development, whereas comparative transcriptomic studies of embryonic stages of hemimetabolous insects are completely lacking. We reconstructed the first comparative transcriptome covering the daily embryonic developmental progression of the blue-tailed damselfly Ischnura elegans (Odonata), an ancient hemimetabolous representative. We identified a "core" set of 6,794 transcripts - shared by all embryonic stages - which are mainly involved in anatomical structure development and cellular nitrogen compound metabolic processes. We further used weighted gene co-expression network analysis to identify transcriptional changes during Odonata embryogenesis. Based on these analyses distinct clusters of transcriptional active sequences could be revealed, indicating that embryos at different development stages have their own transcriptomic profile according to the developmental events and leading to sequential reprogramming of metabolic and developmental genes. Interestingly, a major change in transcriptionally active sequences is correlated with katatrepsis (revolution) during mid-embryogenesis, a 180° rotation of the embryo within the egg and specific to hemimetabolous insects.

discomark: nuclear marker discovery from orthologous sequences using draft genome data.

High-throughput sequencing has laid the foundation for fast and cost-effective development of phylogenetic markers. Here we present the program discomark, which streamlines the development of nuclear DNA (nDNA) markers from whole-genome (or whole-transcriptome) sequencing data, combining local alignment, alignment trimming, reference mapping and primer design based on multiple sequence alignments to design primer pairs from input orthologous sequences. To demonstrate the suitability of discomark, we designed markers for two groups of species, one consisting of closely related species and one group of distantly related species. For the closely related members of the species complex of Cloeon dipterum s.l. (Insecta, Ephemeroptera), the program discovered a total of 78 markers. Among these, we selected eight markers for amplification and Sanger sequencing. The exon sequence alignments (2526 base pairs) were used to reconstruct a well-supported phylogeny and to infer clearly structured haplotype networks. For the distantly related species, we designed primers for the insect order Ephemeroptera, using available genomic data from four sequenced species. We developed primer pairs for 23 markers that are designed to amplify across several families. The discomark program will enhance the development of new nDNA markers by providing a streamlined, automated approach to perform genome-scale scans for phylogenetic markers. The program is written in Python, released under a public licence (GNU GPL version 2), and together with a manual and example data set available at: https://github.com/hdetering/discomark.