A chromosome-scale genome assembly and evaluation of mtDNA variation in the willow leaf beetle Chrysomela aeneicollis.

The leaf beetle Chrysomela aeneicollis has a broad geographic range across Western North America but is restricted to cool habitats at high elevations along the west coast. Central California populations occur only at high altitudes (2,700-3,500 m) where they are limited by reduced oxygen supply and recent drought conditions that are associated with climate change. Here, we report a chromosome-scale genome assembly alongside a complete mitochondrial genome and characterize differences among mitochondrial genomes along a latitudinal gradient over which beetles show substantial population structure and adaptation to fluctuating temperatures. Our scaffolded genome assembly consists of 21 linkage groups; one of which we identified as the X chromosome based on female/male whole genome sequencing coverage and orthology with Tribolium castaneum. We identified repetitive sequences in the genome and found them to be broadly distributed across all linkage groups. Using a reference transcriptome, we annotated a total of 12,586 protein-coding genes. We also describe differences in putative secondary structures of mitochondrial RNA molecules, which may generate functional differences important in adaptation to harsh abiotic conditions. We document substitutions at mitochondrial tRNA molecules and substitutions and insertions in the 16S rRNA region that could affect intermolecular interactions with products from the nuclear genome. This first chromosome-level reference genome will enable genomic research in this important model organism for understanding the biological impacts of climate change on montane insects.

Phylogeny of North Americas largest cicada radiation redefines Tibicinoides and Okanagana (Hemiptera: Auchenorrhyncha: Cicadidae: Tibicininae).

Tibicinoides, with three small endemic California cicada species, has a confusing, intertwined systematic history with Okanagana that we unravel here. An ingroup including all species of Tibicinoides and the majority (84.7%) of Okanagana species were sampled for six gene regions, polarized with Clidophleps, Okanagodes, Subpsaltria, and Tibicina outgroups, and subjected to Bayesian phylogenetic analysis. Although the ingroup was monophyletic from all outgroups including Tibicina, Tibicinoides rendered Okanagana paraphyletic among two major ingroup clades. To bring classification into agreement with phylogeny, we redescribe and redefine Tibicinoides to include all Okanagana species with a hooked uncus in the male genitalia, all of which grouped with the type T. cupreosparsa (Uhler, 1889) in the first of these clades: T. boweni (Chatfield-Taylor & Cole, 2020) comb. n., T. catalina (Davis, 1936) comb. n., T. hesperia (Uhler, 1876) comb. n., T. mercedita (Davis, 1915), T. minuta (Davis, 1915), T. pallidula (Davis, 1917a) comb. n., T. pernix (Bliven, 1964) comb. n., T. rubrovenosa (Davis, 1915) comb. n., T. simulata (Davis, 1921) comb. n., T. striatipes (Haldeman, 1852) comb. n., T. uncinata (Van Duzee, 1915) comb. n., T. utahensis (Davis, 1919) comb. n., and T. vanduzeei (Distant, 1914) comb. n. Okanagana is redescribed and restricted to the species of the second major clade which contained the type O. rimosa (Say, 1830). We describe two new genera for morphologically distinct orphan lineages: Chlorocanta gen. nov. for C. viridis (Davis, 1918) comb. n. and Hewlettia gen. nov. for H. nigriviridis (Davis, 1921) comb. n. We recognize O. rubrobasalis Davis, 1926 stat. rev. as a species and relegate two former species to junior subjective synonyms: O. noveboracensis (Emmons, 1854) = O. canadensis (Provancher, 1889) and O. occidentalis (Walker in Lord, 1866) = O. lurida Davis, 1919. Tibicinoides and Okanagana together represent a rapid radiation that presents challenges to phylogenetic analysis including suboptimal outgroups and short internodes.