- Email: [email protected]
Phylogenetic study of the genus Plasmodium based on the secondary structure-based alignment of the small subunit ribosomal RNA
Molecular and Biochemical Parasitology 90 (1997) 317 – 321
Short communication
Phylogenetic study of the genus Plasmodium based on the secondary structure-based alignment of the small subunit ribosomal RNA Ananias A. Escalante a, Ira F. Goldman a, Peter De Rijk b, Rupert De Wachter b, William E. Collins a, Shoukat H. Qari a, Altaf A. Lal a,* a
Di6ision of Parasitic Diseases, Centers for Disease Control and Pre6ention, Mail Stop F-12, 4770 Buford Hwy., Chamblee, GA 30341, USA b Department Biochemie, Uni6ersiteit Antwerpen (UIA), Uni6ersiteitsplein 1, B-2610 Antwerpen, Belgium Received 28 July 1997; accepted 28 July 1997
Keywords: Malaria; Plasmodium simium; Plasmodium falciparum; Ribosomal RNA; Molecular epidemiology; Virulence
The phylogenetic relationship of the genus Plasmodium has been studied by several investigators using partial or full-length sequences of 18S SSU rRNA genes. Special attention has been focused on the issue of the origin of Plasmodium falciparum [1–4]. Earlier studies suggested that P. falciparum was of recent origin because of a host switch from a nonhuman host. This hypothesis was used to explain the high virulence of P. falciparum in comparison with other human malarial parasites [5,6]. Studies of plasmodial evolution that used 18S SSU rRNA gene-based phylogeny showed that P. * Corresponding author. Tel.: +1 770 4884047; fax: + 1 770 4884454; e-mail: [email protected].
falciparum shared a common ancestor with avian Plasmodium species [1,2]. It was further suggested that this host switch could have taken place at the beginning of agriculture [1,2], supporting the traditional notion that the high virulence of P. falciparum could be explained by the short period of the host–parasite association [5]. Subsequent phylogenetic studies showed that P. reichenowi (a chimpanzee parasite) was closely related to P. falciparum and that the bird parasites shared a common ancestor with Plasmodium parasitic of lizards [3,4]. The complex pattern of expression of the Plasmodium ribosomal genes [7] and the report of partial gene conversion among genes that are expressed at different parasite stages [8], require a more careful analysis of the SSU rRNA data.
0166-6851/97/$17.00 © 1997 Elsevier Science B.V. All rights reserved. PII S 0 1 6 6 - 6 8 5 1 ( 9 7 ) 0 0 1 2 1 - 7
318
A.A. Escalante et al. / Molecular and Biochemical Parasitology 90 (1997) 317–321
We report the results of a phylogenetic analysis based on an alignment that incorporates secondary structure information, reducing the risk of alignment of nonhomologous positions. We have used the available sequences for two types of ribosomal genes found in the genus Plasmodium that are expressed in the asexual (Type A) and sexual stages of the parasite (Type S). We also report the sequences of both types of ribosomal genes for P. simium, a parasite of New World primates. The Plasmodium simium isolate, originally obtained from Dr. L. Deane in Brazil, has been maintained in monkeys at CDC. The SSU rRNA gene was amplified by polymerase chain reaction (PCR), using universal ribosomal primers (AL110: GTC GGA ATT CAA CCT GGT TGA TCT TGC C and AL111: CAG CGG ATC CTA ATG ATC CTT CCG CAG G). The amplified product was purified, cloned and sequenced as previously reported [4]. The sequences for other Plasmodium species have been described elsewhere [1,2,4]. The alignment was made using the DCSE program [9] and the SSU rRNA database maintained at the Department Biochemie, Universiteit Antwerpen. The secondary structure of most of the molecule is well supported; however, the area around E45 – 1 should be considered tentative. The alignment is publicly available via the World Wide Web (WWW) at URL http://rrna.uia.ac.be/. We use, in our phylgenetic analysis, the neighbor joining (NJ) [10] with the substitution rate calibration method developed by Van de Peer et al. [11]. This method converts dissimilarity into genetic distance by considering the substitution rates of the individual nucleotides in a sequence alignment. As a result, the genetic distance is estimated more accurately and biases introduced by rapidly evolving lineages can be corrected for. The equation used in substitution rate calibration depends upon a parameter p which depends on the shape of the spectrum of relative nucleotide substitution rates [12]. In the current study, two different values for p were used. One estimate of p was based on an alignment including only Apicomplexa parasites (p =0.58) and another for eukaryotic SSU rRNA genes (p =0.26). Both p values led to similar results; thus, only those
obtained for p= 0.58 are reported here. Tree reliability was assessed by the bootstrap method [13] with 500 replications. Only bootstrap values above 70% are reported and considered biologically meaningful [14]; however, a rigorous application of bootstrap should use a 95% confidence [15]. The nodes with bootstrap support between 70 and 95% should be considered tentative and require additional data for analysis. All NJ analysis were performed using the program TREECON for Windows [16]. Fig. 1 shows a phylogenetic tree including both type S and type A genes. Overall, the phylogenetic analysis made on an alignment that incorporates information about the secondary structure, reproduces the evolutionary relationships among Plasmodium species that were observed in previous studies that used primary structure-based alignments [1,3,4]. The lizard parasites were originally reported as belonging to the genus Plasmodium [3,4] but their final taxonomic identification is pending. If these isolates of lizard parasites are not considered Plasmodium species, the taxonomic implications of these phylogenetic analyses ([3,4] and the present study) will need to be addressed. A complementary analysis using the Galtier and Gouy model [17] was performed leading to similar results. This model corrects for unequal base composition among the sequences [17] as is the case of this data set. P. simium cannot be separated from P. 6i6ax on the basis of two genetic markers, the CSP [18] and type A SSU rRNA (this study) suggesting that nonhuman primates are active or potential reservoirs for human malaria. However, it is possible to separate these species using type S genes (100% boostrap support). The P. simium–P. 6i6ax separation may be dismissed when more SSU rRNA type S sequences become available or further studies may support that they are different species. The interpretation of these results opens a debate on how gene trees can help us understand species phylogenies. The lack of informative sites due to the time scale of the phylogenetic events may produce gene trees that do not show the species phylogeny [19]. This problem is particularly critical for the identification of reservoirs for
A.A. Escalante et al. / Molecular and Biochemical Parasitology 90 (1997) 317–321
319
Fig. 1. Phylogenetic tree of 14 Plasmodium species inferred from both Type A and type S SSU rRNA gene sequences. Type S sequences are indicated with a ‘S’ following the species code. P. falciparum (Pfa), P. 6i6ax (Pvi), P. o6ale (Pov) and P. malariae (Pma) are from humans. P. cynomolgi (Pcy), P. fragile (Pfr) and P. knowlesi (Pkn) are from macaques. P. simium (Psi) is from new world monkeys. P. reichenowi (Pre) is from chimpanzees. P. gallinaceum (Pga) and P. lophurae are bird parasites. P. berghei (Pbe) is a rodent parasite. L11716 and L11717 were originally reported as P. mexicanum and P. floridense. The numbers in the names indicate different isolates. The sequences have been previously described [1,3,4,8]; sequences from P. simium are reported in this paper. The number on the branches are bootstrap % based on 500 pseudo-replications. Only those values above 70% are reported.
pathogens. Two species identical or very closely related for a given gene, evolving at a slow rate, may be reflecting an event which took place a long time ago that is epidemiologically irrelevant. A molecular phylogeny has been used to suggest that P. falciparum is a new human parasite [1], supporting the notion that it is more severe because of the lack of time for the parasite to become ‘better adapted’ to its host [5,20]. A gene tree per se does not provide a time frame for a given evolutionary event, but some assumptions can be made [3,21]. We would like to suggest that the issues of parasite origin and virulence need to be separated. Virulence is considered to be the result of complex genetic and ecological interactions [22,23]. A broad range of evolutionary and genetic scenarios allow the maintenance of different degrees of virulence.
No relationship between the host–parasite association and virulence was found in lizard malarial parasites [24]. Virulence appears to modify with few passages when parasite strains are maintained in the laboratory, suggesting that a few generations may be enough for changing this trait within the limits of the available polymorphism present in the parasite isolate [6,25]. This study shows that P. simium and P. 6i6ax could be the same species or that they are closely related, providing evidence of a host switch. At least one of the hosts can be considered ‘new’ (humans or South American monkeys) and there is no evidence of differences in the severity of disease [6]. In the specific case of P. falciparum, virulence appears to be a very complex process that includes transmission dynamics and both parasite and host genetic factors [26,27].
320
A.A. Escalante et al. / Molecular and Biochemical Parasitology 90 (1997) 317–321
As far as the origin of parasites is concerned, we want to stress the need for a clear definition of the context where the word ‘origin’ is used. In the specific case of P. falciparum, there is no clear relationship with other primate malarial parasites studied thus far [1–4,21]. However, the data available suggests that the P. falciparum – P. reichenowi clade shares a common ancestor with avian – lizard malarial parasites. This observation has been corroborated by the CSP gene trees [28]. The word ‘origin’ used in this context implies that the P. falciparum– P. reichenowi clade evolved separated from other primate malarial parasites. It is a different issue to determine how ‘old’ or ‘new’ P. falciparum is. A comparative study of human and non-human primate malaria parasites may help reassess the systematic relationships as well as provide greater insight into the origin of human malarias. In summary, we conclude that further genetic analyses of P. 6i6ax and P. simium parasites need to be conducted to better assess the relationship between the two parasites. We have also shown that different genes (i.e. 18S RNA type A vs type S genes) could provide different information. The study also revealed that secondary structure-based alignments yield similar results, at least in the case of Plasmodium species, supporting earlier studies that used sequence alignments that did not consider secondary structure information. We would like to open the discussion regarding the appropriate use of gene trees in studies of molecular epidemiology, as it relates to surveillance and disease manifestations.
Acknowledgements We thank Dr. Y. Van de Peer for updating the software TREECON for windows. This work has been supported by a fellowship to A.A.E. from the Research Associates Program of The American Society for Microbiology and the National Center for Infectious Diseases.
References [1] Waters AP, Higgins DG, McCutchan TF. P. falciparum
[2]
[3]
[4]
[5]
[6]
[7]
[8]
[9]
[10]
[11]
[12]
[13] [14]
[15]
[16]
[17]
appears to have arisen as a result of lateral transfer between avian and human hosts. Proc Natl Acad Sci USA 1991;88:3140 – 4. Waters AP, Higgins DG, McCutchan TF. The phylogeny of Malaria: A useful study. Parasitol Today 1993;9:246 – 50. Escalante AA, Ayala FJ. Phylogeny of the malarial genus Plasmodium, derived from rRNA gene sequences. Proc Natl Acad Sci USA 1994;91:11373 – 7. Qari SH, Shi YP, Pieniazek NJ, Collins WE, Lal AA. Phylogenetic relationship among the malaria parasites based on small subunit rRNA gene sequences: monophyletic nature of the human malaria parasite P. falciparum. Mol Phyl Evol 1996;6:157 – 65. Boyd MF. A comprehensive survey of all aspects of this group of diseases from a global standpoint. In: Boyd MF, editor. Malariology, vol. 1. Philadelphia (PA): Saunders, 1949. Coatney RG, Collins WE, Warren M, Contacos PG. The Primate Malaria. Washington (DC): US Government Printing Office, 1971. McCutchan TF, Li J, McConkey GA, Rogers MJ, Waters AP. The cytoplasmic ribosomal RNAs of Plasmodium spp. Parasitol Today 1995;11:134 – 8. Corredor V, Enea V. The small ribosomal subunit RNA isoforms in Plasmodium cynomolgi. Genetics 1994;136:857 – 65. De Rijk P, De Wachter R. DCSE v2.54, an interactive tool for sequence alignment and secondary structure research. Comput Appl Biosci 1993;9:735 – 40. Saitou N, Nei M. The neighbor-joining method: a new method for reconstructing phylogenetic trees. Mol Biol Evol 1987;4:406 – 25. Van de Peer Y, Neefs JM, De Rijk P, De Watcher R. Reconstructing evolution from eukaryotic small ribosomal subunit RNA sequences: calibration of the molecular clock. J Mol Evol 1993;37:221 – 32. Van de Peer Y, Van der Auwere G, De Watcher R. The evolution of stramenopiles and alveolates as derived by ‘substitution ratecalibration’ of small ribosomal subunit RNA. J Mol Evol 1996;42:201 – 10. Felsenstein J. Confidence limits on phylogenies: An approach using bootstrap. Evolution 1985;39:783 – 91. Hillis DM, Bull JJ. An empirical test of bootstraping as a method for assessing confidence in phylogenetic analysis. Syst Biol 1993;8:189 – 91. Efron B, Halloran E, Holmes S. Bootstrap confidence levels for phylogenetic trees. Proc Natl Acad Sci USA 1996;93:13429– 34. Van de Peer Y, De Watcher R. TREECON for Windows: a software package for the construction and drawing of evolutionary trees for the Microsoft Windows environment. Comput Appl Biosci 1994;10:569 – 70. Galtier N, Gouy M. Inferring phylogenies from DNA sequences of unequal base composition. Proc Natl Acad Sci USA 1995;92:11317– 21.
A.A. Escalante et al. / Molecular and Biochemical Parasitology 90 (1997) 317–321 [18] Escalante AA, Barrio E, Ayala FJ. Evolutionary origin of human and primate malaria: evidence from the circumsporozoite protein gene. Mol Biol Evol 1995;12:616– 26. [19] Graybel A. Evaluating phylogenetic utility of genes: a search for genes informative about deep divergences among vertebrates. Syst Biol 1994;43:174–93. [20] Ewald PW. Evolution of Infectious Disease. New York (NY): Oxford University Press, 1994. [21] Escalante AA, Ayala FJ. Evolutionary origin of Plasmodium and other Apicomplexa based on rRNA genes. Proc Natl Acad Sci USA 1995;92:5793–7. [22] Herre EA. Factors affecting the evolution of virulence: nematode parasites of fig wasps as a case of study. Parasitology 1995;111:S179–91. [23] Ebert D, Herre EA. The evolution of parasitic diseases. Parasitol Today 1996;12:96–100.
.
321
[24] Schall JJ. Virulence of lizard malaria: the evolutionary ecology of an ancient parasite – host association. Parasitology 1990;100:S35 – 52. [25] Alger NE, Branton M, Harant J, Silverman PH. Plasmodium berghei NK65 in the inbred A/J Mouse: Variations in virulence of P. berghei demes. J Protozool 1971;18:598 – 601. [26] Miller LH, Good MF, Milon G. Malaria pathogenesis. Science 1994;264:1878– 83. [27] Gupta S, Hill AVS. Dynamic interactions in malaria: host heterogeneity meets parasite polymorphism. Proc R Soc London B Biol Sci 1995;261:271 – 7. [28] McCutchan TF, Kissinger JC, Touray MG, Rogers MJ, Li J, Sullivan M, Braga EM, Krettli AU, Miller L. Comparison of circumsporozoite proteins from avian and mammalian malaria: biological and phylogenetic implications. Proc Natl Acad Sci USA 1996;93:11889– 94.
Short communication
Phylogenetic study of the genus Plasmodium based on the secondary structure-based alignment of the small subunit ribosomal RNA Ananias A. Escalante a, Ira F. Goldman a, Peter De Rijk b, Rupert De Wachter b, William E. Collins a, Shoukat H. Qari a, Altaf A. Lal a,* a
Di6ision of Parasitic Diseases, Centers for Disease Control and Pre6ention, Mail Stop F-12, 4770 Buford Hwy., Chamblee, GA 30341, USA b Department Biochemie, Uni6ersiteit Antwerpen (UIA), Uni6ersiteitsplein 1, B-2610 Antwerpen, Belgium Received 28 July 1997; accepted 28 July 1997
Keywords: Malaria; Plasmodium simium; Plasmodium falciparum; Ribosomal RNA; Molecular epidemiology; Virulence
The phylogenetic relationship of the genus Plasmodium has been studied by several investigators using partial or full-length sequences of 18S SSU rRNA genes. Special attention has been focused on the issue of the origin of Plasmodium falciparum [1–4]. Earlier studies suggested that P. falciparum was of recent origin because of a host switch from a nonhuman host. This hypothesis was used to explain the high virulence of P. falciparum in comparison with other human malarial parasites [5,6]. Studies of plasmodial evolution that used 18S SSU rRNA gene-based phylogeny showed that P. * Corresponding author. Tel.: +1 770 4884047; fax: + 1 770 4884454; e-mail: [email protected].
falciparum shared a common ancestor with avian Plasmodium species [1,2]. It was further suggested that this host switch could have taken place at the beginning of agriculture [1,2], supporting the traditional notion that the high virulence of P. falciparum could be explained by the short period of the host–parasite association [5]. Subsequent phylogenetic studies showed that P. reichenowi (a chimpanzee parasite) was closely related to P. falciparum and that the bird parasites shared a common ancestor with Plasmodium parasitic of lizards [3,4]. The complex pattern of expression of the Plasmodium ribosomal genes [7] and the report of partial gene conversion among genes that are expressed at different parasite stages [8], require a more careful analysis of the SSU rRNA data.
0166-6851/97/$17.00 © 1997 Elsevier Science B.V. All rights reserved. PII S 0 1 6 6 - 6 8 5 1 ( 9 7 ) 0 0 1 2 1 - 7
318
A.A. Escalante et al. / Molecular and Biochemical Parasitology 90 (1997) 317–321
We report the results of a phylogenetic analysis based on an alignment that incorporates secondary structure information, reducing the risk of alignment of nonhomologous positions. We have used the available sequences for two types of ribosomal genes found in the genus Plasmodium that are expressed in the asexual (Type A) and sexual stages of the parasite (Type S). We also report the sequences of both types of ribosomal genes for P. simium, a parasite of New World primates. The Plasmodium simium isolate, originally obtained from Dr. L. Deane in Brazil, has been maintained in monkeys at CDC. The SSU rRNA gene was amplified by polymerase chain reaction (PCR), using universal ribosomal primers (AL110: GTC GGA ATT CAA CCT GGT TGA TCT TGC C and AL111: CAG CGG ATC CTA ATG ATC CTT CCG CAG G). The amplified product was purified, cloned and sequenced as previously reported [4]. The sequences for other Plasmodium species have been described elsewhere [1,2,4]. The alignment was made using the DCSE program [9] and the SSU rRNA database maintained at the Department Biochemie, Universiteit Antwerpen. The secondary structure of most of the molecule is well supported; however, the area around E45 – 1 should be considered tentative. The alignment is publicly available via the World Wide Web (WWW) at URL http://rrna.uia.ac.be/. We use, in our phylgenetic analysis, the neighbor joining (NJ) [10] with the substitution rate calibration method developed by Van de Peer et al. [11]. This method converts dissimilarity into genetic distance by considering the substitution rates of the individual nucleotides in a sequence alignment. As a result, the genetic distance is estimated more accurately and biases introduced by rapidly evolving lineages can be corrected for. The equation used in substitution rate calibration depends upon a parameter p which depends on the shape of the spectrum of relative nucleotide substitution rates [12]. In the current study, two different values for p were used. One estimate of p was based on an alignment including only Apicomplexa parasites (p =0.58) and another for eukaryotic SSU rRNA genes (p =0.26). Both p values led to similar results; thus, only those
obtained for p= 0.58 are reported here. Tree reliability was assessed by the bootstrap method [13] with 500 replications. Only bootstrap values above 70% are reported and considered biologically meaningful [14]; however, a rigorous application of bootstrap should use a 95% confidence [15]. The nodes with bootstrap support between 70 and 95% should be considered tentative and require additional data for analysis. All NJ analysis were performed using the program TREECON for Windows [16]. Fig. 1 shows a phylogenetic tree including both type S and type A genes. Overall, the phylogenetic analysis made on an alignment that incorporates information about the secondary structure, reproduces the evolutionary relationships among Plasmodium species that were observed in previous studies that used primary structure-based alignments [1,3,4]. The lizard parasites were originally reported as belonging to the genus Plasmodium [3,4] but their final taxonomic identification is pending. If these isolates of lizard parasites are not considered Plasmodium species, the taxonomic implications of these phylogenetic analyses ([3,4] and the present study) will need to be addressed. A complementary analysis using the Galtier and Gouy model [17] was performed leading to similar results. This model corrects for unequal base composition among the sequences [17] as is the case of this data set. P. simium cannot be separated from P. 6i6ax on the basis of two genetic markers, the CSP [18] and type A SSU rRNA (this study) suggesting that nonhuman primates are active or potential reservoirs for human malaria. However, it is possible to separate these species using type S genes (100% boostrap support). The P. simium–P. 6i6ax separation may be dismissed when more SSU rRNA type S sequences become available or further studies may support that they are different species. The interpretation of these results opens a debate on how gene trees can help us understand species phylogenies. The lack of informative sites due to the time scale of the phylogenetic events may produce gene trees that do not show the species phylogeny [19]. This problem is particularly critical for the identification of reservoirs for
A.A. Escalante et al. / Molecular and Biochemical Parasitology 90 (1997) 317–321
319
Fig. 1. Phylogenetic tree of 14 Plasmodium species inferred from both Type A and type S SSU rRNA gene sequences. Type S sequences are indicated with a ‘S’ following the species code. P. falciparum (Pfa), P. 6i6ax (Pvi), P. o6ale (Pov) and P. malariae (Pma) are from humans. P. cynomolgi (Pcy), P. fragile (Pfr) and P. knowlesi (Pkn) are from macaques. P. simium (Psi) is from new world monkeys. P. reichenowi (Pre) is from chimpanzees. P. gallinaceum (Pga) and P. lophurae are bird parasites. P. berghei (Pbe) is a rodent parasite. L11716 and L11717 were originally reported as P. mexicanum and P. floridense. The numbers in the names indicate different isolates. The sequences have been previously described [1,3,4,8]; sequences from P. simium are reported in this paper. The number on the branches are bootstrap % based on 500 pseudo-replications. Only those values above 70% are reported.
pathogens. Two species identical or very closely related for a given gene, evolving at a slow rate, may be reflecting an event which took place a long time ago that is epidemiologically irrelevant. A molecular phylogeny has been used to suggest that P. falciparum is a new human parasite [1], supporting the notion that it is more severe because of the lack of time for the parasite to become ‘better adapted’ to its host [5,20]. A gene tree per se does not provide a time frame for a given evolutionary event, but some assumptions can be made [3,21]. We would like to suggest that the issues of parasite origin and virulence need to be separated. Virulence is considered to be the result of complex genetic and ecological interactions [22,23]. A broad range of evolutionary and genetic scenarios allow the maintenance of different degrees of virulence.
No relationship between the host–parasite association and virulence was found in lizard malarial parasites [24]. Virulence appears to modify with few passages when parasite strains are maintained in the laboratory, suggesting that a few generations may be enough for changing this trait within the limits of the available polymorphism present in the parasite isolate [6,25]. This study shows that P. simium and P. 6i6ax could be the same species or that they are closely related, providing evidence of a host switch. At least one of the hosts can be considered ‘new’ (humans or South American monkeys) and there is no evidence of differences in the severity of disease [6]. In the specific case of P. falciparum, virulence appears to be a very complex process that includes transmission dynamics and both parasite and host genetic factors [26,27].
320
A.A. Escalante et al. / Molecular and Biochemical Parasitology 90 (1997) 317–321
As far as the origin of parasites is concerned, we want to stress the need for a clear definition of the context where the word ‘origin’ is used. In the specific case of P. falciparum, there is no clear relationship with other primate malarial parasites studied thus far [1–4,21]. However, the data available suggests that the P. falciparum – P. reichenowi clade shares a common ancestor with avian – lizard malarial parasites. This observation has been corroborated by the CSP gene trees [28]. The word ‘origin’ used in this context implies that the P. falciparum– P. reichenowi clade evolved separated from other primate malarial parasites. It is a different issue to determine how ‘old’ or ‘new’ P. falciparum is. A comparative study of human and non-human primate malaria parasites may help reassess the systematic relationships as well as provide greater insight into the origin of human malarias. In summary, we conclude that further genetic analyses of P. 6i6ax and P. simium parasites need to be conducted to better assess the relationship between the two parasites. We have also shown that different genes (i.e. 18S RNA type A vs type S genes) could provide different information. The study also revealed that secondary structure-based alignments yield similar results, at least in the case of Plasmodium species, supporting earlier studies that used sequence alignments that did not consider secondary structure information. We would like to open the discussion regarding the appropriate use of gene trees in studies of molecular epidemiology, as it relates to surveillance and disease manifestations.
Acknowledgements We thank Dr. Y. Van de Peer for updating the software TREECON for windows. This work has been supported by a fellowship to A.A.E. from the Research Associates Program of The American Society for Microbiology and the National Center for Infectious Diseases.
References [1] Waters AP, Higgins DG, McCutchan TF. P. falciparum
[2]
[3]
[4]
[5]
[6]
[7]
[8]
[9]
[10]
[11]
[12]
[13] [14]
[15]
[16]
[17]
appears to have arisen as a result of lateral transfer between avian and human hosts. Proc Natl Acad Sci USA 1991;88:3140 – 4. Waters AP, Higgins DG, McCutchan TF. The phylogeny of Malaria: A useful study. Parasitol Today 1993;9:246 – 50. Escalante AA, Ayala FJ. Phylogeny of the malarial genus Plasmodium, derived from rRNA gene sequences. Proc Natl Acad Sci USA 1994;91:11373 – 7. Qari SH, Shi YP, Pieniazek NJ, Collins WE, Lal AA. Phylogenetic relationship among the malaria parasites based on small subunit rRNA gene sequences: monophyletic nature of the human malaria parasite P. falciparum. Mol Phyl Evol 1996;6:157 – 65. Boyd MF. A comprehensive survey of all aspects of this group of diseases from a global standpoint. In: Boyd MF, editor. Malariology, vol. 1. Philadelphia (PA): Saunders, 1949. Coatney RG, Collins WE, Warren M, Contacos PG. The Primate Malaria. Washington (DC): US Government Printing Office, 1971. McCutchan TF, Li J, McConkey GA, Rogers MJ, Waters AP. The cytoplasmic ribosomal RNAs of Plasmodium spp. Parasitol Today 1995;11:134 – 8. Corredor V, Enea V. The small ribosomal subunit RNA isoforms in Plasmodium cynomolgi. Genetics 1994;136:857 – 65. De Rijk P, De Wachter R. DCSE v2.54, an interactive tool for sequence alignment and secondary structure research. Comput Appl Biosci 1993;9:735 – 40. Saitou N, Nei M. The neighbor-joining method: a new method for reconstructing phylogenetic trees. Mol Biol Evol 1987;4:406 – 25. Van de Peer Y, Neefs JM, De Rijk P, De Watcher R. Reconstructing evolution from eukaryotic small ribosomal subunit RNA sequences: calibration of the molecular clock. J Mol Evol 1993;37:221 – 32. Van de Peer Y, Van der Auwere G, De Watcher R. The evolution of stramenopiles and alveolates as derived by ‘substitution ratecalibration’ of small ribosomal subunit RNA. J Mol Evol 1996;42:201 – 10. Felsenstein J. Confidence limits on phylogenies: An approach using bootstrap. Evolution 1985;39:783 – 91. Hillis DM, Bull JJ. An empirical test of bootstraping as a method for assessing confidence in phylogenetic analysis. Syst Biol 1993;8:189 – 91. Efron B, Halloran E, Holmes S. Bootstrap confidence levels for phylogenetic trees. Proc Natl Acad Sci USA 1996;93:13429– 34. Van de Peer Y, De Watcher R. TREECON for Windows: a software package for the construction and drawing of evolutionary trees for the Microsoft Windows environment. Comput Appl Biosci 1994;10:569 – 70. Galtier N, Gouy M. Inferring phylogenies from DNA sequences of unequal base composition. Proc Natl Acad Sci USA 1995;92:11317– 21.
A.A. Escalante et al. / Molecular and Biochemical Parasitology 90 (1997) 317–321 [18] Escalante AA, Barrio E, Ayala FJ. Evolutionary origin of human and primate malaria: evidence from the circumsporozoite protein gene. Mol Biol Evol 1995;12:616– 26. [19] Graybel A. Evaluating phylogenetic utility of genes: a search for genes informative about deep divergences among vertebrates. Syst Biol 1994;43:174–93. [20] Ewald PW. Evolution of Infectious Disease. New York (NY): Oxford University Press, 1994. [21] Escalante AA, Ayala FJ. Evolutionary origin of Plasmodium and other Apicomplexa based on rRNA genes. Proc Natl Acad Sci USA 1995;92:5793–7. [22] Herre EA. Factors affecting the evolution of virulence: nematode parasites of fig wasps as a case of study. Parasitology 1995;111:S179–91. [23] Ebert D, Herre EA. The evolution of parasitic diseases. Parasitol Today 1996;12:96–100.
.
321
[24] Schall JJ. Virulence of lizard malaria: the evolutionary ecology of an ancient parasite – host association. Parasitology 1990;100:S35 – 52. [25] Alger NE, Branton M, Harant J, Silverman PH. Plasmodium berghei NK65 in the inbred A/J Mouse: Variations in virulence of P. berghei demes. J Protozool 1971;18:598 – 601. [26] Miller LH, Good MF, Milon G. Malaria pathogenesis. Science 1994;264:1878– 83. [27] Gupta S, Hill AVS. Dynamic interactions in malaria: host heterogeneity meets parasite polymorphism. Proc R Soc London B Biol Sci 1995;261:271 – 7. [28] McCutchan TF, Kissinger JC, Touray MG, Rogers MJ, Li J, Sullivan M, Braga EM, Krettli AU, Miller L. Comparison of circumsporozoite proteins from avian and mammalian malaria: biological and phylogenetic implications. Proc Natl Acad Sci USA 1996;93:11889– 94.