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, 104 (18), 7495-9

Multiple Molecular Evidences for a Living Mammalian Fossil

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Multiple Molecular Evidences for a Living Mammalian Fossil

Dorothée Huchon et al. Proc Natl Acad Sci U S A.

Abstract

Laonastes aenigmamus is an enigmatic rodent first described in 2005. Molecular and morphological data suggested that it is the sole representative of a new mammalian family, the Laonastidae, and a member of the Hystricognathi. However, the validity of this family is controversial because fossil-based phylogenetic analyses suggest that Laonastes is a surviving member of the Diatomyidae, a family considered to have been extinct for 11 million years. According to these data, Laonastes and Diatomyidae are the sister clade of extant Ctenodactylidae (i.e., gundies) and do not belong to the Hystricognathi. To solve the phylogenetic position of Laonastes, we conducted a large-scale molecular phylogeny of rodents. The analysis includes representatives of all major rodent taxonomic groups and was based on 5.5 kb of sequence data from four nuclear and two mitochondrial genes. To further validate the obtained results, a short interspersed element insertion analysis including 11 informative loci was also performed. Our molecular data based on sequence and short interspersed element analyses unambiguously placed Laonastes as a sister clade of gundies. All alternative hypotheses were significantly rejected based on Shimodaira-Hasegawa tests, supporting the idea that Laonastes does not belong to the Hystricognathi. Molecular dating analysis also supports an ancient divergence, approximately 44 Mya ago, between Ctenodactylidae and Laonastes. These combined analyses support the hypothesis that Laonastes is indeed a living fossil. Protection of this surviving species would conserve an ancient mammalian family.

Conflict of interest statement

The authors declare no conflict of interest.

Figures

Fig. 1.
Fig. 1.
A juvenile L. aenigmamus, captured and released after photography, provides evidence that this species is, indeed, very much alive. Known locally as Kha-nyou, the Laotian rock rat possesses a rat-like head with long whiskers and a furry squirrel-like tail. It lives in the limestone rock outcroppings of central Lao People's Democratic Republic. (Photo by Uthai Treesucon, David Redfield 2006 Lao expedition, and used with permission from Florida State University Research in Review Magazine).
Fig. 2.
Fig. 2.
Phylogenetic hypotheses for L. aenigmamus and Diatomyidae. (A) Based on morphological characters of extant species, Laonastes constitutes a new rodent family at the base of the hystricognaths (2). (B) Based on partial mitochondrial gene sequences, Laonastes constitutes a new rodent family nested within the hystricognaths (2). (C) Based on dental, cranial, and postcranial characters of fossils and extant species, Laonastes is a living fossil of the Diatomyidae family (3). (D) Based on fossil dental evidence, the family Diatomyidae is inferred to be a sister clade of hystricognaths (5). (E) Based on incisor enamel microstructure and cranial characters, Diatomyidae are related to the Pedetidae and Ctenodactylidae (i.e., sciurognathy and hystricomorphy) (6, 7).
Fig. 3.
Fig. 3.
Molecular time scale for the order Rodentia. The chronogram was obtained by using the topology of the best ML tree and a Bayesian relaxed clock method with different substitution models for each gene partition. Fossil constraints are indicated by diamonds on the corresponding nodes: 1, 28.5–50 Mya; 2, >37 Mya; 3, 28.5–37 Mya; 4, 37–90 Mya; 5, 55.4–90 Mya; 6, 25–35 Mya; and 7, 63–90 Mya (detailed references are provided in SI Appendix). The divergence date and the confidence interval of the Laonastes/Ctenodactylidae split are indicated. Circles indicate the phylogenetic support of the corresponding branches. Solid circles indicate branches with maximal support value (ML BP = 100 and Bayesian PP = 1.0); gray circles indicate branches with high support value (100 > BP > 90; PP = 1.0); and white circles indicate nodes with moderate support values (90 > BP > 50; 1.0 > PP > 0.75). Ano., Anomaluromorpha; Cas., Castorimorpha; Cte., Ctenodactylidae; Dia., Diatomyidae; Hys., Hystricognathi; Myo., Myodonta. The terms hystricomorph, myomorph, and sciuromorph indicate both character states and suborders. However, the character states and their corresponding taxonomic divisions disagree. For example, the Gliridae have myomorph characteristics but belong to the sciuromorphs. To avoid confusion, we thus prefer to use the terms, Ctenohystrica, Myodonta, and squirrel-related clade rather than Hystricomorpha, Myomorpha, and Sciuromorpha. CRE, Cretaceous; PAL, Paleocene; EOC, Eocene; OLI, Oligocene; MIO, Miocene; P, PlioPleistocene. Laonastes 25 and 410, specimen vouchers BMNH1998.25 and BMNH1998.410, respectively.
Fig. 4.
Fig. 4.
Phylogenetic affiliations of Laonastes based on presence/absence patterns of retroposed SINEs. The phylogenetic tree indicates the three major rodent clades: the mouse-related clade, the Ctenohystrica, and the squirrel-related clade. Eleven retroposed elements, present in certain mouse-related species (blue circles), were clearly absent in Laonastes. Nine other SINEs, present in certain Hystricognathi species (orange circles), were also absent in Laonastes. The monophyly marker of Ctenohystrica was present in all representatives including Laonastes (black circle) and was absent in members of both the mouse- and squirrel-related clades. Four diagnostic markers were present in Laonastes and Ctenodactylus (red circles) but absent in all other investigated rodents. Detailed information on the 11 investigated loci and diagnostic SINE markers are given in SI Appendix.

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