Integrative phylogenomics reveals a Permian origin of Adephaga beetles

Abstract

Beetles are arguably the most diverse group of animals on Earth with over 400 000 described species. Yet the timing of main diversification events among these insects remains debated. The use of phylogenomic data generated using next‐generation sequencing recently resolved most recalcitrant phylogenetic relationships across Coleoptera. However, limited taxon sampling for some major clades still prevents the use of important fossil calibrations that could provide more accurate estimates of the timing of lineage diversification events among beetles. Here, we present a new fossil‐based dated framework with a focus on the suborder Adephaga. We rely on an integrative phylogenomic approach using a combination of genomic, ultraconserved element and RNAseq transcriptomic datasets, further revealing the prevalent exonic nature of ultraconserved elements in Coleoptera. We infer a robust phylogenomic tree under various optimality criteria and analytical conditions. Our preferred phylogenetic reconstruction is consistent with those of previous phylogenomic studies in recovering the paraphyly of ‘Hydradephaga’, Gyrinidae as sister to all other Adephaga, the monophyly of Geadephaga and Haliplidae as sister to a monophyletic Dytiscoidea. We further recover strong support for paraphyly of Aspidytidae and the placement of Hygrobiidae as part of a clade comprising Aspidytes, Ribera, Beutel, Balke & Vogler, Sinaspidytes Balke, Beutel & Ribera and Amphizoidae. Using 23 carefully chosen fossil calibrations across Coleoptera, we infer the origin of modern beetles ca. 317 Ma in the mid‐Carboniferous, the divergence between Archostemata and Adephaga ca. 296 Ma in the early Permian, and the crown of Adephaga in the end‐Permian ca. 255 Ma. Importantly, our analyses provide more precise estimates of divergence times for internal splits within Adephaga, including ground beetles, tiger beetles and aquatic adephagan lineages. These results represent a major step forward in our understanding of beetle diversification and will serve as a fundamental framework to unravel the evolutionary history of many clades within Adephaga.

Minute moss beetles in the Southern Hemisphere: Molecular phylogeny, historical biogeography and habitat shifts (Coleoptera: Hydraenidae)

“…Since there are no reliable fossil calibrations for the "Gondwana group", we chose to use secondary calibrations from higher-level taxonomic studies of Coleoptera. The recent development of robust dated trees for Coleoptera (e.g., Toussaint et al, 2017a;Zhang et al, 2018;McKenna et al, 2019;Baca et al, 2021) allows the ages of more derived lineages to be constrained with a higher degree of confidence than previously. Zealand .…”

“…Since there are no reliable fossil calibrations for the 'Gondwana group', we chose to use secondary calibrations from higher-level taxonomic studies of Coleoptera. The recent development of robust dated trees for Coleoptera (e.g., Baca et al, 2021;McKenna et al, 2019;Toussaint, Bloom, & Short, 2017;Zhang et al, 2018) allows the ages of more derived lineages to be constrained with a higher degree of confidence = 198.75, 13.34). We used different tree (Yule versus birth-death) and clock priors (one clock for all partitions versus one clock for each partition) to test for potential differences in resulting time estimates.…”

Holocene insect pioneer colonization of post-glacial dune sands exemplified by tiger beetle burrows

“…Although the oldest body fossils of tiger beetles are Early Cretaceous in age (Cassola and Werner, 2004; Zhao et al, 2019), some research has suggested that their ancestors existed by the Triassic with possible crown-group members by the Jurassic (Baca et al, 2021; Pearson and Ghorpade, 1989). Overall, due to their fragile exoskeletons, even compared to other beetles (Smith et al, 2006), body fossils are extremely uncommon with only a few other Cenozoic examples known to date, such as in Eocene Baltic and Rovno amber, Quaternary asphalt deposits from the Caucasus region, Trinidad, and California, and Pleistocene late glacial deposits from the UK and North America (Matalin et al, 2021; Nagano et al, 1982; Wiesner et al, 2017).…”

Phylogenomic and mitogenomic data can accelerate inventorying of tropical beetles during the current biodiversity crisis

“…It is the responsibility of systematic biologists to assemble the natural system, that is, we need to reliably delimit genus- and tribe-level taxa, to make their ecological and distribution attributes informative. But the short fragments are often unsuitable for the building of deep phylogenies and large genomic datasets need to be used ( McKenna et al, 2019 ; Baca et al, 2021 ). These include transcriptomes, whole genome sequences and anchored hybrid capture datasets.…”

“…The applied methods of transcriptome and mtDNA analyses are widely used. The genomic datasets dominate among works focusing on deep relationships (transcriptomes and anchored hybrid capture; Misof et al, 2014 ; Kusy et al, 2019 ; McKenna et al, 2019 ; Baca et al, 2021 ). The mitochondrial markers have been used mainly to study the phylogeny of restricted clades ( Toussaint et al, 2014 ; Sharkey et al, 2021 ).…”