Abstract
Pseudoextinction analyses, which simulate extinction in extant taxa, use molecular phylogenetics to assess the accuracy of morphological phylogenetics. Previous pseudoextinction analyses have shown a failure of morphological phylogenetics to place some individual placental orders in the correct superordinal clade. Recent work suggests that the inclusion of hypothetical ancestors of extant placental clades, estimated by ancestral state reconstructions of morphological characters, may increase the accuracy of morphological phylogenetic analyses. However, these studies reconstructed direct hypothetical ancestors for each extant taxon based on a well-corroborated molecular phylogeny, which is not possible for extinct taxa that lack molecular data. It remains to be determined if pseudoextinct taxa, and by proxy extinct taxa, can be accurately placed when their immediate hypothetical ancestors are unknown. To investigate this, we employed molecular scaffolds with the largest available morphological data set for placental mammals. Each placental order was sequentially treated as pseudoextinct by exempting it from the molecular scaffold and recoding soft morphological characters as missing for all its constituent species. For each pseudoextinct data set, we omitted the pseudoextinct taxon and performed a parsimony ancestral state reconstruction to obtain hypothetical predicted ancestors. Each pseudoextinct order was then evaluated in seven parsimony analyses that employed combinations of fossil taxa, hypothetical predicted ancestors, and a molecular scaffold. In treatments that included fossils, hypothetical predicted ancestors, and a molecular scaffold, only 8 of 19 pseudoextinct placental orders (42%) retained the same interordinal placement as on the molecular scaffold. In treatments that included hypothetical predicted ancestors but not fossils or a scaffold, only four placental orders (21%) were recovered in positions that are congruent with the scaffold. These results indicate that hypothetical predicted ancestors do not increase the accuracy of pseudoextinct taxon placement when the immediate hypothetical ancestor of the taxon is unknown. Hypothetical predicted ancestors are not a panacea for morphological phylogenetics.
Highlights
Charles Darwin [1] provided the world with its first glimpse of a modern phylogeny with contemporary taxa deployed at its tips and ancestors at internal nodes
Mean/median RF distances were much higher for analyses that lacked a molecular scaffold (Table 1)
Because the placement of most extinct taxa cannot be vetted with molecular data, the accuracy of morphological phylogenetics must be assessed with other approaches such as pseudoextinction analyses that are performed upon extant taxa
Summary
Charles Darwin [1] provided the world with its first glimpse of a modern phylogeny with contemporary taxa deployed at its tips and ancestors at internal nodes. Morphological characters were the main source of data for phylogenetic analyses for much of the 20th century [2, 3], but since the 1960s systematists have increasingly relied on different types of genetic data and genomic data with the advent of massively parallel DNA sequencing [3, 4]. Whereas molecular data are readily available for many extant taxa, the procurement of DNA sequences has proven much more challenging for recently extinct species and impossible for long extinct species [7]. The dearth of molecular data for most extinct species, which comprise the vast majority of species that have lived on Earth, mandates the continued use of morphological data to study the phylogenetic relationships of extinct taxa to each other and to extant taxa [5]
Sign-in/Register to view highlights & summary Talk to us
Join us for a 30 min session where you can share your feedback and ask us any queries you have
Schedule a callDisclaimer: All third-party content on this website/platform is and will remain the property of their respective owners and is provided on "as is" basis without any warranties, express or implied. Use of third-party content does not indicate any affiliation, sponsorship with or endorsement by them. Any references to third-party content is to identify the corresponding services and shall be considered fair use under The CopyrightLaw.
