Occasional Papers Museum of Texas Tech University Number 223 13August 2003 Rapidly Evolving Repetitive DNAin a Karyotypically Mecaevolved Genome: Factors That Affect Chromosomal Evolution Robert D. Bradley, Roslyn Martinez, MaryMaltbie, Irene Tiemann-Boege, Holly A. Wichman, and Robert J. Baker Among some congeneric species of mammals, one taxon exhibits chromosomal stasis, whereas the other species possess a radically reorganized karyo¬ type (Baker and Bickham, 1980). This phenomenon of radically reorganizing the G-banded pattern of the karyotype is termed karyotypic megaevolution and it involves an extensive amount of chromosomal evolu¬ tion through the incorporation of both the numbers and kinds and types of rearrangements. The most clas¬ sical example of karyotypic megaevolution is found in two species of Muntiacus where diploid numbers are 2n= 6 for M. muntjak and 2n - 46 for M. re eves i (Fredga, 1977). A significant aspect of this phenom¬ enon is that the euchromatic regions of the genome can be changed substantially while having little or no affect ai the phenotype (morphologic) level, at least not a sufficient amount of change to justify generic distinction. Karyotypic megaevolution probably rep¬ resents the extreme condition for rate of karyotypic change involving complex chromosomal rearrange¬ ments (i.e. tandem fusions, peri and paracentric inver¬ sions). Relative to understanding the factors that af¬ fect chromosomal evolution, karyotypic megaevolution provides examples for studies involving two closely related species where one maintains chromosomal sta¬ sis while the other undergoes numerous chromosomal rearrangements. Many different factors have been proposed to drive chromosomal evolution. These include demo¬ graphic models (Wright, 1941; Wilson et al., 1975; Bush et al., 1977; Lande, 1979) and genetic and mo¬ lecular factors (Pathak et al,, 1973; Hsu et al., 1975; Hatch et al., 1976; Finnegan et al., 1982; Shaw et al., 1983; Wurster-Hill et al., 1988; Graphodatsky, 1989; Baker and Wichman, 1990; Meyne et al., 1990; Redi et al., 1990; Wichman et al., 1991). Of these hypoth¬ eses, only the tandem-repeat model by Wichman et al. (1991) establishes a set of testable predictions. Spe¬ cifically, Wichman et al. (1991) proposed that lineages undergoing rapid karyotypic change would have mul¬ tiple families of tandem repe ats; whereas lineages char¬ acterized by karyotypic stasis would have fewer fami¬ lies and a lower abundance of tandem repeats. In ad¬ dition, taxa possessing multiple repeats would be ex¬ pected to have these repeats actively changing chro¬ mosomal fields, as suggested by Lima-De-Faria (1980), whereas in taxa expressing karyotypic stasis, these repeats would be restricted to a single chromosomal field. From a population genetics standpoint, litter- 2 Occasional Papers, Museum of Texas Tech University size, effective population size, and generation time (i.e, demographic and populational characteristics) do not vary so radically in congeneric taxa that they could explain the extreme differences in rates and types of chromosomal rearrangements observed in karyotypic megaevolution. The tandem-repeat model (Wichman et al., 1991) was based on studies of genome organization in equids. Equids have been proposed to be the most rapidly evolv¬ ing karyotypic group of mammals (Wilson etal,, 1975). Within the genome of six species of equids, it was found that families of tandem repeats were diverse and that the chromosomal fields (Lima-De-Faria, 1980) occupied by these repeats varied substantially among closely related species. Using bats as a model, Bradley and Wichman (1994) tested the hypothesis that chromosomal evolu¬ tion was associated with the occurrence of tandemly repeated DNA sequences. The phylogenetic screen¬ ing method (Wichman et al. 1985, 1990) was used to evaluate the activity of tandemly repeated sequences in a conservatively evolving genome represented by the bat species Macrotus waterhousii compared to the activity of tandem repeats in the more rapidly evolving genome of the outgroup taxon {Artibeus jamaicensis). Their findings indicated that the number of families of repeated sequences were lower in M. waterhousii than in A Jamaicensis; thus providing initial support for the Wichman et al. (1991) predictions concerning karyo¬ typic evolution. However, the study by Bradley and Wichman (1994) represented only one end of the com¬ parative spectrum. What was lacking was an evalua¬ tion of the families and abundance of tandemly evolv¬ ing repeats from a taxon with a radically reorganized karyotype (megaevolved) compared to a more con¬ servatively evolving karyotype (chromosomal stasis). In this study, tandemly repeated DNA sequences were examined from the bat species Rhinophylla pumilio . This species was selected for two reasons. First, if. pumilio possesses a radically evolved karyo¬ type having accumulated > 20 rearrangements com¬ pared to its sister taxon R, fischerae, This extensive reorganization makes it impossible to compare to the G-banded karyotype of if. pumilio to the proposed primitive karyotype (Al. waterhousii) for the family Phyllostomidae (Baker, 1979; Baker et al., 1989). On the other hand, if. fischerae has a karyotype that dif¬ fers from the primitive condition by seven rearrange¬ ments: four fusions, one inversion, and two terminal translocations (Baker et al. 1987). This characteristic suggests that if. pumilio possesses one of, if not the most evolved karyotype in the family Phyllostomidae, Second, if. pumilio belongs to the same family (Phyllostomidae) as A Jamaicensis and M, waterhousii allowing for a comparison of tandemly repeated se¬ quences in a known phylogenetic framework. Spe¬ cifically, our goal was to compare the number of rap¬ idly evolving tandemly repeated DNA sequences found in a species undergoing karyotypic megaevolution (if, pumilio) to that found in a taxon demonstrating chro¬ mosomal stasis (M. waterhousii ). If the number of tandemly repeated sequences in if. pumilio statistically exceeds that found in M. waterhousii, then the hy¬ pothesis of Wichman et al. (1991) remains viable. Methods and Materials High molecular weight DNA was isolated from Sau3Al. Digests were electrophoresed on low melt- approximately 0.5 g of liver tissue of A. jamaicensis ing point agarose gels. DNA fragments in the 4-6 kb (TK 32042, male, Cuba: Guantanoma Province; range were extracted, ligated into the BamRl site of Guantanoma Bay Naval Base) and if. pumilio (TK pUC 18 vector, and transformed by electroporation 17565, female, Surinam: Marowijne; 3 km SWAlbina). into the JM103 strain of E. colt Methods for DNA isolation, cloning, digestion, trans¬ fer, and hybridization followed that of Bradley and Operationally, clones were not amplified during Wichman (1994). Specifically, a genomic library was the transformation pro cess; thus each clone represented constructed from if, pumilio by generating partial di- a unique DNA fragment and was treated as such by gests of genomic DNA using the restriction enzyme assigning each an identification number. DNA from Bradley et al.— Factors that Affect Chromosomal Evolution 3 each clone was triple digested with EcoRl, Hindlll , and Bam HI, electrophoresed on 0.8% agarose gels, and DNA transferred to two positively charged nylon membranes (Boehringer Mannheim) by placing filters above and below the gel following a modified tech¬ nique of Southern (1975). This generated two identical membranes each with bound DNA from R. pumilio clones that were used for the phylogenetic screening procedure (Wichman et al., 1985). Each filter was hybridized to labeled genomic probes, one from R. pumilio (ingroup) and the other from A. jamaicensis (outgroup). Probes were constructed from genomic DNA labeled with [ 32 P]dCTP using random-primed labeling techniques. Hybridization conditions were standardized with those of Bradley and Wichman (1994) to provide a compari¬ son among bat species, and to compare rates obtained from rodents (Wichman et al., 1990) and primates (Lloyd et al., 1987). A second verification was performed, hybridiz¬ ing the same membranes using the ECL Direct kit (Amersham). Membranes were washed previous to the hybridization in lx SSC, 1%SDS at 65°C for one hour and rinsed two times in 2xSSC for five minutes at room temperature. Genomic DNA of A. jamaicensis and R . pumilio was sonicated and 1.5 pg were la¬ beled. DNA was hybridized at 42°C overnight in 150 ml hybridization solution (ECL kit). Post-hybridiza¬ tion washes included two washes in 2xSSC for five minutes at room temperature, two washes in ECL post hybridization solution (6M urea, 04% SDS, 0.5xSSC) at 42°C for 10 minutes, and two washes in 2xSSC for five minutes. Membranes were blotted and submerged in reagents I and II for one minute and exposed on film. Autoradiograms of the two sets of filters (from both experiments) were overlaid and compared for ab¬ sence or presence of hybridization of R . pumilio or A. jamaicensis genomic DNA with the done fragments. In addition, the difference in intensity was compared by scoring bands as faint, medium, or strong. Under these conditions, only repetitive sequences show de¬ tectable hybridization because single copy sequences are under-represented in a total genomic probe. The presence or absence of a band indicates the gain or loss of a repetitive element or portion of the element, whereas the difference in intensity indicates the num¬ ber of copies of that element. Clones identified as different between the ingroup and outgroup were verified by repeating the phyloge¬ netic screening procedure and were designated as hypervariable. Hypervariable clones were sorted into families by Southern blot cross-hybridization (South¬ ern, 1975). If clones possessed multiple bands (frag¬ ments), each band was numbered sequentially begin¬ ning with the largest fragment. Cross-hybridization experiments involved labeling the hypervariable band(s) of each clone and using it to probe the other hypervariable clones. The bands of interest were ex¬ cised from 0.8% agarose gels, extracted and purified with the Prep-A-Gene kit (Bio-Rad), radiolabeled, hy¬ bridized, and scored as described above. These ex¬ periments were repeated until all clones were assigned to at least one family. Results Phylogenetic screening methods (Wichman et al., 1985) were used to screen 747 clones from a genomic library constructed from J?. pumilio DNA. Of these, 103 did not show any detectable hybridization to A. jamaicensis or self genomic DNA, indicating that they probably represented single or low copy sequences. The average insert size per clone was approximately 4.9 kb. If bats possess a genome size that is approxi¬ mately 60-80% of the typical mammalian genome (Manfredi-Romanini, 1985; Burton et al., 1989), then the 747 clones examined represent approximately 1/ 1000 of the bat genome. Two clones (Rp59 and Rp435) were identified as hypervariable, in that they were present in the ingroup (R, pumilio) but absent in the outgroup (A. jamaicensis). The low intensity of hy¬ bridization of these two clones suggests that they are members of a family of repeats characterized by low copy number. Four additional clones (Rp418, Rp607, Rp612, and Rp627) showed more intense hybridiza¬ tion in R. pumilio than in A, jamaicensis hut were not 4 Occasional Papers, Museum of Texas Tech University considered as representing hypervariable clones as these sequences would not be expected to contribute to the hypotheses as outlined in Wichman et al. (1990). The potential intenrelationship (sequence similar¬ ity) of these two clones was examined using cross¬ hybridization experiments. For each clone, bands (DNA fragment) generated by the triple digest of BamH\, £coRI, and FfmdIII were used as probes (Fig. 1). In each case, the labeled fragment hybridized to itself and other fragments from that clone; however, no frag¬ ment cross-hybridized to any other clone. in oo T— o *d- W (0 K CM h- cn o O © CM *3 *— <*> <£> <£> to © tO 00 T- O Vi to t- CSI r-- 00 T— h* TT © o © y— •t Y- 00 to to to to to 5090 bp 4072 bp 3045 bp 2036 bp 1636 bp Figure 1. Autoradiogram depicting the phylogenetic screening process for representative clones (DNA se¬ quences) isolated from a library constructed from genomic DNA obtained from Rhinophylla pumilio. Clones were triple digested with-Sa/wHI, EcoKL, and Hindi II restriction enzymes and were then hybridized to a radioac- tively-labeled probe constructed from total genomic DNA from Rhinophylla pumilio (left) and Artibeus jamaicensis (right). Only hybridization to repetitive elements is visible under these conditions. Discussion Seven hundred forty seven inserts were exam¬ ined in this study. Of these, 103 did not show detect¬ able hybridization to total genomic DNA and thus are thought to contain single or low copy sequences; con¬ sequently, they were removed from further consider¬ ation. The majority of the remaining clones (638 of 644) contained repetitive sequences that do not appear to show different patterns of evolution since the di¬ vergence of R . pumilio and A. jamaicensis . Of the remaining six clones, only two meet the criteria of hypervariable as defined by Wichman et al. (1991). These two DNA sequences appear to have originated since R. pumilio and A. jamaicensis shared a common ancestor. In addition, these clones appear to represent different DNA sequence families, as they share no ap¬ parent sequence similarity in cross-hybridization ex¬ periments. Alternatively, these sequences could con¬ tain portions of a larger repeat. Bradley et al.— Factors that Affect Chromosomal Evolution 5 Results of this study (Table 1) were similar to that obtained from the phylogenetic screening of the Macrotus genome (Bradley and Wichman, 1994), Both genomes contained a paucity of hypervariable clones and families of hypervariable sequences. However, these data differed substantially from similar studies of rodents (Wichman et al., 1985; 1990), primates (Lloyd et al., 1987), and equids (Wichman et al., 1990; 1991). Table 1. Comparison of results from phylogenetic screening efforts of rodents (Wichman et al, 1985; 1990), equids (Wichman et al, 1990; 1991), primates (Lloyd et al, 1987), and bats (Bradley and Wichman, 1994; this study). Taxon % Genome Examined # Variable Clones # Variable Families Average Genome Size of Order (Mb) Peromyscus 0.1 11 4 3400 Equus 0.1 34 6 3019 Homo 0.17 20 3 3000 Macrotus 0.1 I 1 1890 Rhinophylla 0.1 2 2 1890 Interpretation of the data generated from this study require the rejection of the prediction by Wichman et al. (1991) that lineages that undergo rapid karyo¬ typic change would have multiple families of tandemly repeated sequences. However in rejecting this hypoth¬ esis, three alternative scenarios must be examined. First, it may be that bats possess fewer repetitive se¬ quences than do other mammals. This possibility is supported by the observation of Manfredi Romanini (1985) and Burton et al, (1989) that bats possess ap¬ proximately 60-80% of the DNA found in typical mam¬ malian species. Although, the hypothesis that genome size is proportional to the number of repeats or repeat activity has been debated recently (Mouse Genome Sequencing Consortium, 2002). Second, our phylogenetic screening procedure may not have detected the presence of some hypervariable sequences. In this study, we choose A. jamaicensis as the outgroup taxon for evaluating the evolution of genomic sequences in the rapidly evolv¬ ing genome of R, pumilio, It may be that the genome of A, jamaicensis contains many of the potentially rap¬ idly evolving sequences found in the R. pumilio ge¬ nome. It is known that A. jamaicensis possesses a moderately evolving genome as calculated from the accumulation of chromosomal rearrangements since its divergence from the base of the Phyllostomid clade (Baker et al., 1989). Additionally, it may be that the ingroup taxon is too closely related to the outgroup taxon. What may be more valuable is a comparison of Rhinophytla to Macrotus. This would provide for a more conservative test. Third, for bats, it may be that tandemly repeated sequences do not drive chromosomal evolution as is hypothesized for equids (Wichman et al., 1990,1991). Alternatively, some other molecular mechanism is re¬ sponsible for this pattern of karyotypic megaevolution. For example, the rate of insertions/deletions or substi¬ tutions is very high in repeats of chiropterans and thus these divergent families of repeats would be missed by our stringent hybridization conditions. The com¬ parison of the mouse and human genome showed that substitution rates among repeats vary significantly. Of course, the longer the repeat the less the effect of the substitution rate on the hybridization. Sequencing the hypervariable clones would give us an indication of the type and length of the repeat (Mouse Genome Se¬ quencing Consortium, 2002). Another possibility is that sequences with a large number of repeats are difficult to clone. The selection of 4-6kb fragment sizes could have also contributed to the loss of repeat sequences. 6 Occasional Papers, Museum of Texas Tech University Acknowledgments We thank F. Mendez-Harclerode, S. Reeder, B. Amman, and M, Haynie for reviewing earlier versions of this manuscript. Thanks to B. Walker for assis¬ tance in the laboratory. Tissue samples were kindly provided by the Natural Science Research Laboratory, Museum of Texas Tech University. Support for this research was obtained from the Albert R. and Alma Shadle Fellowship, American Society of Mammalo- gists (RDB), Howard Hughes Medical Institute, Un¬ dergraduate Biological Sciences Education Program to Texas Tech University (RM), NIH Grant GM 38727 (HAW), NSF Grants BSR-86-00646 and BSR-90- 06797 (RJB). Literature Cited Baker, R. J. 1979. Karyology, Pp. 107-156 in Biology of bats of the New World family Phyllostomidae, Part ID (R. J. Baker, J. K. Jones Jr., and D, C. Carter, eds.). Special Publications, The Museum, Texas Tech University, Lubbock, Texas. Baker, R, J., and J. W. Bickham. 1980. Karyotypic evolu¬ tion in bats: evidence of extensive and conser¬ vative chromosomal evolution in closely related taxa. 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Bradley Department of Biological Sciences and Museum Texas Tech University Lubbock, Texas 79409-3131 e-mail: robert.bradley@ttu.edu Roslyn Martinez Wichman, H, A., C. T. Payne, and T. W. Reeder. 1990. Intrageneric variation in repetitive sequences iso¬ lated by phylogenetic screening of mammalian genomes, Pp. 153-160 /k Molecular Evolution (M. Clegg and S. J. O’Brien, eds.). Alan R. Liss Inc., New York. Wichman, H. A., S. S, Potter, and D. S. Pine. 1985. Mys, a family of mammalian transposable elements iso¬ lated by a phylogenetic screening procedure. Na¬ ture, 317:77-81. Wichman, H. A., C. T. Payne, O. A. Ryder, M. J. Hamilton, M, Maltbie, and R. J. Baker. 1991. Genomic dis¬ tribution of heterochromatin sequences in equids: implications to rapid chromosomal evo- 1 uti on. Joum al of Heredity, 82:369-377. Wilson, A. C., G. L. Bush, S. M, Case, and M. C, King. 1975. Social structuring of mammalian popula¬ tions and rate of chromosomal evolution. 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Mary Maltbie Los Alamos National Laboratory Life Sciencse Division Mail Stop M880 Los Alamos ; New Mexico 87545 Current Address: Therion International, LLC 36 Phila Street Saratoga Springs, New York 12866 e-mail: maltbie@theriondnaxom Department of Biological Sciences Texas Tech University Lubbock, Texas 79409-3131 Current Address: 8023 Garden Court San Antonio, Texas 78239 e-mail: roslyn76@flash.net 8 Occasional Papers, Museum of Texas Tech University Irene Tiemann-Boege Department of Biological Sciences Texas Tech University Lubbock, Texas 79409-3131 Current Address: Molecular and Computational Biology Program University of Southern California Los Angeles , California 90089-1340 e-mail; tiemanbo@usc.edu Holly A. Wichman Department of Biological Sciences University of Idaho Moscow, Idaho 83843 e-mail: hwichman@uidaho.edu Robert J. Baker Department of Biological Sciences and Museum Texas Tech University Lubbock, Texas 79409-3131 e-mail: rjbaker@ttu.edu Publications of the Museum of Texas Tech University Subscriptions are available through the Museum of Texas Tech University, attn: NSRL Publications Secretary, Box 43191, Lubbock, TX 79409-3191, Individuals may also purchase separate num¬ bers of the Occasional Papers directly from the Museum of Texas Tech University. ISSN 0149-175X Museum of Texas Tech University, Lubbock, TX 79409-3191