Deciphering the timing of the placental mammal radiation is a longstanding problem in evolutionary biology, but consensus on the tempo and mode of placental diversification remains elusive. Nevertheless, an accurate timetree is essential for understanding the role of important events in Earth history (e.g., Cretaceous Terrestrial Revolution, KPg mass extinction) in promoting the taxonomic and ecomorphological diversification of Placentalia. Archibald and Deutschman described three competing models for the diversification of placental mammals, which are the Explosive, Long Fuse, and Short Fuse Models. More recently, the Soft Explosive Model and Trans-KPg Model have emerged as additional hypotheses for the placental radiation. Here, we review molecular and paleontological evidence for each of these five models including the identification of general problems that can negatively impact divergence time estimates. The Long Fuse Model has received more support from relaxed clock studies than any of the other models, but this model is not supported by morphological cladistic studies that position Cretaceous eutherians outside of crown Placentalia. At the same time, morphological cladistics has a poor track record of reconstructing higher-level relationships among the orders of placental mammals including the results of new pseudoextinction analyses that we performed on the largest available morphological data set for mammals (4,541 characters). We also examine the strengths and weaknesses of different timetree methods (node dating, tip dating, and fossilized birth-death dating) that may now be applied to estimate the timing of the placental radiation. While new methods such as tip dating are promising, they also have problems that must be addressed if these methods are to effectively discriminate among competing hypotheses for placental diversification. Finally, we discuss the complexities of timetree estimation when the signal of speciation times is impacted by incomplete lineage sorting (ILS) and hybridization. Not accounting for ILS results in dates that are older than speciation events. Hybridization, in turn, can result in dates than are younger or older than speciation dates. Disregarding this potential variation in "gene" history across the genome can distort phylogenetic branch lengths and divergence estimates when multiple unlinked genomic loci are combined together in a timetree analysis.
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.
Contagious diseases are unavoidable realities of life. Thus, understanding pathogens and their respective diseases is important in many biological subfields including evolution, ecology, health sciences, microbiology, and others. While all college students will have encountered pathogenic diseases at some point in their lives, many will not have studied them in a classroom setting. As a result, students may not be able to accurately formulate a comprehensive definition of pathogenic disease on their own. Here, I provide an engaging activity where students construct a definition of pathogenic disease based on their lived experiences using the think-pair-share technique. Students are asked to define pathogenic disease individually, then in small groups, and finally as an entire class. At the end of this activity, the class will have agreed upon one definition for pathogenic disease. Following this, the students are asked to put their new definition into practice by completing a categorization activity where they must sort different diseases into the following categories: genetic, environmental, or pathogenic. This immediate application of new knowledge helps foster long-term learning. Students were highly engaged with the material, and this lesson also fostered a sense of classroom community as it encouraged students to share their knowledge while completing the categorization assignment. An end-of-term review activity showcased that the students were able to recall the information learned during this lesson at the end of the course. This lesson is easy to implement and can help students understand pathogenic disease in both introductory and advanced courses.
We set out to create a fun and engaging activity using recognizable fictional characters, so students get a chance to practice using Greek and Latin roots to create binomial names. Students in biology courses are faced with a plethora of scientific jargon that are often composed of Greek and Latin roots that hint at their definitions. Students often struggle to understand and apply these terms due to a lack of familiarity with these roots. With this scaffolded activity we attempt to alleviate these concerns by first having students define biological terms by looking up the roots that the word is composed of. We then provide examples of real species and their binomial names with Greek and Latin roots to give examples of how species characteristics are used to create their scientific names. Lastly the students work in groups to group Pokémon™ into genera and give each Pokémon™ a binomial name. Students were engaged in the activity and reported that it helped improve their understanding of Greek and Latin roots for future projects and exams. This activity can enrich introductory and advanced biology courses of any size.
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