A genome‐wide phylogeny and the diversification of genus Liriomyza (Diptera: Agromyzidae) inferred from anchored phylogenomics

Abstract

The genus Liriomyza Mik (Diptera: Agromyzidae) is a diverse and globally distributed group of acalyptrate flies. Phylogenetic relationships among Liriomyza species have remained incompletely investigated and have never been fully addressed using molecular data. Here, we reconstruct the phylogeny of the genus Liriomyza using various phylogenetic methods (maximum likelihood, Bayesian inference, and gene tree coalescence) on target-capture-based phylogenomic datasets (nucleotides and amino acids) obtained from anchored hybrid enrichment (AHE). We have recovered tree topologies that are nearly congruent across all data types and methods, and individual clade support is strong across all phylogenetic analyses. Moreover, defined morphological species groups and clades are well-supported in our best estimates of the molecular phylogeny. Liriomyza violivora (Spencer) is a sister group to all remaining sampled Liriomyza species, and the well-known polyphagous vegetable pests [L. huidobrensis (Blanchard), L. langei Frick, L. bryoniae. (Kaltenbach), L. trifolii (Burgess), L. sativae Blanchard, and L. brassicae (Riley)].belong to multiple clades that are not particularly closely related on the trees. Often, closely related Liriomyza species feed on distantly related host plants. We reject the hypothesis that cophylogenetic processes between Liriomyza species and their host plants drive diversification in this genus. Instead, Liriomyza exhibits a widespread pattern of major host shifts across plant taxa. Our new phylogenetic estimate for Liriomyza species provides considerable new information on the evolution of host-use patterns in this genus. In addition, it provides a framework for further study of the morphology, ecology, and diversification of these important flies.

Population genetics and ecological niche modelling provide insights into management strategies of the herbivorous pest Phytomyza horticola (Diptera: Agromyzidae)

“…The unique geographical and climatic features of this region have played an important role in driving the speciation and genetic divergence of populations (Che et al, 2010;Chen et al, 2022;Ding et al, 2018;Lu et al, 2014;Zhu et al, 2022). This may also help explain the great genetic differenti- Xuan et al, 2022); however, we did not observe an obvious influence of host plants on the differentiation of P. horticola populations. In general, high levels of gene flow among genetically divergent populations could offset random genetic drift, selection and mutation, and ultimately homogenize the populations (Endersby et al, 2005;Lyons et al, 2012;Wang et al, 2017Wang et al, , 2022.…”

“…However, low levels of differentiation and high levels of gene flow have been observed among most geographical populations within the large genetic lineages. In addition, studies have shown that host specialization may lead to genetic differentiation in leaf‐mining fly populations and may even promote the development of many new species (Scheffer et al, 2007; Scheffer & Lewis, 2005, 2006; Spencer, 1964; Winkler, Mitter, et al, 2009; Winkler, Scheffer, et al, 2009; Xuan et al, 2022); however, we did not observe an obvious influence of host plants on the differentiation of P. horticola populations. In general, high levels of gene flow among genetically divergent populations could offset random genetic drift, selection and mutation, and ultimately homogenize the populations (Endersby et al, 2005; Lyons et al, 2012; Wang et al, 2017, 2022).…”

Phylotranscriptomics reveals the phylogeny of Asparagales and the evolution of allium flavor biosynthesis

“…Several insect larvae, such as Delia antiqua 39 , and leaf miners, such as Phytomyza gymnostoma, commonly feed on Allium species. Considering the concurrent diversification of insects 40,41 , it is plausible that the expansion of these two genes may serve as a defense mechanism against insect predation.…”