Showing papers by "Niklas Wahlberg published in 2023"

Genome-wide gene birth-death dynamics are associated with diet breadth variation in Lepidoptera

Abstract: Comparative analyses of gene birth-death dynamics (GBDD) have the potential to reveal gene families that played an important role in the evolution of morphological, behavioral, or physiological variation. Here, we used whole genomes of 30 species of butterflies and moths to identify GBDD among the Lepidoptera that are associated with specialist or generalist feeding strategies. Our work advances this field by using a uniform set of annotated proteins for all genomes, investigating associations while correcting for phylogeny, and assessing all gene familes rather than a priori subsets. We discovered that the sizes of several important gene families (e.g., those associated with pesticide resistance, xenobiotic detoxification, and/or protein digestion) are significantly correlated with diet breadth. We also found 12 gene families showing significant shifts in GBDD at the butterfly (Papilionoidea) crown node, the most notable of which was a family of pheromone receptors that underwent a contraction potentially linked with a shift to visual-based mate recognition. Our findings highlight the importance of uniform annotations, phylogenetic corrections and unbiased gene family analyses in generating a list of candidate genes that warrant further exploration. Significance Statement Gene duplications and gene deaths are important for the development of novel traits, but their study is often complicated by methodological issues, such as input data coming from different sources with different biases. Here, we address many of these issues in an analysis of gene duplication and death across 30 species of moths by using standardized, genome-wide input data. Importantly, our analysis uses a model that can correlate gene family sizes with any quantitative trait, while also accounting for relatedness between species. Using this model, we provide novel evolutionary insights by showing that the sizes of several important gene families are correlated with increases or decreases in the number of host plant orders that Lepidoptera eat.

A phylogenomic perspective on the relationships of subfamilies in the family Geometridae (Lepidoptera)

Abstract: Geometrid moths, the second largest radiation of Lepidoptera, have been the target of extensive phylogenetic studies. Those studies have flagged several problems in tree topology that have remained unanswered. We address three of those: (i) deep nodes of Geometridae (subfamilies Sterrhinae + Larentiinae, or Sterrhinae alone as sister to all other subfamilies), (ii) the taxonomic status of subfamily Orthostixinae and (iii) the systematic position of the genus Eumelea (classified in Desmobathrinae: Eumeleini or incertae sedis earlier). We address these questions by using a phylogenomic approach, a novel method on these moths, with up to 1000 protein-coding genes extracted from whole-genome shotgun sequencing data. Our datasets include representatives from all geometrid subfamilies and we analyse the data by using three different tree search strategies: partitioned models, GHOST model and multispecies coalescent analysis. Despite the extensive data, we found incongruences in tree topologies. Eumelea did not associate with Desmobathrinae as suggested earlier, but instead, it was recovered in three different phylogenetic positions, either as sister to Oenochrominae, Geometrinae or as sister to Oenochrominae + Geometrinae. Orthostixinae, represented by its type species, falls within Desmobathrinae. We propose the following taxonomic changes: we raise Eumeleini to subfamily rank as Eumeleinae stat. nov. and we treat Orthostixinae as a junior synonym of Desmobathrinae syn. nov.

DNA barcodes of the Greater Antillean butterflies (Lepidoptera: Papilionoidea) suggest a richer, more isolated fauna and higher endemism

Abstract: We provide the first comprehensive assessment of the Greater Antilles butterfly fauna from a molecular perspective. We gathered COI barcodes for 82% of the archipelago’s 367 species. Barcodes perform relatively well for species identification. A barcode gap separates 83% of the 270 species (represented by at least two sequences) from its nearest neighbour (NN). Of the 31 species represented by single barcodes, 26 have minimum distances from their NN above 2%. Maximum intraspecific distances are higher than 2% for 57 species (21%); however, values are lower within single islands suggesting that a part of these species has evolved into endemic lineages overlooked or unrecognized until today. Barcodes are diagnostic for only 80 of the currently accepted 180 subspecies represented by at least two sequences suggesting numerous conflicts with the infraspecific classification and highlighting its subjectivity. For 20 species, and several subspecies within them, we propose a split into two or more species and elevating several subspecies to the species category. Other data sources including novel or previously ignored morphological characters of adults and immature stages, natural history and/or additional nuclear sequences support these taxonomic changes.