Molecular Biology and Evolution 17:915-928 (2000)
© 2000 Society for Molecular Biology and Evolution
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L1 (LINE-1) Retrotransposon Evolution and Amplification in Recent Human History
,Section on Genomic Structure and Function, Laboratory of Molecular and Cellular Biology, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, Maryland
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Abstract |
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 TOP Abstract IntroductionMaterials and MethodsResultsDiscussionConclusionsAcknowledgementsliterature cited |
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L1 (LINE-1) elements constitute a large family of mammalian retrotransposons that have been replicating and evolving in mammals for more than 100 Myr and now compose 20% or more of the DNA of some mammals. Here, we investigated the evolutionary dynamics of the active human Ta L1 family and found that it arose ~4 MYA and subsequently differentiated into two major subfamilies, Ta-0 and Ta-1, each of which contain additional subsets. Ta-1, which has not heretofore been described, is younger than Ta-0 and now accounts for at least 50% of the Ta family. Although Ta-0 contains some active elements, the Ta-1 subfamily has replaced it as the replicatively dominant subfamily in humans; 69% of the loci that contain Ta-1 inserts are polymorphic for the presence or absence of the insert in human populations, as compared with 29% of the loci that contain Ta-0 inserts. This value is 90% for loci that contain Ta-1d inserts, which are the youngest subset of Ta-1 and now account for about two thirds of the Ta-1 subfamily. The successive emergence and amplification of distinct Ta L1 subfamilies shows that L1 evolution has been as active in recent human history as it has been found to be for rodent L1 families. In addition, Ta-1 elements have been accumulating in humans at about the same rate per generation as recently evolved active rodent L1 subfamilies.
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Introduction |
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TOPAbstractIntroductionMaterials and MethodsResultsDiscussionConclusionsAcknowledgementsliterature cited |
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L1 (LINE-1) elements (fig. 1 ) are mammalian long interspersed repeated DNA elements that replicate by retrotransposition (Voliva et al. 1984
; Hattori et al. 1986
; Fanning and Singer 1987a
; Mathias et al. 1991
; Furano 2000
). Most L1 copies are defective and accumulate mutations at the pseudogene (neutral) rate (e.g., Voliva et al. 1983
; Hardies et al. 1986
; Pascale et al. 1993
). They have been replicating and evolving in mammals since before the marsupial/placental divergence (~170 MYA) and account for ~14% of the mass of the human genome (Smit 1999
). Thus, L1 activity has had a major and perhaps defining effect on the structure and function of modern genomes.
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However, an important unresolved issue is the effect of L1 replication on present-day populations. In addition to causing polymorphisms and genetic defects (reviewed in Kazazian and Moran 1998
), L1 insertion could also affect the structural (Usdin and Furano 1989
; Schwartz et al. 1998
; Moran, DeBerardinis, and Kazazian 1999
) and regulatory properties of the genome (Wade et al. 1997
; Yang et al. 1998
). Although some L1 transposition takes place in modern humans, it has been suggested that L1 amplification occurs at such a low rate that the impact on the genome could be considered minor (DeBerardinis et al. 1998
). In contrast, there is clear evidence in murine rodents (Old World rats and mice) for novel, rapidly expanding families of L1 elements (Cabot et al. 1997
; DeBerardinis et al. 1998
; Naas et al. 1998
; Saxton and Martin 1998
). These novel L1 families are the latest products of a vigorous evolutionary process that has exemplified rodent L1 evolution for at least the last 10 Myr (e.g., Adey et al. 1994
; Casavant and Hardies 1994
; Cabot et al. 1997
; Saxton and Martin 1998
; Verneau, Catzeflis, and Furano 1998
).
A subset of human L1 elements called the Ta family (Skowronski, Fanning, and Singer 1988
) is the source of 11 of 12 de novo L1 insertions identified so far (quoted in Kimberland et al. 1999
), and two active elements belonging to this family have been isolated (Dombroski et al. 1991
; Holmes et al. 1994
). In addition, several other full-length Ta elements were shown to be active in a cell culture–based retrotransposition assay (Moran et al. 1996
; Sassaman et al. 1997
). However, the evolutionary dynamics of the Ta family has yet to be examined.
Here, we show that the Ta family emerged ~4 MYA, somewhat after the divergence (6 MYA; Goodman et al. 1998
) of humans and chimpanzees. Since then, the Ta family has differentiated into two major subfamilies, Ta-0 and Ta-1, each of which spawned additional subsets. Ta-0 is older than Ta-1, and although Ta-0 retains some active elements, Ta-1 now accounts for about one half of the Ta family and has largely replaced Ta-0 as the replicatively dominant subfamily in humans. The youngest subset of Ta-1, Ta-1d, arose about 1.4 MYA and accounts for about two thirds of the Ta-1 subfamily. The extensive differentiation of the Ta L1 family, typified by the emergence of, and eventual replacement by, novel active subsets, recapitulates the active evolution typical of murine L1 elements (Adey et al. 1994
; Casavant and Hardies 1994
; Cabot et al. 1997
; Saxton and Martin 1998
; Verneau, Catzeflis, and Furano 1998
). In addition, the Ta family has been expanding at about the same rate per generation as the most active rodent L1 families. Thus, human and murine genomes are being altered to about the same extent by L1 activity.
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Materials and Methods |
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TOPAbstractIntroductionMaterials and MethodsResultsDiscussionConclusionsAcknowledgementsliterature cited |
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Sequence and Phylogenetic Analysis
The BLAST (Altschul et al. 1990
) search program was used to find every sequence in the GenEMBL database with a perfect match to a 20mer sequence cognate to different regions of the L1 sequence. For example, to identify all of the Ta elements in the database, we performed the search using the sequence of oligonucleotide 3 depicted in figure 4
, which is cognate to the 3' untranslated region (UTR) ACA motif characteristic of the Ta family. Sequences were initially aligned using the GCG Pileup program (Wisconsin Package, version 10.0, Genetics Computer Group, Madison, Wis.) and refined manually. Phylogenetic analyses were performed using PAUP, version 4.0b2a (Swofford 1998
).
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Quantification of Ta and Ta-1 Elements
One and two micrograms of human DNA were transferred using a slot-blotter to Bio-Rad Zeta-Probe GT nylon membranes, as well as about 300, 600, 1,200, or 2,400 haploid genomic equivalents of a Ta-1 PCR product mixed with 2 µg of rat DNA. Membranes were hybridized to an oligonucleotide probe cognate to either the Ta (oligonucleotide 3 on fig. 4 ) or the Ta-1 (oligonucleotide 1 on fig. 4 ) subfamilies, together with their respective competitor oligonucleotides, as previously described (Verneau, Catzeflis, and Furano 1997
). The Ta- and Ta-1-type probes were hybridized overnight at 43°C and 45°C, respectively. Blots were washed three times in 0.3 M NaCl, 0.03 M Nacitrate (pH 7.4). The amount of radioactivity hybridized to each slot was quantified by analyzing the scanned autoradiograms using NIH Image (Wayne Rasband, NIH). In control experiments, we found that oligonucleotide 1 was specific to the Ta-1 subfamily, since it did not hybridize to a cloned Ta-0 element (sequence U09116 in clone JM104-Lre2; Moran et al. 1996
).
PCR
PCRs were performed in either an Idaho Technology Air-Thermo Cycler or an MJ Research PTC 100 thermocycler. In both cases, the reactions contained (as suggested by Idaho Technology) 50 mM Tris-Cl (pH 8.3), 2 mM MgCl2, 0.2 mM of each dNTP, 250 µg/ml bovine serum albumin, 2% sucrose, 0.1 mM Cresol Red (as an electrophoretic dye marker), and 0.5 µM primers. The primers used to determine the phylogenetic distribution of the Ta family are shown on figure 4
. The specificity of primers to amplify different L1 sequences was verified with clones of known sequence. Fifty to one hundred nanograms of genomic DNA was amplified in a total volume of 25 µl using the following conditions: denaturation at 94°C for 0 s (30 s in the MJ instrument), primer annealing at 40–50°C (depending on the pair of primers used) for 0 s (30 s), and chain extension at 72°C for 10 s (40 s), for 30 cycles.
We determined the polymorphism of each L1 insert using two PCRs and the primers listed in the appendix: one included the primer pair cognate to the non-L1 flanking sequence, and the second included the primer for the 3' flank and one specific for a 3' region of open reading frame (ORF) II (oligonucleotides 2 or 5; fig. 4 ). All of the human DNAs used in this study were purchased from the Coriell Institute for Medical Research. Nonhuman primate DNAs were gifts from Dr. C. Roos.
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Results |
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TOPAbstractIntroductionMaterials and MethodsResultsDiscussionConclusionsAcknowledgementsliterature cited |
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The Ta Family Consists of at Least Two Major Subfamilies: Ta-0 and Ta-1
We identified 91 Ta elements in the GenEMBL database (as of August 13, 1999; see appendix). Of these, 18 were obtained in studies designed to select L1 elements (Dombroski et al. 1991
; Dombroski, Scott, and Kazazian 1993
; Holmes et al. 1994
; Sassaman et al. 1997
), and 73 were the result of nonselective sequencing. The size distribution of all of the nonselected elements of known size (71 of 73) is shown in figure 1
. Interestingly, 34% of the nonselected Ta elements are full-length. This is considerably higher than the previous estimates of 5%–10% full-length elements in primates and mice (Fanning and Singer 1987b
), but it is about the proportion of full-length L1 elements in the rat genome (D'Ambrosio et al. 1986
). Most (81%) of the partial elements represent simple truncations. However, the remaining 19% contain inversions, some of which contained deletions (see legend to fig. 1
). These types of L1 structures have long been noted and are thought to be generated during L1 insertion (Rogers 1985
; Hutchison et al. 1989
; Casavant 1994
).
Figure 2
shows an alignment of all 42 full-length Ta elements (24 of the nonselected plus 18 of the selected elements), along with two "pre-Ta" elements (see below) and five ancestral non-Ta elements (Smit et al. 1995
). The 150 (of 6,048) positions (numbers given across the top of the fig. 2
) at which a character difference from the consensus is shared by three or more elements are presented. We do not show the additional 108 informative positions at which a difference is shared between just two elements, because these additional data do not change any of the conclusions and make inspection of the alignment unwieldy. We also aligned all of the non–full–length Ta elements and found no subsets other than those revealed here (results not shown). The full alignment of all informative positions of the full-length elements is available in the file Boissinot.Ta-align and can be obtained by anonymous ftp from helix.nih.gov in pub/avf.
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Since only five ancestral non-Ta elements were included in the alignment, the consensus sequence is that of the Ta elements. The Ta-defining ACA character in the 3' UTR is boxed. There has been little differentiation of the 3' UTR among the Ta elements. Elements ac00632 and ac007043 (arrows in fig. 2 ) might be considered "pre-Ta" elements because they contain ACg instead of the ACA character. However, these elements clearly belong in Ta, because they share numerous characters with bona fide Ta elements in other regions of the sequence. In addition, at least some of these elements retain activity, as one generated an insert in the factor VIII gene (Kazazian et al. 1988
).
The sequence alignment of the 5' UTR, ORF I, and ORF II reveals obvious subdivisions within the Ta family. For example, the Ta family can be divided into two groups based on the nucleotide pair at positions (5557, 5560) of ORF II. One, which we call Ta-1, has (T, G) at these positions, and the second one, Ta-0, almost always has (G, C). Although some ancestral non-Ta elements contain (T, G), (G, C) is quite likely the ancestral character at these positions. First, this (G, C) was invariably found associated with the ancestral LPA2 and LPA3 non-Ta L1 families in an earlier survey of primate L1 sequences (Smit et al. 1995
; the Ta family was designated LPA1 in this study). Second, a BLAST search of GenEMBL with a 20mer sequence cognate to this region of ORF II returned 500 L1 entries containing the (G, C) ORF-II sequence (500 is the maximal number returned by BLAST) but only 50 L1 entries containing the (T, G) sequence. Of these, 44 were Ta L1 elements, which we here call Ta-1. Third, as figure 3A
shows, the (G, C)-containing Ta-0 subfamily is, on the whole, more divergent than Ta-1. Sequence divergence within an L1 subfamily is positively correlated with its age (Pascale et al. 1993
; Adey et al. 1994
; Casavant and Hardies 1994
; Furano et al. 1994
; Verneau, Catzeflis, and Furano 1998
) Therefore, the results in figure 3A
suggest that most Ta-0 elements have resided longer in the genome than have most Ta-1 elements. This would be consistent with the ancestral nature of the (G, C) character.
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Figure 2 also reveals additional subdivisions within both the Ta-1 and the Ta-0 subfamilies. A deletion at position 74 of the 5' UTR (and several other characters) divides Ta-1 into two groups, Ta-1nd (no deletion) and Ta-1d, and the latter group itself harbors a subset consisting of the first four elements (in the gray box) in the alignment. As was the case for the Ta-1 and Ta-0 subfamilies, the distinction between the Ta-1d and Ta-1nd subsets based on the alignment is also evident by a difference between their divergence; figure 3B shows that Ta-1d is considerably less divergent (younger) than Ta-1nd. In addition, the Ta-0 subfamily also contains several apparent subsets (boxed). The divergence between the members of the top two subsets are, respectively, ~0.5% and ~0.4% less than the ~1.1% divergence of the Ta-0 subfamily on the whole (results not shown and fig. 3A ). As we show below, these younger Ta-1 and Ta-0 subsets were supported by phylogenetic analysis. (The pair of sequences [al096677 and u93573] that compose the bottommost Ta-0 subset differ at just one position and may actually be the same sequence; see legend to fig. 2 .)
Expansion of the Ta Family in Humans
Given the correlation between sequence divergence and age, we converted the percentage of divergence of the Ta-1 and Ta-0 subfamilies into time by using a molecular clock calibrated from the ~7% average divergence between human-specific and orangutan-specific L1 subfamilies (unpublished data). Assuming that humans and orangutans diverged 14 MYA (Goodman et al. 1998
), we obtained a nucleotide substitution rate per lineage of ~0.25% per Myr, which is ~15% to ~60% higher than other estimates of the hominid pseudogene rate (e.g., Casane et al. 1997
; Easteal and Herbert 1997
). Since this difference would not materially change any of our conclusions, we used the L1-derived rate, as it is based on structurally similar sequences.
We estimated that the Ta family emerged as early as ~4 MYA but that most of the amplification occurred in the last 3 Myr (fig. 3A
). We confirmed this recent origin of the Ta family by PCR. Ta family–specific primers generated a product only from humans but not from its closest relative, the chimpanzee, which diverged from humans ~6 MYA (Goodman et al. 1998
) (fig. 4
). In contrast, primers specific for older primate L1 families generated products in both humans and other primates (fig. 4
). The data in figure 3A
indicate that the Ta-1 subfamily first arose about 2.5 MYA, with most (75%) of the Ta-1 elements having been generated during the last ~1.6 Myr. In contrast, 80% of the Ta-0 elements had apparently already been inserted before ~1.6 MYA.
Slot blot analysis showed that the haploid human genome contains ~700 Ta elements (fig. 5 ). At the time of our search, ~13% of the human genome had been sequenced and this portion contained 73 Ta elements (after removal of the entries that had been purposely cloned). This would extrapolate to ~560 elements, which agrees reasonably well with the hybridization data (table 1 , cf. columns 2 and 5). Of these 73 "nonselected" Ta elements, 55 (75%) were long enough (fig. 1 ) to be classified as either Ta-1 or Ta-0. Applying this proportion to the ~700 Ta elements detected by hybridization gives a value of ~525 classifiable Ta elements (table 1 , column 3). Hybridization revealed ~300 sequences that hybridize to the Ta-1 (T, G) character (figs. 2, 4, and 5 and table 1 ). As mentioned above, ~12% of this hybridization may be due to non-Ta elements and correction for these yields ~265 Ta-1 elements per haploid genome (table 1 ). Thus, amplification of the Ta-1 subfamily accounts for at least half of the Ta family. This value is consistent with the proportion of these elements (counting only the nonselected ones) present in the GenEMBL database (cf. columns 3 and 6 in table 1 ).
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Although Ta-1 elements account for at least half of the Ta family, the Ta-1 subfamily had not been recognized earlier. In particular, no full-length Ta-1d elements (which account for about two thirds of Ta-1; see Discussion) were recovered in a previous search for full-length Ta elements (Sassaman et al. 1997
). As figure 2 shows, Ta-1d elements contain a deletion in the 5' UTR at what would be position 74, and we noted that the oligonucleotide (oligonucleotide A) used to select full- length elements in the above study was cognate to the nondeleted version of the 5' UTR (Sassaman et al. 1997
). Figure 6
shows that oligonucleotide A hybridizes very poorly to the deleted version of the 5' UTR. Thus, it is not surprising that of the 13 full-length elements isolated (Sassaman et al. 1997
), only 3 were Ta-1 elements, each of which (U93566, U93572, U93568) belonged to the smaller and older Ta-1nd subset that is not deleted at position 74 (fig. 2 ).
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Figure 1 shows that 34% of the 71 nonselected L1 Ta elements analyzed are full-length. Extrapolating this value to the ~700 present in the entire haploid genome indicates that it contains ~240 full-length Ta elements, or about three times the 80 previously reported (Sassaman et al. 1997
). Sassaman et al. (1997)
estimated the number of full-length Ta elements by hybridization of a Ta-specific oligonucleotide (e.g., analogous to oligonucleotide 3 in fig. 4
) to a ~6-kb L1 fragment on a blot of electrophoretically fractionated genomic DNA that had been digested with the AccI restriction endonuclease. Except for Ta-0 element ac003080, AccI sites are present at positions 41 and 5987 in every Ta and pre-Ta element shown in figure 2
. Therefore, the presence of a subset of Ta elements that lacks either of the AccI sites seems not to explain the apparent underestimation of full-length Ta elements in this earlier study (Sassaman et al. 1997
).
Polymorphic Ta Inserts
Figures 2 and 3
show that the Ta family has a distinct subfamily structure and that these subfamilies are of different but somewhat overlapping divergence. If these differences actually reflect different ages (fig. 3
), then we would expect that the loci which contain inserts of the less divergent (younger) subfamilies would be polymorphic (for the presence or absence of the L1 insert) compared with the loci that contain inserts of the older L1 subfamilies. For brevity, we refer to these insert-containing loci as polymorphic and fixed L1 inserts, respectively. We designed oligonucleotide primers cognate to the 5' (F) and 3' (R) flanking sequences of each of 14 nonselected Ta-0 and 25 nonselected Ta-1 elements present in GenEMBL (fig. 1
). Figure 7
summarizes the results of duplicate PCR reactions with these oligonucleotides (one with the F/R pair, the second with R and an L1 (L) oligonucleotide on a single individual from each of eight populations. Whereas 17 (68%) of 25 Ta-1 inserts were polymorphic, only 3 (22%) of 14 Ta-0 inserts were. These results are consistent with the difference between the divergency (age) of the Ta-1 and Ta-0 subfamilies (fig. 3A
). Since we sampled only a single individual from each of the eight populations, it is possible that some "fixed" L1-containing loci may be absent in some individuals. However, this would not change the fact that any arbitrarily sampled Ta-1–containing locus is much rarer in humans than an arbitrarily chosen Ta-0–containing locus.
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This correlation was even more dramatic when we mapped polymorphic Ta inserts on a phylogenetic tree of the Ta family. Figure 8 shows a single neighbor-joining tree (Saitou and Nei 1987
) of all of the full-length Ta elements. Several nodes (circled) within the Ta family are supported by bootstrap values of ~70% or greater. This would correspond to an ~95% confidence level, since the extents (and presumably the rate) of character change are not very different among the members of our data set (Hillis and Bull 1993
). One of these nodes groups the Ta-1d elements as a distinct subset within Ta-1, separate from the Ta-1nd elements. The Ta-1d subset is distinctly less divergent (younger) than the Ta-1nd subset (fig. 3B
) and 10 of the 11 (91%) Ta-1d elements tested (here or by others, see legend to fig. 8
and appendix) were polymorphic. In contrast, only one of five tested Ta-1nd elements was polymorphic (fig. 8
).
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10% that of the others, and the elements in parentheses contain open reading frames interrupted by a termination codon or a frameshift (or both)Figure 8 also shows that the generally older Ta-0 subfamily contains at least two well-supported subsets of elements. These subsets are young, as their members are quite similar to each other (connected by short branch lengths). This implies that these elements are recent inserts and all four of the elements tested from these subsets were polymorphic. On the other hand, none of five Ta-0 elements outside of these subsets was polymorphic. Thus, within both the Ta-1 and the Ta-0 subfamilies, there is a consistent correlation between low divergency and polymorphism.
Figure 8
also compares our results with previous studies of Ta elements using the cell culture retrotransposition assay (Sassaman et al. 1997
; Kimberland et al. 1999
). Although the earlier failure to clone Ta-1d elements (see above) somewhat limits the comparison, there is nonetheless a generally excellent correlation between the grouping of an element within a young cluster (i.e., in Ta-1 or the "young" Ta-0 subsets) and whether the element is active in the retrotransposition assay. In particular, those elements that are among the most active in this assay (l19088, L1.3; l19092, L1.4; af148856, L1RP) are all Ta-1d elements (Sassaman et al. 1997
; Kimberland et al. 1999
).
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Discussion |
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TOPAbstractIntroductionMaterials and MethodsResultsDiscussionConclusionsAcknowledgementsliterature cited |
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Sequence alignment revealed that the human Ta L1 family consists of distinct subsets of elements. We defined two major groups (subfamilies) based on the presence or absence of a number of ancestral nucleotide characters. For example, all members of the Ta-0 subfamily retain the ancestral C at 5560, most retained the ancestral G's at (4920, 5557) and the ancestral T at 5413, and about one half retained the ancestral A at 2188 and the ancestral G at 2380 (fig. 2 ). In contrast, none of these characters have been retained by any (or most) of the Ta-1 elements. The presence of the Ta-1 (T, G) character at (5557, 5560) in several non-Ta elements does not invalidate its use as a hallmark of the Ta-1 subfamily. This character was found only about 12% of the time in non-Ta elements, and the ancestral (G, C) character is invariably associated with ancestral primate L1 families (Smit et al. 1995
). We are now investigating whether these sites represent mutational hot spots. Both Ta-0 and Ta-1 harbor additional subsets of elements, and although the various Ta subgroups are clearly distinguished by a number of nucleotide characters, the alignment in figure 2 shows that determining the genealogical relationship between them could be difficult. First, while some characters are exclusively (or largely) confined to a particular subset (e.g., the deletion at position 74 or the T at position 1820), others are shared between several members of two or more subsets: the C at position 155, the G at position 1645, the G at position 2380, the T at position 5131. Furthermore, although the T at position 1820 that distinguishes Ta-1d is an apparent derived character (this T is not present in the five ancestral non-Ta elements), the diagnostic G at position 355 of Ta-1d may be an ancestral character being present in some of the ancestral non-Ta elements. This inconsistent pattern of shared characters and admixture of derived and ancestral characters will confound phylogenetic methods, like maximum parsimony or maximum likelihood, that rely on the pattern of inherited characters. Additionally, all of the Ta sequences are quite similar; most Ta-0 elements are 0.7%–1.1% divergent from most Ta-1 elements. Nonetheless, the neighbor-joining method, which is a distance method and groups sequences based on their overall sequence similarity, did generate some well-supported subsets, including Ta-1d (fig. 8 ).
The different subsets within the Ta family could also be distinguished by their degree of sequence divergence (fig. 3
) and the extent to which their inserts are polymorphic in human populations (figs. 7 and 8
). The excellent correlation between the low sequence divergence of a particular Ta subset and the high degree of polymorphism of its members again validates the use of sequence divergence within an L1 subfamily as a measure of its age (Pascale et al. 1993
; Adey et al. 1994
; Casavant and Hardies 1994
; Furano et al. 1994
; Verneau, Catzeflis, and Furano 1998
). Thus, the differentiation within the Ta family was the result of the successive amplification of different L1 subfamilies over the last ~4 Myr since it first arose.
The distributions of pairwise divergence between members of the Ta-1 and Ta-0 subfamilies (fig. 3A
) suggest that the amplification of Ta-1, and particularly Ta-1d (fig. 3B
), generally coincided with a decline of transpositional activity of Ta-0 elements, despite the fact that Ta-0 still retains some active subsets (fig. 8
). This apparent replacement of a preexisting active subfamily by a more recent one recapitulates the mode of L1 evolution in rats (Cabot et al. 1997
; Hayward, Zavanelli, and Furano 1997
) and mice (Adey et al. 1994
; Casavant and Hardies 1994
; Saxton and Martin 1998
). The distributions of pairwise divergence shown in figure 3
closely resemble those expected when L1 families are the product of a single lineage of replication-competent elements (the "master model") (Clough et al. 1996
). This model, wherein novel L1 subfamilies belonging to a single dominant lineage are generated successively in time, describes L1 evolution in most of the studied mammalian taxa. Although distinct active L1 subsets may coexist for short periods, a single lineage usually prevails (Rikke, Garvin, and Hardies 1991
; Pascale et al. 1993
; Adey et al. 1994
; Casavant and Hardies 1994
; Furano et al. 1994
).
The differentiation of a single 3' UTR lineage into distinct subfamilies that have waxed and waned over the past ~4 Myr describes the evolutionary dynamics of the human Ta family. This has also been observed for a recent rat L1 family (Cabot et al. 1997
). Figure 2
shows that the Ta 3' UTR sequence has hardly changed since it first arose in hominids ~4 MYA. In contrast, significant variation has taken place in all other regions of the Ta family. Selective constraint on the 3' UTR sequence or adaptive changes in the non-3' UTR sequence (or both) could account for this difference. An essential role for the 3' UTR sequence in L1 replication, as has been demonstrated for L1-like elements in insects (Luan and Eickbush 1995
; Mathews et al. 1997
), could account both for the conservation of the Ta 3' UTR sequence shown here and for the persistence of certain sequence motifs in the 3' UTR throughout mammalian L1 evolution (Howell and Usdin 1997
). On the other hand, adaptive changes in the non-3' UTR region could have enabled the element to either evade host repression or gain replicative superiority over existing elements. Whatever the case, competition for replicative dominance could explain the successive replacement of existing L1 subfamilies by novel ones (e.g., fig. 3
) and the expansion of one L1 subfamily at the expense of another (Casavant and Hardies 1994
; Cabot et al. 1997
).
In addition to mimicking the evolutionary dynamics of murine L1 evolution, Ta has also been accumulating at about the same rate per generation as its murine counterparts. The average accumulation (haploid) rate of the Ta family since it began amplifying in earnest ~3.5 MYA (fig. 3A
) is ~0.2 elements per 1,000 years (700 ÷ 3,500; table 1
). The most recent active L1 subfamilies in murine rodents have accumulated ~12 elements per 1,000 years for the L1Rnmlvi2-rn subfamily in Rattus norvegicus (~5,600 elements per 450,000 years; Cabot et al. 1997
) and ~5 elements per 1,000 years for the mouse Mus musculus Tf subfamily (~1,825 elements per 325,000 years, the average of three published determinations; DeBerardinis et al. 1998
; Naas et al. 1998
; Saxton and Martin 1998
). Because the impact of L1 amplification would be related to the number of elements accumulating per generation, we normalized the accumulation rates using generation times of ~20 years for humans and ~0.5 years for rodents. The normalized accumulation rates are ~0.006 elements per generation in rats and ~0.0025 elements per generation in mice, as compared with ~0.004 elements per generation in humans. These accumulation rates reflect the rate of both L1 transposition and L1 elimination by either selection (in the case of deleterious or lethal insertions) or genetic drift. Although these factors could be very different between these species, our results suggest that L1 transpositional activity might play equally important roles in the genetic diversity and evolution of both human and rodent genomes.
About 90% of the Ta-1d and a smaller percentage of Ta-1nd and Ta-0 insertions are polymorphic and could be useful for gene mapping or population genetics studies. The number of polymorphic inserts due to Ta-1d alone may well number several hundred in world human populations. L1 insertions have several advantages over commonly used polymorphic markers such as microsatellites and single-nucleotide polymorphisms. Parallelism (i.e., independent retrotransposition into the same chromosomal location) is unlikely, and the ancestral state of the polymorphism is known (i.e., the absence of inserts). Therefore, Ta insertions, like Alu insertions, could be used as robust markers to root population trees (e.g., Batzer et al. 1994
; Novick et al. 1998
) or allele phylogenies (e.g., Hammer 1994
).
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Conclusions |
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TOPAbstractIntroductionMaterials and MethodsResultsDiscussionConclusionsAcknowledgementsliterature cited |
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Evolutionary analysis of the Ta L1 family has shown that the tempo and mode of L1 evolution in recent human history recapitulates the process in murine rodents and that L1 activity may have affected the genomes of these taxa similarly. Furthermore, by identifying the most recently active human L1 subfamily(s), we now might possibly identify those factors responsible for its replicative success. To this end, we recently isolated every member of the Ta-1 subfamily and can compare such parameters as the genetic environment and the regulatory and enzymatic properties of various members of the Ta-1 subsets. Finally, by identifying the entire insertional history of the Ta-1 subfamily in several human populations, we may be better able to estimate the effect of this most current wave of L1 replication on present-day humans.
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Acknowledgements |
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TOPAbstractIntroductionMaterials and MethodsResultsDiscussionConclusionsAcknowledgementsliterature cited |
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We thank C. Roos for the primate DNA samples and Dr. John Moran for clone JM104-Lre2.
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Footnotes |
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Thomas Eickbush, Reviewing Editor
1 Keywords: L1/LINE-1
human
evolution
polymorphism
retrotransposon 
1 Present address: Institut des Sciences de l'Evolution, Case courrier 064, Université Montpellier II, Montpellier, France.
3 Address for correspondence and reprints: Anthony V. Furano, National Institutes of Health, Building 8, Room 203, 8 Center Drive MSC 0830, Bethesda, Maryland 20892-0830. E-mail: avf{at}helix.nih.gov
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