Determining and dating recent rodent speciation events by using L1 (LINE-1) retrotransposons - PubMed (original) (raw)

Determining and dating recent rodent speciation events by using L1 (LINE-1) retrotransposons

O Verneau et al. Proc Natl Acad Sci U S A. 1998.

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, approximately 2.7 Mya, produced at least five lineages in <0.3 My; a second began approximately 1.2 Mya and may still be continuing.

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Figures

Figure 1

Figure 1

Rat L1 subfamilies. This is an alignment of the consensus sequences calculated for 45 rat L1 subfamilies and the individual sequence of 5 additional L1 elements. Only 100 bp of the 215- to 320-bp region of the 3′ UTR that was sequenced is shown here. All mammalian L1 elements contain four regions: a 5′ UTR involved in regulation; ORF I, which encodes an RNA-binding protein; ORF II, which encodes a reverse transcriptase; and the 3′ UTR. As explained elsewhere, the evolution of the 3′ UTR appears to occur rapidly enough to make it a useful source of phylogenetic characters for analyzing recent or rapid speciations (4). The names of the subfamilies (or individual elements) are given on the left, and the number (N) of members of each subfamily and its approximate age (in My) are given on the right. Alternate names also are listed on the right: letters for cross-reference to Fig. 2 and in parentheses are previously used designations (e.g., refs. and 19). The dots indicate identity with the consensus calculated from the listed sequences, the dashes indicate gaps, and the letters indicate differences. The numbered boxes indicate the sequence of the oligonucleotide hybridization probes derived from this part of the alignment. For oligonucleotides 55, 54, and 30, the sequence extends a few bases beyond the displayed alignment. This alignment begins at base 10 of our previously published partial alignment of this region (6).

Figure 2

Figure 2

The phylogeny of rats. This tree was built by using shared L1 oligonucleotide characters such as those numbered in Fig. 1. An open rectangle signifies that more than one oligonucleotide defines the branch, and an open square indicates that only one oligonucleotide character was used. The position of the oligonucleotide characters on a branch is arbitrary and not related to the “age” of the phylogenetic character. The length of the branches or positions of nodes in My was estimated, where possible, from the age of the indicated L1 subfamilies as described in the text. These subfamilies are a subset those in Fig. 1 and are positioned on the tree according to their age (solid circles). When no L1 subfamily was available to date a node or estimate a branch length they were drawn arbitrarily.

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