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Unit Chapters
Genomics
Proteins & Proteomics
Evolution & Phylogenetics
Introduction
A Brief History of Classification
Cladistics and Classification
Applications of Molecular Phylogenetics
HIV and Forensic Uses of Phylogenetics
The Origin of Bats and Flight
Challenges
Coda: The Renaissance of Comparative Biology
Microbial Diversity
Emerging Infectious Diseases
HIV & AIDS
Genetics of Development
Cell Biology & Cancer
Human Evolution
Neurobiology
Biology of Sex & Gender
Biodiversity
Genetically Modified Organisms
The Origin of Bats and Flight

Molecular phylogenetics are often most useful when there is conflict among the phylogenies constructed with different morphological character data sets. For instance, molecular data have helped settle the question of whether bats are a monophyletic group - that is, whether they share a common ancestor not shared by non-bats. In the 1980s several morphological analyses challenged the traditional view that bats (order Chiroptera) were monophyletic. The studies proposed that the large fruit-eating Megachiroptera (megabats) were actually more closely related to primates than they were to the smaller insect-eating Microchiroptera (microbats). The studies based the megabat-primate grouping on synapomorphies that included features of the penis, brain, and limbs. The implication of this reclassification was that flight evolved more than once within mammals.
Figure 5 Monophyly and Diphyly of Bat Evolution

Spurred by this controversy, several research groups performed cladistic analyses of bats using molecular data during the early 1990s. For example, Loren Ammerman and David Hillis sequenced mitochondrial DNA sequences from many mammals, including two species of microbats, two species of megabats, a tree shrew, a primate, and several outgroups. From their data, the most parsimonious tree that assumed bat monophyly was ten steps shorter than the most parsimonious tree that assumed bats were not monophyletic. Statistical analysis showed that bat monophyly was significantly more parsimonious than the absence of bat monophyly. Other molecular phylogenetic studies, using a variety of different classes of genes, showed the same pattern of bat monophyly. These researchers also indicated that convergence is the most likely reason why some derived morphological character states seem to be shared by
Figure 5a Megabat
primates and bats.5

Other researchers raised the objection that these early molecular phylogenetic studies did not take into account biases in the way that sequences evolve. Specifically, the critics noted that both microbats and macrobats have DNA with a higher proportion of G's and C's than A's and T's. It is well known that organisms that have higher metabolic rates will have higher G-C content. Thus, the critics argued, perhaps the apparent monophyly of bats that was observed in the molecular studies is due to convergent evolution toward high G-C content and not homology. Using various methods, subsequent molecular phylogenetic studies took the bias in nucleotide changes into account. One simple method was to split the DNA sequences into A-T rich and G-C rich regions and do a
Figure 5b: Mexican freetail bat
separate analysis on each. Even after nucleotide sequence bias was discounted, the most parsimonious phylogenies still showed that all bats had a single common ancestor. This support for bats as a monophyletic group is also strong evidence for flight evolving only once in mammals.

The monophyly of bats is an example where molecular data shored up the traditional phylogeny against challenges posed by some morphological characters. In contrast, there are also occasions where analysis of the molecular data provided an unexpected answer. One such example is the example of the evolutionary history of whales, which is discussed in detail in the video.
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