Hyper-specialized bamboo lemurs possess a reduced suite of xenobiotic-metabolizing cytochrome P450 genes

Subfamilies of cytochrome P450 proteins have been strongly linked to the metabolism of physiologically disruptive compounds such as alkaloids, terpenoids, and other xenobiotics. Consistent with this function, these genes have adaptively evolved in response to environmental pressures exerted on animals, such as herbivores, that consume elevated amounts of toxic xenobiotics or plant secondary metabolites (PSMs). Theory on evolutionary tradeoffs predicts that highly specialized herbivores should exhibit a relatively narrow toolkit of adaptations to accommodate the concomitantly narrow arrays of PSMs in their diets. The bamboo lemurs of Madagascar (genera Prolemur and Hapalemur) represent an interesting test case for this theory because of their dietary hyper-specialization, as these lemurs consume bamboo and grasses at rates otherwise unseen in the order Primates. To test whether the hyper-specialized folivory of these primates is reflected in a similarly specialized and narrow P450 gene s..., Data gathering  
In addition to a novel genome assembly for Hapalemur griseus, we mined data from publicly available genome assemblies for 14 species: Prolemur simus (Hawkins et al., 2018), Lemur catta (Palmada-Flores et al., 2022), Eulemur flavifrons and E. macaco (Meyer et al. 2015), Propithecus coquereli (Lowe and Eddy 1997; Guevara et al. 2021), Indri indri (accession number: GCA_004363605.1), Daubentonia madagascariensis (accession number: GCA_004027145.1), Mirza coquereli (accession number: GCA_004024645.1), Mirza zaza (Hunnicutt et al., 2020), and Microcebus murinus (Averdam et al., 2011; Lecompte et al., 2016), as well as the following additional species of mouse lemur: Mic. griseorufus, Mic. mittermeieri, Mic. ravelobensis, and Mic. tavaratra (Hunnicutt et al., 2020). These assemblies, along with any associated annotation files, were downloaded locally and formatted into BLAST databases within Geneious Prime, version 2022.1.1.
We located the loci for all annotated CYP1-3 homolo..., , # Hyper-specialized bamboo lemurs possess a reduced suite of xenobiotic-metabolizing cytochrome P450 genes.

This dataset contains all the input data needed to reproduce results from a manuscript of the same title. The data herein include alignments (standard format and LASTZ format), as well as output trees and statistics from the programs PhyML and jModelTest.

## Description of the data and file structure

The tar.gz archive contains three subdirectories: LASTZ, CDS, and PhyML. The **LASTZ** folder contains the pairwise alignments used to find genes for nearly all downstream parts of the paper. For each alphanumeric subfamily (representing individual cytochrome P450 gene-subfamilies), there are .gb files for the reference species (in order to provide some information about reference-gene locations) and .bam files for all query species. The **CDS** subdirectory contains all the codon alignments required to to replicate the HyPhy analyses in the previously mentioned manuscript. All ...