Bibliography and Index of the Sirenia and Desmostylia  

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"Springer, Mark S."

Springer, Mark S.: SEE ALSO Amrine & Springer, 1999; Lavergne et al., 1996; Stanhope et al., 1998. (detail)
Springer, Mark S.; Kirsch, John A. W. (detail)
A molecular perspective on the phylogeny of placental mammals based on mitochondrial 12S rDNA sequences, with special reference to the problem of the Paenungulata.
Jour. Mamm. Evol. 1(2): 149-166. 2 tabs. 7 figs. June 1993.
–All analyses united Loxodonta and Dugong, with Procavia as their sister group, supporting the Paenungulata clade.
Lavergne, Anne; Douzery, Emmanuel; Stichler, Todd; Catzeflis, François M.; Springer, Mark S. (detail)
Interordinal mammalian relationships: evidence for paenungulate monophyly is provided by complete mitochondrial 12S rRNA sequences.
Molec. Phylogenetics & Evol. 6(2): 245-258. Oct. 1996.
–The most strongly supported clade among mammalian orders was found to be the Paenungulata (Sirenia + Proboscidea + Hyracoidea); the Tethytheria (Sirenia + Proboscidea) grouping was also observed but less stably supported. This may be due to a short elapsed time between the divergences of hyracoids and tethytheres. Paenungulates are estimated to have originated at the end of the Cretaceous.
Springer, Mark S.; Cleven, Gregory C.; Madsen, Ole; De Jong, Wilfried W.; Waddell, Victor G.; Amrine, Heather M.; Stanhope, Michael J. (detail)
Endemic African mammals shake the phylogenetic tree.
Nature 388(6637): 61-64. 3 tabs. 1 fig. July 3, 1997.
–Reports evidence from DNA sequences that supports a close relationship of sirs. with hyracoids, proboscideans, golden moles, elephant shrews, and aardvarks.
Stanhope, Michael J.; Madsen, Ole; Waddell, Victor G.; Cleven, Gregory C.; De Jong, Wilfried W.; Springer, Mark S. (detail)
Highly congruent molecular support for a diverse superordinal clade of endemic African mammals.
Molec. Phylog. Evol. 9(3): 501-508. June 1998.
Amrine, Heather M.; Springer, Mark S. (detail)
Maximum-likelihood analysis of the tethythere hypothesis based on a multigene data set and a comparison of different models of sequence evolution.
Jour. Mamm. Evol. 6(2): 161-176. 7 tabs. 1 fig. June 1999.
Springer, Mark S.; Stanhope, M. J.; Madsen, Ole; De Jong, Wilfried W. (detail)
Molecules consolidate the placental mammal tree.
Trends in Ecol. & Evol. 19(8): 430-438. 1 tab. 4 figs. Aug. 2004.
Meredith, Robert W.; Gatesy, John; Murphy, William J.; Ryder, Oliver A.; Springer, Mark S. (detail)
Molecular decay of the tooth gene enamelin (ENAM) mirrors the loss of enamel in the fossil record of placental mammals.
PLoS Genetics 5(9): 1-12. 6 figs. e1000634. doi: 10.1371/journal.pgen.1000634 Sept. 4, 2009.
–Includes Dugong dugon in cladogram (fig. 1, p. 3), showing that its enamelin gene is not degenerate (despite the vestigial state of its tooth enamel). Sirs. are not mentioned in the text.
Springer, Mark S.; Signore, Anthony V.; Paijmans, Johanna L. A.; Vélez-Juarbe, Jorge; Domning, Daryl Paul; Bauer, Cameron E.; He, Kai; Crerar, Lorelei D.; Campos, Paula F.; Murphy, William J.; Meredith, Robert W.; Gatesy, John; Willerslev, Eske; MacPhee, Ross D. E.; Hofreiter, Michael; Campbell, Kevin L. (detail)
Interordinal gene capture, the phylogenetic position of Steller's sea cow based on molecular and morphological data, and the macroevolutionary history of Sirenia.
Molecular Phylogenetics & Evolution 91: 178-193. 5 tabs. 5 figs. 9 tabs. in online Supplementary Material. DOI:10.1016/j.ympev.2015.05.022 Publ. online June 4, 2015.
–ABSTRACT: The recently extinct (ca. 1768) Steller's sea cow (Hydrodamalis gigas) was a large, edentulous North Pacific sirenian. The phylogenetic affinities of this taxon to other members of this clade, living and extinct, are uncertain based on previous morphological and molecular studies. We employed hybridization capture methods and second generation sequencing technology to obtain >30 kb of exon sequences from 26 nuclear genes for both H. gigas and Dugong dugon. We also obtained complete coding sequences for the tooth-related enamelin (ENAM) gene. Hybridization probes designed using dugong and manatee sequences were both highly effective in retrieving sequences from H. gigas (mean = 98.8% coverage), as were more divergent probes for regions of ENAM (99.0% coverage) that were designed exclusively from a proboscidean (African elephant) and a hyracoid (Cape hyrax). New sequences were combined with available sequences for representatives of all other afrotherian orders. We also expanded a previously published morphological matrix for living and fossil Sirenia by adding both new taxa and nine new postcranial characters. Maximum likelihood and parsimony analyses of the molecular data provide robust support for an association of H. gigas and D. dugon to the exclusion of living trichechids (manatees). Parsimony analyses of the morphological data also support the inclusion of H. gigas in Dugongidae with D. dugon and fossil dugongids. Timetree analyses based on calibration density approaches with hard- and soft-bounded constraints suggest that H. gigas and D. dugon diverged in the Oligocene and that crown sirenians last shared a common ancestor in the Eocene. The coding sequence for the ENAM gene in H. gigas does not contain frameshift mutations or stop codons, but there is a transversion mutation (AG to CG) in the acceptor splice site of intron 2. This disruption in the edentulous Steller's sea cow is consistent with previous studies that have documented inactivating mutations in tooth-specific loci of a variety of edentulous and enamelless vertebrates including birds, turtles, aardvarks, pangolins, xenarthrans, and baleen whales. Further, branch-site dN/dS analyses provide evidence for positive selection in ENAM on the stem dugongid branch where extensive tooth reduction occurred, followed by neutral evolution on the Hydrodamalis branch. Finally, we present a synthetic evolutionary tree for living and fossil sirenians showing several key innovations in the history of this clade including character state changes that parallel those that occurred in the evolutionary history of cetaceans.
Gaudry, Michael J.; Jastroch, Martin; Treberg, Jason R.; Hofreiter, Michael; Paijmans, Johanna L. A.; Starrett, James; Wales, Nathan; Signore, Anthony V.; Springer, Mark S.; Campbell, Kevin L. (detail)
Inactivation of thermogenic UCP1 as a historical contingency in multiple placental mammal clades.
Science Advances 3: e1602878 (14 pp.). 4 figs. + online supplementary materials. DOI: 10.1126/sciadv.1602878 July 12, 2017.
–ABSTRACT: Mitochondrial uncoupling protein 1 (UCP1) is essential for nonshivering thermogenesis in brown adipose tissue and is widely accepted to have played a key thermoregulatory role in small-bodied and neonatal placental mammals that enabled the exploitation of cold environments. We map ucp1 sequences from 133 mammals onto a species tree constructed from a ~51-kb sequence alignment and show that inactivating mutations have occurred in at least 8 of the 18 traditional placental orders, thereby challenging the physiological importance of UCP1 across Placentalia. Selection and timetree analyses further reveal that ucp1 inactivations temporally correspond with strong secondary reductions in metabolic intensity in xenarthrans and pangolins, or in six other lineages coincided with a ~30 million–year episode of global cooling in the Paleogene that promoted sharp increases in body mass and cladogenesis evident in the fossil record. Our findings also demonstrate that members of various lineages (for example, cetaceans, horses, woolly mammoths, Steller's sea cows) evolved extreme cold hardiness in the absence of UCP1-mediated thermogenesis. Finally, we identify ucp1 inactivation as a historical contingency that is linked to the current low species diversity of clades lacking functional UCP1, thus providing the first evidence for species selection related to the presence or absence of a single gene product.

Daryl P. Domning, Research Associate, Department of Paleobiology, National Museum of Natural History, Smithsonian Institution, Washington, D.C. 20560, and Laboratory of Evolutionary Biology, Department of Anatomy, College of Medicine, Howard University, Washington, D.C. 20059.
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