macroevolutionary patterns behind a classic case of coevolution: uncovering the evolution of milkweed longhorn beetles Tetraopes, Cerambycidae

Tetraopes beetles are known for their resistance to milkweed plant toxins and their coevolutionary dynamics with milkweed plants (Asclepias). This association is considered a textbook example of coevolution, in which each species of Tetraopes is specialized to feed on one species of Asclepias. A major challenge to investigating coevolution and molecular ecology studies lies in the limited understanding of the evolutionary history of Tetraopes. By integrating genomic, morphological, paleontological, and geographical data, we present a robust phylogeny of Tetraopes and their relatives, using three inference methods with varying subsets of data, encompassing 2 to 12 thousand UCE loci. We elucidate the diversification patterns of Tetraopes species across major biogeographical regions and their colonization of the Americas. Our findings suggest that the genus originated in Central America approximately 21 million years ago during the Miocene and diversified from the Mid-Miocene to the Pleist..., DNA extraction and library preparation
DNA was extracted from body tissue and legs; legs were punctured to facilitate the action of proteinase-k. MagAttract HMW DNA Kit was used to isolate high molecular weight genomic DNA from T. tetrophthalmus following the manufacturer’s protocol for solid frozen tissue and recommendations from 10x Chromium DNA Extraction from Single Insects [25]. OmniPrep DNA Extraction kit, DNeasy Blood & Tissue Kit, and Qlamp mini kit were used for DNA extractions of other specimens. DNA fragment size was quantified using Qbit 2.0 fluorometric quantification (Invitrogen, USA), a Bioanalyzer, and 0.5% agarose gel electrophoresis. In some cases, DNA was sheared before library preparation in a Covaris M220 (Covaris Inc., USA).
After DNA extraction, samples were divided into two groups for library preparation and sequencing. The first included 30 specimens for which library preparation was performed at the Center for Comparative Genomics of the California Academy ..., , # Macroevolutionary patterns behind a classic case of coevolution: Uncovering the evolution of milkweed longhorn beetles (Tetraopes, Cerambycidae)

[https://doi.org/10.5061/dryad.gmsbcc2vh](https://doi.org/10.5061/dryad.gmsbcc2vh)

Here are the genome assemblies and UCE custom probes that are part of the project titled 'Macroevolutionary patterns behind a classic case of coevolution: Uncovering the evolution of milkweed longhorn beetles (*Tetraopes*, Cerambycidae)'. Code is available at: [https://github.com/NayeliGutierrez/2023_MacroevolTetraopes ](https://github.com/NayeliGutierrez/2023_MacroevolTetraopes)

## Description of the data and file structure

* The files with the extension '**_scaffolds.fasta**' correspond to the genome assemblies of the beetle species included in the analysis. The first section of the file name indicates the species to which they correspond.

The genome of *T. tetraophthalmus* was assembled in Supernova 2.1 [27], the software designed for Chromium-prepared ...