@article {22984, title = {Chromosomal-level genome assembly of the Coffee Bee Hawk Moth reveals the evolution of chromosomes and the molecular basis of distinct phenotypes}, journal = {Genome Biology and Evolution}, volume = {15}, year = {2023}, month = {09/2023}, pages = {evad141}, chapter = {evad141}, abstract = {

\"Cephonodes hylas, the coffee bee hawk moth is a hawk moth species with unique characteristics, such as larvae feeding on gardenia, overcoming the toxicity of its iridoid glycosides, diurnal adults, and transparent wings. Although C. hylas is a fascinating model for molecular biological research, genome sequence analysis-based genetic approaches to elucidate these peculiarities have not yet been undertaken. We successfully achieved de novo genome assembly at the chromosome level of C. hylas comparable to the Lepidoptera model organism, silkworm. Additionally, 16,854 protein-coding genes were annotated, and the constructed genome sequence and annotated genes were of the highest quality BUSCO completion compared to closely related species. Comparative genome analysis revealed the process of chromosomal evolution from the Bombycoidea ancestral (n = 31) genome and changes in turnover at the chromosome level associated with chromosomal fusion events, such as the rate of repetitive sequence insertion. These analyses were only possible because the genome was constructed at the chromosome level. Additionally, increased the nonsynonymous/synonymous rate (dN/dS) ratios were observed in multiple photoreceptor-related genes that were strongly associated with the acquisition of diurnal activity. Furthermore, tandemly duplicated expanded genes containing many digestive and other enzymes and larval midgut-specific expression were also confirmed. These genes may be involved in the metabolism of genipin, a toxin found in gardenias. Using the genome sequence of C. hylas determined at the chromosome level, we have successfully identified new insights into the chromosomal evolution of Bombycoidea, as well as the relationship between the genome sequence and its characteristic traits.\"

}, keywords = {CEPHONODES, CHROMOSOME ASSEMBLY, CHROMOSOMES, DETOXIFICATION, DIURNALISM, EVOLUTION, FOODPLANT CHEMISTRY, FOODPLANT SPECIFICITY, GENOME ASSEMBLY, HYLES, MANDUCA, OPSIN, SPHINGIDAE, WING TRANSPARENCY}, url = {https://doi.org/10.1093/gbe/evad141}, author = {Yamabe, T. and Kajitani, R. and Toyoda, A. and Itoh, T.} } @article {22014, title = {Genome-wide SNP Data reveal an overestimation of species diversity in a group of hawkmoths}, journal = {Genome Biology and Evolution}, volume = {11}, year = {2019}, month = {08/2019}, pages = {2136-2150}, chapter = {2136}, abstract = {

\"The interface between populations and evolving young species continues to generate much contemporary debate in systematics depending on the species concept(s) applied but which ultimately reduces to the fundamental question of \“when do nondiscrete entities become distinct, mutually exclusive evolutionary units\”? Species are perceived as critical biological entities, and the discovery and naming of new species is perceived by many authors as a major research aim for assessing current biodiversity before much of it becomes extinct. However, less attention is given to determining whether these names represent valid biological entities because this is perceived as both a laborious chore and an undesirable research outcome. The charismatic spurge hawkmoths (Hyles euphorbiae complex, HEC) offer an opportunity to study this less fashionable aspect of systematics. To elucidate this intriguing systematic challenge, we analyzed over 10,000 ddRAD single nucleotide polymorphisms from 62 individuals using coalescent-based and population genomic methodology. These genome-wide data reveal a clear overestimation of (sub)species-level diversity and demonstrate that the HEC taxonomy has been seriously oversplit. We conclude that only one valid species name should be retained for the entire HEC, namely Hyles euphorbiae, and we do not recognize any formal subspecies or other taxonomic subdivisions within it. Although the adoption of genetic tools has frequently revealed morphologically cryptic diversity, the converse, taxonomic oversplitting of species, is generally (and wrongly in our opinion) accepted as rare. Furthermore, taxonomic oversplitting is most likely to have taken place in intensively studied popular and charismatic organisms such as the HEC.\"

}, keywords = {CATALOGUE, ddRAD, GENE FLOW, HYLES, OVERSPLITTING, SPECIATION, SPECIES DELIMITATION, SPHINGIDAE, TAXONOMY, WORLDMAP1}, doi = {10.1093/gbe/evz113}, author = {Hundsdoerfer, A.K. and Lee, K.M. and Kitching, I.J. and Mutanen, M.} } @article {21298, title = {Conservation, duplication, and divergence of five opsin genes in insect evolution}, journal = {Genome Biology and Evolution}, volume = {8}, year = {2016}, month = {02/2016}, pages = {579-587}, chapter = {579}, abstract = {

\"Opsin proteins covalently bind to small molecular chromophores and each protein-chromophore complex is sensitive to particular wavelengths of light. Multiple opsins with different wavelength absorbance peaks are required for color vision. Comparing opsin responses is challenging at low light levels, explaining why color vision is often lost in nocturnal species. Here, we investigated opsin evolution in 27 phylogenetically diverse insect species including several transitions between photic niches (nocturnal, diurnal, and crepuscular).We find widespread conservation of five distinct opsin genes, more than commonly considered.\  These comprise one c-opsin plus four r-opsins (long wavelength sensitive or LWS, blue sensitive, ultra violet [UV] sensitive and the often overlooked Rh7 gene). Several recent opsin gene duplications are also detected. The diversity of opsin genes is consistent with color vision in diurnal, crepuscular, and nocturnal insects. Tests for positive selection in relation to photic niche reveal evidence for adaptive evolution in UVsensitive opsins in day-flying insects in general, and in LWS opsins of day-flying Lepidoptera specifically.\"

}, keywords = {BOMBYCIDAE, BOMBYX, C-OPSINS, COLOUR VISION, DAY/NIGHT TRANSITIONS, EREBIDAE, EVOLUTION, GENE DUPLICATION, INSECTA, LWS-OPSIN, MANDUCA, OPSIN, PHYLOGENY, R-OPSINS, SPHINGIDAE, VISION}, doi = {10.1093/gbe/evw015}, author = {Feuda, R. and Marl{\'e}taz, F. and Bentley, M.A. and Holland, P.W.H.} } @article {17015, title = {Phylotranscriptomics: saturated third codon positions radically influence the estimation of trees based on next-gen data}, journal = {Genome Biology and Evolution}, volume = {5}, year = {2013}, month = {10/2013}, pages = {2082-2092}, chapter = {2082}, abstract = {

\"Recent advancements in molecular sequencing techniques have led to a surge in the number of phylogenetic studies that incorporate large amounts of genetic data. We test the assumption that analyzing large number of genes will lead to improvements in tree resolution and branch support using moths in the superfamily Bombycoidea, a group with some interfamilial relationships that have been difficult to resolve. Specifically, we use a next-gen data set that included 19 taxa and 938 genes (\∼1.2M bp) to examine how codon position and saturation might influence resolution and node support among three key families. Maximum likelihood, parsimony, and species tree analysis using gene tree parsimony, on different nucleotide and amino acid data sets, resulted in largely congruent topologies with high bootstrap support compared with prior studies that included fewer loci. However, for a few shallow nodes, nucleotide and amino acid data provided high support for conflicting relationships. The third codon position was saturated and phylogenetic analysis of this position alone supported a completely different, potentially misleading sister group relationship. We used the program RADICAL to assess the number of genes needed to fix some of these difficult nodes. One such node originally needed a total of 850 genes but only required 250 when synonymous signal was removed. Our study shows that, in order to effectively use next-gen data to correctly resolve difficult phylogenetic relationships, it is necessary to assess the effects of synonymous substitutions and third codon positions.\"

}, keywords = {ACTIAS, ANTHERAEA, BOMBYCIDAE, BOMBYX, CERATOMIA, DARAPSA, DNA, ENYO, HEMARIS, INCOMPLETE, MANDUCA, MAXIMUM LIKELIHOOD, PARSIMONY, PHYLOGENY, RADICAL, RAXML, SAMIA, SATURATION, SATURNIIDAE, SPHINGIDAE, SYNONYMOUS SUBSTITUTIONS, TRANSCRIPTOMICS}, doi = {10.1093/gbe/evt157}, url = {https://doi.org/10.1093/gbe/evt157}, author = {Breinholt, J.W. and Kawahara, A.Y.} }