DOI: 10.5061/dryad.9w0vt4bc9
title: Museomics of tree squirrels: a dense taxon sampling of mitogenomes reveals hidden diversity, phenotypic convergence, and the need of a taxonomic overhaul

description: Background: Tree squirrels (Sciuridae, Sciurini), in particular the highly
 diverse Neotropical lineages, are amongst the most rapidly diversifying
 branches of the mammal tree of life but also some of the least known.
 Negligence of this group by phylogeneticists is likely a product of the
 scarcity or unavailability of fresh tissue samples for DNA sequencing.
 Lack of comprehensive phylogenies result in highly discrepant taxonomic
 arrangements that are based exclusively on morphological
 data—impressively, these are the only classification schemes available for
 the group. Here we used high-throughput sequencing and an unprecedented
 sampling effort of museum specimens to provide the first comprehensive
 phylogenetic analysis of tree squirrels, with a special emphasis on
 Neotropical taxa. Results: We gathered mitochondrial genome data from 232
 modern and historical samples, representing 40 out of the 43 currently
 recognized species of Sciurini. We found no correlation between specimen
 age and completeness of mitogenomes recovered for historical samples. Our
 phylogenetic analyses—performed with datasets differing on levels of
 missing data and taxa under distinctanalytical methods— strongly support
 the monophyly of Sciurini and consistently recovered 12 major clades
 within the tribe. We found evidence that the diversity of Neotropical tree
 squirrels is underestimated, with at least seven lineages that might
 represent taxa to be named or revalidated. Ancestral state reconstructions
 of number of upper premolars and number of pairs of mammae indicated that
 alternative conditions of both characters must have evolved multiple times
 along the evolutionary history of tree squirrels. Conclusions: We were
 able to obtain complete mitogenomes for samples as old as 120 years,
 reinforcing the potential of historical samples for phylogenetic and
 evolutionary inferences of elusive lineages of the tree of life. None of
 the taxonomic arrangements ever proposed for tree squirrels fully
 corresponded to our phylogenetic reconstruction, with only a few of the
 currently recognized genera recovered as monophyletic. By investigating
 the evolution of two morphological traits widely employed in the taxonomy
 of the group, we revealed that their homoplastic nature can help to
 explain the incongruence between phylogenetic results and classification
 schemes presented so far, and we recommend a substantial taxonomic
 overhaul.
description: Datasets used on the phylogenetic analyses of the tribe Sciurini, generated considering distinct percentages of mitogenome completeness per sample, as follow: Dataset 1 included only complete mitochondrial genomes (92 specimens with no missing data); Dataset 2 included samples with at least 80% of the mitogenome (162 specimens with &lt;20% of missing data per sample); Dataset 3 included samples with at least 60% of the mitogenome (186 specimens with &lt;40% of missing data per sample); Dataset 4 included samples with at least 40% of the mitogenome (210 specimens with &lt;60% of missing data per sample); and Dataset 5 included samples with at least 20% of the mitogenome (232 specimens with &lt;80% of missing data per sample).