Novacek, Michael J., American Museum of Natural History, EF 0629811 Murphy, William J., Texas A & M Research Foundation, EF 0629849 O'Leary, Maureen A., SUNY Stony Brook, EF 0629836 Luo, Zhe-Xi, Carnegie Institute, EF 0629959 Springer, Mark, Univ. California, Riverside, EF 0629860
Abstract Only a few of the myriad biological groups now thriving on this planet have fossil records that chronicle their evolutionary past. One of these few is Mammalia, known from about 5,000 extant species distributed among 1135 living genera, including our own human lineage, and more than 4,000 extinct genera, a four-to-one ratio of fossil genera to living genera that can hardly be matched elsewhere in the biota. Mammals display a spectacular range in size, form, and adaptations. They are closely linked to human health, welfare, and experience. No tree of all life could be regarded as complete without a comprehensive phylogeny of Mammalia. This conviction has inspired a surge of work in paleontology, comparative anatomy, and molecular biology. Despite these significant gains, many aspects of mammalian phylogeny are unresolved or highly controversial, even at some of the major branching points on the mammalian tree. PIs propose to examine species exemplars for 135 extant families, the majority of some 350 extinct families, and to extend this sample to a generic-level data set of 500 extant and nearly 500 extinct genera for combined analysis of genes and morphology. Their molecular team will continue to sample taxa toward a goal of covering 95% of all living genera outside the murids (rats, mice, and kin) and sciurids (squirrels). For character evidence, PIs plan to sample 30Kb in gene sequences from 34 genes for at least one exemplar of all living families. For the larger generic-level phases of the project, they will sample at least 6Kb of sequence. Morphologists will collect a projected 2,000 characters. Completion of a broad scale phylogeny for mammals will provide a model system in evolutionary and comparative biology with numerous applications in conservation and wildlife management, human health, biomedicine, and other areas. In addition, PIs intend to compile an integrated and image rich database for mammalian characters and convert it into a powerful toolkit for conservation management, education, and outreach through training programs and web resources.
Mammals are one of the most conspicuous elements of the world’s fauna and comprise ~5,500 species that are deployed in diverse habitats across far flung regions of the globe. Mammalian species are arranged into 26 orders and ~150 families. Relationships among these groups have proved difficult to resolve with anatomical data owing to convergent evolution, which occurs when similar features arise independently in different groups in response to similar environmental conditions. To remedy this problem, we assembled a large molecular data set for mammalian families that included DNA sequences for 26 genes in 164 mammalian species. Analyses of evolutionary relationships based on our molecular data set yielded a robust phylogeny for mammalian families. Molecular dating analyses that employed 82 fossil calibrations resulted in a timetree for mammalian families that elucidates important events in the evolutionary history of Mammalia. The Cretaceous Terrestrial Revolution, which witnessed the diversification of flowering plants, and the Cretaceous-Paleogene (KPg) mass extinction, which resulted in the final demise of non-avian dinosaurs, both played important roles in opening up ecospace that promoted mammalian diversification. Additional studies targeted genes that have played important roles in the adaptive radiation of mammals, including genes that are involved in tooth formation and vision. In the case of tooth formation, we examined several genes that are necessary for proper enamel formation. Enamel is the hardest substance in the vertebrate body and one of the essential genes for making enamel is enamelin. Most mammals have teeth that are capped with enamel, but there are also lineages without teeth (anteaters, pangolins, baleen whales) or with enamelless teeth (armadillos, sloths, aardvarks). All mammals without teeth or without enamel are descended from ancestral forms that possessed teeth with enamel. Given this ancestry, we predicted that toothless and enamelless mammals would have copies of the gene that encodes the enamelin protein, but that the enamelin gene in these species would exhibit signatures of molecular decay that abrogate normal function. To test this hypothesis, we sequenced most of the protein-coding region of the enamelin gene in all groups of placental mammals that lack teeth or have enamelless teeth. In every case, we discovered mutations in the enamelin gene that disrupt the proper function of this gene so that enamel cannot be manufactured. Our results link evolutionary change at the molecular level to morphological change in the fossil record and provide transparent evidence for the enormous predictive power of Charles Darwin’s theory of descent with modification. In the case of genes that are associated with vision, we provide the first molecular evidence for complete loss of color vision pigments in a mammalian species. Specifically, we identified five different lineages of deep-diving cetaceans, including the blue whale and the giant sperm whale, where all vestiges of color vision have been lost in favor of more acute vision in low light conditions. We also discovered molecular evidence for this condition, known as rod monochromacy, in golden moles and the nine-banded armadillo. This condition also occurs in human populations with a frequency of 1:30,000 and results in severely compromised vision. The identification of multiple mammalian species with natural rod monochromacy provides an opportunity to identify possible genetic causes of this condition that is maladaptive in our own species.
