Interordinal gene capture, the phylogenetic position of Steller’s sea cow based on molecular and morphological data, and the macroevolutionary history of Sirenia

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 >30kb 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.

Evidence for two sympatric sirenian species (Mammalia, Tethytheria) in the early Oligocene of Central Europe

“…The present paper does not attempt to resolve this issue, but the hypothesis that dental replacement may be lost in the process of full elimination of a tooth or locus could well match with the observations in K. bronni. This find especially supports the successive reduction of the antemolar dentition during the evolution of Sirenia (Springer et al, 2015). Besides both extant genera, Trichechus (e.g., Domning, 1982) and Dugong (e.g., Lanyon and Sanson, 2006), fossil taxa such as Metaxytherium krahuletzi (Domning and Pervesler, 2001), M. floridanum (Domning, 1988), and M. albifontanum (Velez-Juarbe and Domning, 2014), all of which are more derived than Kaupitherium n. gen., lack permanent premolars.…”

“…The dental formula is highly informative, as shown in the most recent phylogenetic approach on Sirenia (Springer et al, 2015, fig. 5), where the loss of canines, incisors, and permanent premolars is plotted on a tree.…”

Targeted resequencing of codingDNAsequences forSNPdiscovery in nonmodel species

“…Baits do of course not need to be explicitly designed with the aim of discovering SNPs for genetic monitoring purposes. Thus, baits designed for other purposes (e.g., resolving taxonomic uncertainties, Yuan et al, 2016; identifying regulatory sequences, Yoshihara et al, 2016; identifying adaptive genes, Roffler et al, 2016; investigating loci linked to traits, Springer et al, 2015) can be used to screen samples from related species for intraspecific variation. via, Estonia and Norway.…”

A taxonomic and morphological re-evaluation of “Halitherium” cristolii Fitzinger, 1842 (Mammalia, Sirenia) from the late Oligocene of Austria, with the description of a new genus

“…The family Dugongidae Gray, 1821 has also been considered to be paraphyletic as, for instance, in the phylogenetic analyses by Domning (1994) and Voss (2013), who included an extensive set of taxa representing the order Sirenia. In contrast, although a number of dugongid taxa were neglected, such as the multispecific genera Eosiren and Prototherium, Springer et al (2015) included representatives of all major groups and recovered the Dugongidae as monophyletic. Other recent works using smaller datasets (e.g., VelezJuarbe & Domning 2014a support this hypothesis and consider the taxon studied herein as a member of the family Dugongidae.…”

“…This taxon proved to be invalid for two reasons: 1) the type genus Halitherium is declared a nomen dubium, and 2) this subfamily is considered paraphyletic in all known studies (e.g., Domning 1994;Velez-Juarbe et al 2012;Springer et al 2015), and this study aims at using a classification comprising only monophyletic taxa. The family Dugongidae Gray, 1821 has also been considered to be paraphyletic as, for instance, in the phylogenetic analyses by Domning (1994) and Voss (2013), who included an extensive set of taxa representing the order Sirenia.…”