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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.
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