Proc. Natl. Acad. Sci. USA
Vol. 95, pp. 11284–11289, September 1998
Evolution

Determining and dating recent rodent speciation events by using
L1 (LINE-1) retrotransposons
¸OIS CATZEF LIS‡,
OLIVIER VERNEAU*†, FRANC

AND

A NTHONY V. FURANO*§

*Laboratory of Molecular and Cellular Biology, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD
´ Montpellier 2, 34095 Montpellier, France
20892-0830; and ‡Institut des Sciences de l’Evolution, Case Courrier 064, Universite

Communicated by Herbert Tabor, National Institute of Diabetes and Digestive and Kidney Diseases, Bethesda, MD, July 24, 1998 (received for review May 22, 1998)

This difference stems from the distinct biological properties of these elements. L1 elements are prolific, self-replicating mammalian retrotransposons that rapidly generate distinct novel subfamilies consisting mostly of defective (pseudo) copies (see legend to Fig. 1). The defective subfamily members are retained in the genome and diverge from each other with time at the pseudogene (neutral) rate. The rapid generation of novel L1 characters keeps pace with speciation, and the sequence divergence of the various defective subfamily members theoretically permits the dating of the speciations (4). By contrast, although SINE elements can be organized into subfamilies, they are not self-replicating and there are not enough distinct SINE families to generate high-resolution trees (11). Although individual SINE insertions are very robust phylogenetic characters and can generate detailed phylogenies, they cannot be used to date phylogenetic events (12).
Here we demonstrate that the L1 phylogenetic character can determine and date phylogenetic events within Rattus sensu stricto. These rodents consist of Ϸ50 very closely related taxa that evolved very recently and have been largely refractory to phylogenetic analysis (13–16). We found that the Rattus sensu stricto lineage, which we redefine partially here, emerged
Ϸ7.5–5.5 million years ago (Mya). Rattus sensu stricto then underwent two intense speciations: one occurred Ϸ2.7 Mya and generated five Rattus lineages in less than 0.3 My; a second began Ϸ1.2 Mya and may still be continuing.

ABSTRACT
Phylogenies based on the inheritance of shared derived characters will be ambiguous when the shared characters are not the result of common ancestry. Such characters are called homoplasies. Phylogenetic analysis also can be problematic if the characters have not changed sufficiently, as might be the case for rapid or recent speciations.
The latter are of particular interest because evolutionary processes may be more accessible the more recent the speciation. The repeated DNA subfamilies generated by the mammalian L1 (LINE-1) retrotransposon are apparently homoplasy-free phylogenetic characters. L1 retrotransposons are transmitted only by inheritance and rapidly generate novel variants that produce distinct subfamilies of mostly defective copies, which then ‘‘age’’ as they diverge. Here we show that the L1 character can both resolve and date recent speciation events within the large group of very closely related rats known as Rattus sensu stricto. This lineage arose 5–6 million years ago (Mya) and subsequently underwent two episodes of speciation: an intense one, Ϸ2.7 Mya, produced at least five lineages in <0.3 My; a second began Ϸ1.2 Mya and may still be continuing.
Cladistics is a phylogenetic approach for classifying organisms into taxa based on shared inherited characters (1). The emphasis on inherited couples taxonomic classification to the evolutionary history of the examined taxa. This makes cladistics intellectually appealing since phylogeny is based on genealogy. The shared characters can range from classical morphological and biochemical to molecular sequence data.
However, the major problem for cladistics is determining whether a shared character is inherited or arose independently because of convergence,