@article {22562, title = {Hidden phylogenomic signal helps elucidate arsenurine silkmoth phylogeny and the evolution of body size and wing shape trade-offs}, journal = {Systematic Biology}, volume = {71}, year = {2022}, month = {06/2022}, pages = {859{\textendash}874}, chapter = {859}, abstract = {

\"One of the key objectives in biological research is understanding how evolutionary processes have produced Earth\’s diversity. A critical step toward revealing these processes is an investigation of evolutionary tradeoffs\—that is, the opposing pressures of multiple selective forces. For millennia, nocturnal moths have had to balance successful flight, as they search for mates or host plants, with evading bat predators. However, the potential for evolutionary trade-offs between wing shape and body size are poorly understood. In this study, we used phylogenomics and geometric morphometrics to examine the evolution of wing shape in the wild silkmoth subfamily Arsenurinae (Saturniidae) and evaluate potential evolutionary relationships between body size and wing shape. The phylogeny was inferred based on 782 loci from target capture data of 42 arsenurine species representing all 10 recognized genera. After detecting in our data one of the most vexing problems in phylogenetic inference\—a region of a tree that possesses short branches and no \“support\” for relationships (i.e., a polytomy), we looked for hidden phylogenomic signal (i.e., inspecting differing phylogenetic inferences, alternative support values, quartets, and phylogenetic networks) to better illuminate the most probable generic relationships within the subfamily. We found there are putative evolutionary trade-offs between wing shape, body size, and the interaction of fore- and hindwing (HW) shape. Namely, body size tends to decrease with increasing HW length but increases as forewing (FW) shape becomes more complex. Additionally, the type of HW (i.e., tail or no tail) a lineage possesses has a significant effect on the complexity of FW shape. We outline possible selective forces driving the complex HW shapes that make Arsenurinae, and silkmoths as a whole, so charismatic.\"

}, keywords = {ANCHORED HYBRID ENRICHMENT, ARSENURINAE, GEOMETRIC MORPHOMETRICS, PHYLOGENOMICS, SATURNIIDAE, TRADE-OFFS, TRAITS, WING SHAPE}, doi = {10.1093/sysbio/syab090}, author = {Hamilton, C.A. and Winiger, N. and Rubin, J.J. and Breinholt, J. and Rougerie, R. and Kitching, I.J. and Barber, J.R. and Kawahara, A.Y.} } @article {21525, title = {Resolving relationships among the megadiverse butterflies and moths with a novel pipeline for anchored phylogenomics}, journal = {Systematic Biology}, year = {2017}, type = {Early view}, abstract = {

\"The advent of next-generation sequencing technology has allowed for the collection of large portions of the genome for phylogenetic analysis. Hybrid enrichment and transcriptomics are two techniques that leverage next-generation sequencing and have shown much promise. However, methods for processing hybrid enrichment data are still limited. We developed a pipeline for anchored hybrid enrichment (AHE) read assembly, orthology determination, contamination screening, and data processing for sequences flanking the target \“probe\” region. We apply this approach to study the phylogeny of butterflies and moths (Lepidoptera), a megadiverse group of more than 157,000 described species with poorly understood deep-level phylogenetic relationships. We introduce a new, 855 locus AHE kit for Lepidoptera phylogenetics and compare resulting trees to those from transcriptomes. The enrichment kit was designed from existing genomes, transcriptomes, and expressed sequence tags and was used to capture sequence data from 54 species from 23 lepidopteran families. Phylogenies estimated from AHE data were largely congruent with trees generated from transcriptomes, with strong support for relationships at all but the deepest taxonomic levels.We combineAHEand transcriptomic data to generate a new Lepidoptera phylogeny, representing 76 exemplar species in 42 families. The tree provides robust support for many relationships, including those among the seven butterfly families. The addition of AHE data to an existing transcriptomic dataset lowers node support along the Lepidoptera backbone, but firmly places taxa with AHE data on the phylogeny. Combining taxa sequenced for AHE with existing transcriptomes and genomes resulted in a tree with strong support for (Calliduloidea + Gelechioidea + Thyridoidea) + (Papilionoidea + Pyraloidea + Macroheterocera). To examine the efficacy of AHE at a shallowtaxonomic level, phylogenetic analyseswere also conducted on a sister group representing a more recent divergence, the Saturniidae and Sphingidae. These analyses utilized sequences from the probe region and data flanking it, nearly doubled the size of the dataset; resulting trees supported new phylogenetics relationships, especially within the Saturniidae and Sphingidae (e.g., Hemarina derived in the latter). We hope that our data processing pipeline, hybrid enrichment gene set, and approach of combining AHE data with transcriptomes will be useful for the broader systematics community.\"

}, keywords = {ANCHORED HYBRID ENRICHMENT, HEMARINI, HIGHER CLASSIFICATION, LEPIDOPTERA, METHODOLOGY, PHYLOGENOMICS, PHYLOGENY, PIPELINE, SATURNIIDAE, SPHINGIDAE}, doi = {10.1093/sysbio/syx048}, author = {Breinholt, J.W. and Earl, C. and Lemmon, A.R. and Moriarty_Lemmon, E. and Xiao, L. and Kawahara, A.Y.} } @article {21255, title = {Species-level para- and polyphyly in DNA barcode gene trees: strong operational bias in European Lepidoptera}, journal = {Systematic Biology}, year = {2016}, type = {Early view}, abstract = {

\"The proliferation of DNA data is revolutionizing all fields of systematic research. DNA barcode sequences, now available for millions of specimens and several hundred thousand species, are increasingly used in algorithmic species delimitations. This is complicated by occasional incongruences between species and gene genealogies, as indicated by situations where conspecific individuals do not form a monophyletic cluster in a gene tree. In two previous reviews, non-monophyly has been reported as being common in mitochondrial DNA gene trees. We developed a novel web service \“Monophylizer\” to detect non-monophyly in phylogenetic trees and used it to ascertain the incidence of species non-monophyly in COI (a.k.a. cox1) barcode sequence data from 4977 species and 41,583 specimens of European Lepidoptera, the largest data set of DNA barcodes analyzed from this regard. Particular attention was paid to accurate species identification to ensure data integrity. We investigated the effects of tree-building method, sampling effort, and other methodological issues, all of which can influence estimates of non-monophyly. We found a 12\% incidence of non-monophyly, a value significantly lower than that observed in previous studies. Neighbor joining (NJ) and maximum likelihood (ML) methods yielded almost equal numbers of non-monophyletic species, but 24.1\% of these cases of non-monophyly were only found by one of these methods. Non-monophyletic species tend to show either low genetic distances to their nearest neighbors or exceptionally high levels of intraspecific variability. Cases of polyphyly in COI trees arising as a result of deep intraspecific divergence are negligible, as the detected cases reflected misidentifications or methodological errors. Taking into consideration variation in sampling effort, we estimate that the true incidence of non-monophyly is \∼23\%, but with operational factors still being included. Within the operational factors, we separately assessed the frequency of taxonomic limitations (presence of overlooked cryptic and oversplit species) and identification uncertainties. We observed that operational factors are potentially present in more than half (58.6\%) of the detected cases of non-monophyly. Furthermore, we observed that in about 20\% of non-monophyletic species and entangled species, the lineages involved are either allopatric or parapatric\—conditions where species delimitation is inherently subjective and particularly dependent on the species concept that has been adopted. These observations suggest that species-level non-monophyly in COI gene trees is less common than previously supposed, with many cases reflecting misidentifications, the subjectivity of species delimitation or other operational factors.\"

}, keywords = {BARCODE GAP, BARCODING, COI, DNA, EUROPE, GENE TREE, LEPIDOPTERA, MAXIMUM LIKELIHOOD, MONOPHYLIZER, NEIGHBOR-JOINING, PARAPHYLY, POLYPHYLY, SPECIES DELIMITATION, SPECIES MONOPHYLY}, doi = {10.1093/sysbio/syw044}, author = {Mutanen, M. and Kivel{\"a}, S.M. and Vos, R.A. and Doorenweerd, C. and Ratnasingham, S. and Hausmann, A. and Huemer, P. and Dinca, V. and van Nieukerken, E.J. and Lopez-Vaamonde, C. and Vila, R. and Aarvik, L. and Deca{\"e}ns, T. and Efetov, K.A. and Hebert, P.D.N. and Johnsen, A. and Karsholt, O. and Pentinsaari, M. and Rougerie, R. and Segerer, A. and Tarmann, G. and Zahiri, R. and Godfray, H.C.J.} } @article {16807, title = {Biogeography and floral evolution of baobabs ({IAdansonia}, Bombacaceae) as inferred from multiple data sets}, journal = {Systematic Biology}, volume = {47}, year = {1998}, month = {1998}, pages = {181-207}, keywords = {ADANSONIA, BAOBAB, BATS, BIOGEOGRAPHY, CPDNA, ITS, MALVACEAE, MAXIMUM LIKELIHOOD, MORPHOLOGY, PARSIMONY, PHYLOGENY, POLLINATION, RESTRICTION SITES, RP116 INTRON, SPHINGIDAE}, author = {Baum, D. A. and Small, R. L. and Wendel, J. F.} }