Diversification shifts in leafroller moths linked to continental colonization and the rise of angiosperms

Hierarchical architecture of neo-sex chromosomes and accelerated adaptive evolution in tortricid moths

Sex chromosomes can expand through fusion with autosomes, thereby acquiring unique evolutionary patterns. In butterflies and moths (Lepidoptera), these sex chromosome-autosome (SA) fusions occur relatively frequently, suggesting possible evolutionary advantages. Here, we investigated how SA fusion affects chromosome features and molecular evolution in leafroller moths (Lepidoptera: Tortricidae). Phylogenomic analysis showed that Tortricidae diverged ∼124 million years ago, accompanied by an SA fusion between the Merian elements M(20 + 17) and MZ. In contrast to partial autosomal fusions, the fused neo-Z Chromosome developed a hierarchical architecture, in which the three elements exhibit heterogeneous sequence features and evolutionary patterns. Specifically, the M17 part had a distinct base composition and chromatin domains. Unlike M20 and MZ, M17 was expressed at the same levels as autosomes in both sexes, compensating for the lost gene dosage in females. Concurrently, the SA fusion drove M17 as an evolutionary hotspot, accelerating the evolution of several genes related to ecological adaptation (e.g., ABCCs) and facilitating the divergence of closely related species, whereas the undercompensated M20 did not show such an effect. Thus, accelerated evolution under a novel pattern of dosage compensation may have favored the adaptive radiation of this group. This study demonstrates the association between a karyotype variant and adaptive evolution and explains the recurrent SA fusion in the Lepidoptera.

Rapid diversification of St-genome-sharing species in wheat grasses (Triticeae: Poaceae) accompanied by diversifying selection of chloroplast genes

BACKGROUND

The St-genome-sharing taxa are highly complex group of the species with the St nuclear genome and monophyletic origin in maternal lineages within the Triticeae, which contains more than half of polyploid species that distributed in a wide range of ecological habitats. While high level of genetic heterogeneity in plastome DNA due to a reticulate evolutionary event has been considered to link with the richness of the St-genome-sharing taxa, the relationship between the dynamics of diversification and molecular evolution is lack of understanding.

RESULTS

Here, integrating 106 previously and 12 newly sequenced plastomes representing almost all previously recognized genomic types and genus of the Triticeae, this study applies phylogenetic reconstruction methods in combination with lineage diversification analyses, estimate of sequence evolution, and gene expression to investigate the dynamics of diversification in the tribe. Phylogenomic analysis confirmed previous phylogenetic relationships, with the St/E/V lineages (Pseudoroegneria/Lophopyrum + Thinopyrum/Dasypyrum) being suffered from a chloroplast capture event prior to polyploidization events. Analyses of diversification rates detected a significant acceleration approximately five million years ago in the St-genome-sharing taxa. Molecular tests of evolution and gene expression further indicated that radiation within the accelerated group has been accompanied by adaptive genetic changes in a few chloroplast-encoded genes directly or indirectly related to photosynthesis.

CONCLUSIONS

Our results support an important role for adaptive evolution in plastomes during accelerated diversification. In combination with plastome data, further investigations using other genomes, such as the nuclear genome, are urgently needed to enhance our understanding of the evolutionary history of the St-genome-sharing taxa, especially to determine whether adaptive changes in the nuclear genome are accelerated as well because plastome represents the maternal inheritation in angiosperms.

Nuclear and mitochondrial genomes of Polylopha cassiicola: the first assembly in Chlidanotinae (Tortricidae)

Tortricidae is one of the largest families in Lepidoptera, including subfamilies of Tortricinae, Olethreutinae, and Chlidanotinae. Here, we assembled the gap-free genome for the subfamily Chlidanotinae using Illumina, Nanopore, and Hi-C sequencing from Polylopha cassiicola, a pest of camphor trees in southern China. The nuclear genome is 302.03 Mb in size, with 36.82% of repeats and 98.4% of BUCSO completeness. The karyotype is 2n = 44 for males. We identified 15412 protein-coding genes, 1052 tRNAs, and 67 rRNAs. We also determined the mitochondrial genome of this species and annotated 13 protein-coding genes, 22 tRNAs, and one rRNA. These high-quality genomes provide valuable information for studying phylogeny, karyotypic evolution, and adaptive evolution of tortricid moths.

Molecular phylogeny, divergence time, biogeography and trends in host plant usage in the agriculturally important tortricid tribe Grapholitini (Lepidoptera: Tortricidae: Olethreutinae)

The leaf-roller moth tribe Grapholitini comprises about 1200 described species and contains numerous notorious pests of fruits and seeds. The phylogeny of the tribe has been little studied using contemporary methods, and the monophyly of several genera remains questionable. In order to provide a more robust phylogenetic framework for the group, we conducted a multiple-gene phylogenetic analysis of 104 species representing 27 genera of Grapholitini and 29 outgroup species. Divergence time, ancestral area, and host plant usage were also inferred to explore evolutionary trends in the tribe. Our analyses indicate that Larisa and Corticivora, traditionally assigned to Grapholitini, are best excluded from the tribe. After removal of these two genera, the tribe is found to be monophyletic, represented by two major lineages-a Dichrorampha clade and a Cydia clade, the latter of which can be divided into seven generic groups. The genus Grapholita was found to be polyphyletic, comprising three different clades, and we propose three genera to accommodate these groups: Grapholita (sensu stricto), Aspila (formerly a subgenus of Grapholita) and Ephippiphora (formerly considered a synonym of Grapholita). We summarize each generic group, including related genera not included in our analysis, providing morphological, pheromone and food plant characters that support particular branches within the molecular hypotheses. Biogeographical analyses indicate that Grapholitini probably originated in the Nearctic, Afrotropical and Neotropical regions in the Lutetian of the middle Eocene (ca. 44.3 Ma). Our results also indicate that most groups in Grapholitini originated from Fabaceae-feeding monophagous or oligophagous ancestors, and that host plant shifts probably promoted species diversification within the tribe.

Features and evolution of control regions in leafroller moths (Lepidoptera: Tortricidae) inferred from mitochondrial genomes and phylogeny

The control region (CR) of the mitochondrial genome (mitogenome) represents a major noncoding fragment with several special structural features that are thought to be responsible for the initiation of mitogenome transcription and replication. However, few studies have revealed the evolutionary patterns of CR in the phylogenetic context. Here, we explain the characteristics and evolution of CR in Tortricidae, inferred from a mitogenome-based phylogeny. The first complete mitogenomes of the genera Meiligma and Matsumuraeses were sequenced. Both mitogenomes are double-stranded circular DNA molecules with lengths of 15,675 bp and 15,330 bp, respectively. Phylogenetic analyses derived from 13 protein-coding genes and two ribosomal RNAs showed that most tribes, including subfamilies Olethreutinae and Tortricinae, were recovered as monophyletic clades, similar to previous studies based on morphological or nuclear data. Moreover, comprehensive comparative analyses of the structural organization and role of tandem replications on the length variation and high AT content of CR sequences were conducted. The results reveal a significant positive correlation between the total length and AT content of tandem repeats and whole CR sequences in Tortricidae. The structural organization in CR sequences is diverse, even between closely related tribes, which demonstrates the plasticity of the mitochondrial DNA molecule in Tortricidae.

“Lepidoptera Flies”, but Not Always…Interactions of Caterpillars and Chrysalis with Soil

Lepidoptera, an order of insects traditionally linked to the aerial habitat, are much more diverse in their living environment than the clichéd image we may have of them. The imago stage, which is the most visible in these insects, is not the one that has the most interaction with the environment (usually caterpillars) nor the one that lasts the longest (very often chrysalises). These two stages are often directly related to litter and soil, although only the interaction at the pupal stage seems to follow a phylogenetic logic with two independent evolutionary events for the preference with soil: Use of litter and the upper “O” horizon as protection against predation for the evolutionarily oldest Lepidoptera families, pupation at greater depths (up to 60 centimetres in extreme cases) for the most derived Lepidoptera families; this probably to take advantage of the thermal and moisture buffer provided by the soil. An estimate suggests that about 25% of lepidopteran species worldwide have more or less obligatory interactions with soil.

Complete mitochondrial genome analysis and molecular phylogenetic implications of Kennelia xylinana (Lepidoptera: Tortricidae)

Kennelia is a small genus in Tortricidae that is distributed in the Oriental and Palaearctic regions, and its taxonomic position within the subfamily Olethreutinae is controversial. For a comprehensive understanding of the genus, we sequenced the mitogenome of Kennelia xylinana, the type species of Kennelia, and Ancylis unculana, a species of Enarmoniini; analyzed the mitogenome characteristics of K. xylinana; and explored its phylogenetic position. Similar to other members of Lepidoptera, the mitogenome of K. xylinana is 15,762-bp long and consists of 13 protein-coding genes (PCGs), two ribosomal RNA genes, 22 transfer RNA genes, and a noncoding control region. In particular, we found a structure (TATAATTAATAA)₁₁ in the middle of the AT-rich region. Based on the Bayesian inference and maximum likelihood analyses of the 13 PCGs of 40 tortricid species, representing 8 tribes of 2 subfamilies, K. xylinana was clustered with two members of Enarmoniini, A. unculana and Loboschiza koenigiana, and formed highly supported monophyly. The results indicate that Kennelia should be placed in the tribe Enarmoniini.

The Spruce Budworm Genome: Reconstructing the Evolutionary History of Antifreeze Proteins

Insects have developed various adaptations to survive harsh winter conditions. Among freeze-intolerant species, some produce "antifreeze proteins" (AFPs) that bind to nascent ice crystals and inhibit further ice growth. Such is the case of the spruce budworm, Choristoneura fumiferana (Lepidoptera: Tortricidae), a destructive North American conifer pest that can withstand temperatures below -30°C. Despite the potential importance of AFPs in the adaptive diversification of Choristoneura, genomic tools to explore their origins have until now been limited. Here we present a chromosome-scale genome assembly for C. fumiferana, which we used to conduct comparative genomic analyses aimed at reconstructing the evolutionary history of tortricid AFPs. The budworm genome features 16 genes homologous to previously reported C. fumiferana AFPs (CfAFPs), 15 of which map to a single region on chromosome 18. Fourteen of these were also detected in five congeneric species, indicating Choristoneura AFP diversification occurred before the speciation event that led to C. fumiferana. Although budworm AFPs were previously considered unique to the genus Choristoneura, a search for homologs targeting recently sequenced tortricid genomes identified seven CfAFP-like genes in the distantly related Notocelia uddmanniana. High structural similarity between Notocelia and Choristoneura AFPs suggests a common origin, despite the absence of homologs in three related tortricids. Interestingly, one Notocelia AFP formed the C-terminus of a "zonadhesin-like" protein, possibly representing the ancestral condition from which tortricid AFPs evolved. Future work should clarify the evolutionary path of AFPs between Notocelia and Choristoneura and assess the role of the "zonadhesin-like" protein as precursor of tortricid AFPs.

A second view on the evolution of flight in stick and leaf insects (Phasmatodea)

BACKGROUND

The re-evolution of complex characters is generally considered impossible, yet, studies of recent years have provided several examples of phenotypic reversals shown to violate Dollo's law. Along these lines, the regain of wings in stick and leaf insects (Phasmatodea) was hypothesised to have occurred several times independently after an ancestral loss, a scenario controversially discussed among evolutionary biologists due to overestimation of the potential for trait reacquisition as well as to the lack of taxonomic data.

RESULTS

We revisited the recovery of wings by reconstructing a phylogeny based on a comprehensive taxon sample of over 500 representative phasmatodean species to infer the evolutionary history of wings. We additionally explored the presence of ocelli, the photoreceptive organs used for flight stabilisation in winged insects, which might provide further information for interpreting flight evolution. Our findings support an ancestral loss of wings and that the ancestors of most major lineages were wingless. While the evolution of ocelli was estimated to be dependent on the presence of (fully-developed) wings, ocelli are nevertheless absent in the majority of all examined winged species and only appear in the members of few subordinate clades, albeit winged and volant taxa are found in every euphasmatodean lineage.

CONCLUSION

In this study, we explored the evolutionary history of wings in Phasmatodea and demonstrate that the disjunct distribution of ocelli substantiates the hypothesis on their regain and thus on trait reacquisition in general. Evidence from the fossil record as well as future studies focussing on the underlying genetic mechanisms are needed to validate our findings and to further assess the evolutionary process of phenotypic reversals.

The mitochondrial genomes of Tortricidae: nucleotide composition, gene variation and phylogenetic performance

BACKGROUND

Mitochondrial genomes (mitogenomes) have greatly improved our understanding of the backbone phylogeny of Lepidoptera, but few studies on comparative mitogenomics below the family level have been conducted. Here, we generated 13 mitogenomes of eight tortricid species, reannotated 27 previously reported mitogenomes, and systematically performed a comparative analysis of nucleotide composition, gene variation and phylogenetic performance.

RESULTS

The lengths of completely sequenced mitogenomes ranged from 15,440 bp to 15,778 bp, and the gene content and organization were conserved in Tortricidae and typical for Lepidoptera. Analyses of AT-skew and GC-skew, the effective number of codons and the codon bias index all show a base bias in Tortricidae, with little heterogeneity among the major tortricid groups. Variations in the divergence rates among 13 protein-coding genes of the same tortricid subgroup and of the same PCG among tortricid subgroups were detected. The secondary structures of 22 transfer RNA genes and two ribosomal RNA genes were predicted and comparatively illustrated, showing evolutionary heterogeneity among different RNAs or different regions of the same RNA. The phylogenetic uncertainty of Enarmoniini in Tortricidae was confirmed. The synonymy of Bactrini and Olethreutini was confirmed for the first time, with the representative Bactrini consistently nesting in the Olethreutini clade. Nad6 exhibits the highest phylogenetic informativeness from the root to the tip of the resulting tree, and the combination of the third coding positions of 13 protein-coding genes shows extremely high phylogenetic informativeness.

CONCLUSIONS

This study presents 13 mitogenomes of eight tortricid species and represents the first detailed comparative mitogenomics study of Tortricidae. The results further our understanding of the evolutionary architectures of tortricid mitogenomes and provide a basis for future studies of population genetics and phylogenetic investigations in this group.

Food Plant Shifts Drive the Diversification of Sack-Bearer Moths

AbstractLepidoptera are a highly diverse group of herbivorous insects; however, some superfamilies have relatively few species. Two alternative hypotheses for drivers of Lepidoptera diversity are shifts in food plant use or shifts from concealed to external feeding as larvae. Many studies address the former hypothesis but with bias toward externally feeding taxa. One of the most striking examples of species disparity between sister lineages in Lepidoptera is between the concealed-feeding sack-bearer moths (Mimallonoidea), which contain about 300 species, and externally feeding Macroheterocera, which have over 74,000 species. We provide the first dated tree of Mimallonidae to understand the diversification dynamics of these moths in order to fill a knowledge gap pertaining to drivers of diversity within an important concealed-feeding clade. We find that Mimallonidae is an ancient Lepidoptera lineage that originated in the Cretaceous ∼105 million years ago and has had a close association with the plant order Myrtales for the past 40 million years. Diversification dynamics are tightly linked with food plant usage in this group. Reliance on Myrtales may have influenced diversification of Mimallonidae because clades that shifted away from the ancestral condition of feeding on Myrtales have the highest speciation rates in the family.

Evolution of the codling moth pheromone via an ancient gene duplication

BACKGROUND

Defining the origin of genetic novelty is central to our understanding of the evolution of novel traits. Diversification among fatty acid desaturase (FAD) genes has played a fundamental role in the introduction of structural variation in fatty acyl derivatives. Because of its central role in generating diversity in insect semiochemicals, the FAD gene family has become a model to study how gene family expansions can contribute to the evolution of lineage-specific innovations. Here we used the codling moth (Cydia pomonella) as a study system to decipher the proximate mechanism underlying the production of the ∆8∆10 signature structure of olethreutine moths. Biosynthesis of the codling moth sex pheromone, (E8,E10)-dodecadienol (codlemone), involves two consecutive desaturation steps, the first of which is unusual in that it generates an E9 unsaturation. The second step is also atypical: it generates a conjugated diene system from the E9 monoene C12 intermediate via 1,4-desaturation.

RESULTS

Here we describe the characterization of the FAD gene acting in codlemone biosynthesis. We identify 27 FAD genes corresponding to the various functional classes identified in insects and Lepidoptera. These genes are distributed across the C. pomonella genome in tandem arrays or isolated genes, indicating that the FAD repertoire consists of both ancient and recent duplications and expansions. Using transcriptomics, we show large divergence in expression domains: some genes appear ubiquitously expressed across tissue and developmental stages; others appear more restricted in their expression pattern. Functional assays using heterologous expression systems reveal that one gene, Cpo_CPRQ, which is prominently and exclusively expressed in the female pheromone gland, encodes an FAD that possesses both E9 and ∆8∆10 desaturation activities. Phylogenetically, Cpo_CPRQ clusters within the Lepidoptera-specific ∆10/∆11 clade of FADs, a classic reservoir of unusual desaturase activities in moths.

CONCLUSIONS

Our integrative approach shows that the evolution of the signature pheromone structure of olethreutine moths relied on a gene belonging to an ancient gene expansion. Members of other expanded FAD subfamilies do not appear to play a role in chemical communication. This advises for caution when postulating the consequences of lineage-specific expansions based on genomics alone.

Phylogeny and diversification of the true water bugs (Insecta: Hemiptera: Heteroptera: Nepomorpha)

Climate fluctuations and tectonic reconfigurations associated with environmental changes play large roles in determining patterns of adaptation and diversification, but studies documenting how such drivers have shaped the evolutionary history and diversification dynamics of limnic organisms during the Mesozoic are scarce. Members of the heteropteran infraorder Nepomorpha, or aquatic bugs, are ideal for testing the effects of these determinants on their diversification pulses because most species are confined to aquatic environments during their entire life. The group has a relatively mature taxonomy and is well represented in the fossil record. We investigated the evolution of Nepomorpha based on phylogenetic analyses of morphological and molecular characters sampled from 115 taxa representing all 13 families and approximately 40% of recognized genera. Our results were largely congruent with the phylogenetic relationships inferred from morphology. A divergence dating analysis indicated that Nepomorpha began to diversify in the late Permian (approximately 263 Ma), and diversification analyses suggested that palaeoecological opportunities probably promoted lineage diversification in this group.

A Cretaceous peak in family-level insect diversity estimated with mark-recapture methodology

The history of insects' taxonomic diversity is poorly understood. The two most common methods for estimating taxonomic diversity in deep time yield conflicting results: the 'range through' method suggests a steady, nearly monotonic increase in family-level diversity, whereas 'shareholder quorum subsampling' suggests a highly volatile taxonomic history with family-level mass extinctions occurring repeatedly, even at the midpoints of geological periods. The only feature shared by these two diversity curves is a steep increase in standing diversity during the Early Cretaceous. This apparent diversification event occurs primarily during the Aptian, the pre-Cenozoic interval with the most described insect occurrences, raising the possibility that this feature of the diversity curves reflects preservation and sampling biases rather than insect evolution and extinction. Here, the capture-mark-recapture (CMR) approach is used to estimate insects' family-level diversity. This method accounts for the incompleteness of the insect fossil record as well as uneven sampling among time intervals. The CMR diversity curve shows extinctions at the Permian/Triassic and Cretaceous/Palaeogene boundaries but does not contain any mass extinctions within geological periods. This curve also includes a steep increase in diversity during the Aptian, which appears not to be an artefact of sampling or preservation bias because this increase still appears when time bins are standardized by the number of occurrences they contain rather than by the amount of time that they span. The Early Cretaceous increase in family-level diversity predates the rise of angiosperms by many millions of years and can be better attributed to the diversification of parasitic and especially parasitoid insect lineages.

The early wasp plucks the flower: disparate extant diversity of sawfly superfamilies (Hymenoptera: ‘Symphyta’) may reflect asynchronous switching to angiosperm hosts

The insect order Hymenoptera originated during the Permian nearly 300 Mya. Ancestrally herbivorous hymenopteran lineages today make up the paraphyletic suborder ‘Symphyta’, which encompasses c. 8200 species with very diverse host-plant associations. We use phylogeny-based statistical analyses to explore the drivers of diversity dynamics within the ‘Symphyta’, with a particular focus on the hypothesis that diversification of herbivorous insects has been driven by the explosive radiation of angiosperms during and after the Cretaceous. Our ancestral-state estimates reveal that the first symphytans fed on gymnosperms, and that shifts onto angiosperms and pteridophytes – and back – have occurred at different time intervals in different groups. Trait-dependent analyses indicate that average net diversification rates do not differ between symphytan lineages feeding on angiosperms, gymnosperms or pteridophytes, but trait-independent models show that the highest diversification rates are found in a few angiosperm-feeding lineages that may have been favoured by the radiations of their host taxa during the Cenozoic. Intriguingly, lineages-through-time plots show signs of an early Cretaceous mass extinction, with a recovery starting first in angiosperm-associated clades. Hence, the oft-invoked assumption of herbivore diversification driven by the rise of flowering plants may overlook a Cretaceous global turnover in insect herbivore communities during the rapid displacement of gymnosperm- and pteridophyte-dominated floras by angiosperms.

Multiple origins of sexual dichromatism and aposematism within large carpenter bees

The evolution of reversed sexual dichromatism and aposematic coloration has long been of interest to both theoreticians and empiricists. Yet despite the potential connections between these phenomena, they have seldom been jointly studied. Large carpenter bees (genus Xylocopa) are a promising group for such comparative investigations as they are a diverse clade in which both aposematism and reversed sexual dichromatism can occur either together or separately. We investigated the evolutionary history of dichromatism and aposematism and a potential correlation of these traits with diversification rates within Xylocopa, using a newly generated phylogeny for 179 Xylocopa species based on ultraconserved elements (UCEs). A monochromatic, inconspicuous ancestor is indicated for the genus, with subsequent convergent evolution of sexual dichromatism and aposematism in multiple lineages. Aposematism is found to covary with reversed sexual dichromatism in many species; however, reversed dichromatism also evolved in non-aposematic species. Bayesian Analysis of Macroevolutionary Models (BAMM) did not show increased diversification in any specific clade in Xylocopa, whereas support from Hidden State Speciation and Extinction (HiSSE) models remained inconclusive regarding an association of increased diversification rates with dichromatism or aposematism. We discuss the evolution of color patterns and diversification in Xylocopa by considering potential drivers of dichromatism and aposematism.

Convergent herbivory on conifers by Choristoneura moths after boreal forest formation

Mitogenomes are useful markers for phylogenetic studies across a range of taxonomic levels. Here, we focus on mitogenome variation across the tortricid moth genus Choristoneura and particularly the spruce budworm (Choristoneura fumiferana) species complex, a notorious pest group of North American conifer forests. Phylogenetic relationships of Tortricidae, representing two subfamilies, four tribes and nine genera, were analyzed using 21 mitogenomes. These included six newly-sequenced mitogenomes for species in the spruce budworm complex plus three additional Choristoneura species and 12 previously published mitogenomes from other tortricids and one from the Cossidae. We evaluated the phylogenetic informativeness of the mitogenomes and reconstructed a time-calibrated tree with fossil and secondary calibrations. We found that tortricid mitogenomes had conserved protein and ribosomal regions, and analysis of all protein-coding plus ribosomal genes together provided an efficient marker at any taxonomic rank. The time-calibrated phylogeny showed evolutionary convergence of conifer feeding within Choristoneura, with two independent lineages, the Nearctic spruce budworm complex and the Palearctic species Choristoneura murinana, both shifting onto conifers about 11 million years ago from angiosperms. These two host-plant shifts both occurred after the formation of boreal forest in the late Miocene. Haplotype diversification within the spruce budworm complex occurred in the last 4 million years, and is probably linked to the initial cooling cycles of the Northern Hemisphere in the Pliocene.