Dataset Information

Museomics of tree squirrels: a dense taxon sampling of mitogenomes reveals hidden diversity, phenotypic convergence, and the need of a taxonomic overhaul.

ABSTRACT: 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 systematists is likely a product of the difficulties in assessing morphological informative traits and of the scarcity or unavailability of fresh tissue samples for DNA sequencing. The highly discrepant taxonomic arrangements are a consequence of the lack of phylogenies and the exclusive phenotypic-based classifications, which can be misleading in a group with conservative morphology. Here we used high-throughput sequencing and an unprecedented sampling of museum specimens to provide the first comprehensive phylogeny of tree squirrels, with a special emphasis on Neotropical taxa. RESULTS:We obtained complete or partial mitochondrial genomes from 232 historical and modern samples, representing 40 of the 43 currently recognized species of Sciurini. Our phylogenetic analyses-performed with datasets differing on levels of missing data and taxa under distinct analytical 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 six lineages that represent taxa to be named or revalidated. Ancestral state reconstructions of number of upper premolars and number of mammae indicated that alternative conditions of both characters must have evolved multiple times throughout the evolutionary history of tree squirrels. CONCLUSIONS:Complete mitogenomes were obtained from museum specimens as old as 120?years, reinforcing the potential of historical samples for phylogenetic 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 explain the incongruence between phylogenetic results and the classification schemes presented so far. Based on our phylogenetic results we suggest a tentative supraspecific taxonomic arrangement for Sciurini, employing 13 generic names used in previous taxonomic classifications.

SUBMITTER: de Abreu-Jr EF

PROVIDER: S-EPMC7320592 | biostudies-literature | 2020 Jun

REPOSITORIES: biostudies-literature

ACCESS DATA

Publications

Museomics of tree squirrels: a dense taxon sampling of mitogenomes reveals hidden diversity, phenotypic convergence, and the need of a taxonomic overhaul.

de Abreu-Jr Edson Fiedler EF Pavan Silvia E SE Tsuchiya Mirian T N MTN Wilson Don E DE Percequillo Alexandre R AR Maldonado Jesús E JE

BMC evolutionary biology 20200626 1

<h4>Background</h4>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 systematists is likely a product of the difficulties in assessing morphological informative traits and of the scarcity or unavailability of fresh tissue samples for DNA sequencing. The highly discrepant taxonomic arrangements are a consequence of t ...[more]

PMID: 32590930

Similar Datasets

Project description:The Indonesian island of Sulawesi has a complex geological history. It is composed of several landmasses that have arrived at a near modern configuration only in the past few million years. It is the largest island in the biodiversity hotspot of Wallacea-an area demarcated by the biogeographic breaks between Wallace's and Lydekker's lines. The mammal fauna of Sulawesi is transitional between Asian and Australian faunas. Sulawesi's three genera of squirrels, all endemic (subfamily Nannosciurinae: Hyosciurus, Rubrisciurus and Prosciurillus), are of Asian origin and have evolved a variety of phenotypes that allow a range of ecological niche specializations. Here we present a molecular phylogeny of this radiation using data from museum specimens. High throughput sequencing technology was used to generate whole mitochondrial genomes and a panel of nuclear ultraconserved elements providing a large genome-wide dataset for inferring phylogenetic relationships.Our analysis confirmed monophyly of the Sulawesi taxa with deep divergences between the three endemic genera, which predate the amalgamation of the current island of Sulawesi. This suggests lineages may have evolved in allopatry after crossing Wallace's line. Nuclear and mitochondrial analyses were largely congruent and well supported, except for the placement of Prosciurillus murinus. Mitochondrial analysis revealed paraphyly for Prosciurillus, with P. murinus between or outside of Hyosciurus and Rubrisciurus, separate from other species of Prosciurillus. A deep but monophyletic history for the four included species of Prosciurillus was recovered with the nuclear data.The divergence of the Sulawesi squirrels from their closest relatives dated to ~9.7-12.5 million years ago (MYA), pushing back the age estimate of this ancient adaptive radiation prior to the formation of the current conformation of Sulawesi. Generic level diversification took place around 9.7 MYA, opening the possibility that the genera represent allopatric lineages that evolved in isolation in an ancient proto-Sulawesian archipelago. We propose that incongruence between phylogenies based on nuclear and mitochondrial sequences may have resulted from biogeographic discordance, when two allopatric lineages come into secondary contact, with complete replacement of the mitochondria in one species.

Project description:BACKGROUND: Discrepancies exist between what resident and attending physicians perceive as adequate supervision. We documented current practices in a university-based, categoric, internal medicine residency to characterize these discrepancies and the types of mixed messages that are communicated to residents, as well as to assess their potential effect on resident supervision and patient safety. METHODS: We surveyed residents and attending physicians separately about their current attitudes and behaviors regarding resident supervision. Both groups responded to 2 different measures of resident supervision: (1) 6 clinical vignettes that involved patient safety concerns, and (2) 9 frequently reported phrases communicated by attending physicians to residents before leaving the hospital during on-call admission days. RESULTS: There were clear and substantial differences between the perceptions of resident and attending physicians about when the supervising attending physician should be notified in each of the 6 vignettes. For example, 85% of attending physicians reported they wanted to be notified of an unexpected pneumothorax that required chest tube placement, but only 31% of resident physicians said they would call their attending physician during those circumstances. Common phrases, such as "page me if you need me," resulted in approximately 50% of residents reporting they would "rarely" or "never" call and another 41% reporting they would only "sometimes" call their attending physicians. CONCLUSIONS: Our study found that attending physicians reported they would want more frequent communication and closer supervision than routinely perceived by resident physicians. Although this discrepancy exists, commonly used phrases, such as "page me if you need me," rarely resulted in a change in resident behavior, and attending physicians appeared to be aware of the ineffectiveness of these statements. These mixed messages may increase the difficulty of balancing the dual goals of appropriate attending supervision and progressive independence during residency training.

Dataset Information

Museomics of tree squirrels: a dense taxon sampling of mitogenomes reveals hidden diversity, phenotypic convergence, and the need of a taxonomic overhaul.

Publications

Museomics of tree squirrels: a dense taxon sampling of mitogenomes reveals hidden diversity, phenotypic convergence, and the need of a taxonomic overhaul.

Similar Datasets

OmicsDI is part of the ELIXIR infrastructure

Tweets