Neutral Polymorphisms in Putative Housekeeping Genes and Tandem Repeats Unravels the Population Genetics and Evolutionary History of Plasmodium vivax in India

Abstract

The evolutionary history and age of Plasmodium vivax has been inferred as both recent and ancient by several studies, mainly using mitochondrial genome diversity. Here we address the age of P. vivax on the Indian subcontinent using selectively neutral housekeeping genes and tandem repeat loci. Analysis of ten housekeeping genes revealed a substantial number of SNPs (n = 75) from 100 P. vivax isolates collected from five geographical regions of India. Neutrality tests showed a majority of the housekeeping genes were selectively neutral, confirming the suitability of housekeeping genes for inferring the evolutionary history of P. vivax. In addition, a genetic differentiation test using housekeeping gene polymorphism data showed a lack of geographical structuring between the five regions of India. The coalescence analysis of the time to the most recent common ancestor estimate yielded an ancient TMRCA (232,228 to 303,030 years) and long-term population history (79,235 to 104,008) of extant P. vivax on the Indian subcontinent. Analysis of 18 tandem repeat loci polymorphisms showed substantial allelic diversity and heterozygosity per locus, and analysis of potential bottlenecks revealed the signature of a stable P. vivax population, further corroborating our ancient age estimates. For the first time we report a comparable evolutionary history of P. vivax inferred by nuclear genetic markers (putative housekeeping genes) to that inferred from mitochondrial genome diversity.

Author Summary

Plasmodium vivax is the most prevalent human malaria parasite outside Africa, responsible for significant morbidity, although it is commonly referred to as a benign malaria agent with respect to P. falciparum. Inferring the evolutionary history of an infectious agent provides important information for designing control measures. In this study, we developed a panel of novel molecular markers including housekeeping genes, minisatellites and microsatellites to infer the evolutionary history of P. vivax on the Indian subcontinent. The panel of markers uncovered an ancient and long evolutionary history and a stable population structure of P. vivax in India.

Introduction

Plasmodium vivax is the most prevalent malaria species outside Africa, causing widespread morbidity that can be severe and fatal [1], [2], [3], [4], [5], [6]. The fixation of the Duffy negativity trait (P. vivax resistance factor) in tropical African populations restricts infection by this parasite there [7]. P. vivax is distantly related to the more virulent Plasmodium falciparum, as inferred from mitochondrial and nuclear DNA variation [8], [9], [10], [11]; the former appears to have evolved from a monkey malaria parasite between 20–35 million years ago via host switching [12]. Various studies on the age and origin of extant P. vivax strongly support it as an ancient human malaria parasite that evolved in Southeast Asia [12], [13], [14], [15].

Single nucleotide polymorphisms (SNPs) have been used by several researchers to elucidate the population history of P. falciparum and P. vivax [12], [16], [17], [18]. These studies established the importance of using selectively neutral loci for determining the molecular age, origin, and evolutionary history of the parasites, assuming a “molecular clock” hypothesis. Many population studies have exploited polymorphisms in two kinds of neutral loci: SNPs in putative housekeeping genes, and repeat polymorphisms in tandem repeats such as microsatellites [19], [20], [21]. Genome sequencing of P. vivax has revealed a higher SNP density [22] and fewer microsatellite markers than in P. falciparum [23], [24].

India contributes about 78% of the total malaria cases in South Asia, and P. vivax accounts for 50–55% of this [25]. The paucity of information about the age and evolutionary history of P. vivax in Indian populations [15], [26] makes such investigations highly relevant. In this paper, we use an evolutionary genetics approach to unravel the evolutionary history of P. vivax on the Indian subcontinent. We have developed putative housekeeping gene, microsatellite, and minisatellite markers for investigating the population and evolutionary history of P. vivax on the Indian subcontinent.

Materials and Methods

Identification of putative housekeeping genes

Putative housekeeping genes were identified from the P. vivax genome database PlasmoDB (http://www.plasmodb.org). The major parameters used for selecting housekeeping genes from PlasmoDB were constitutive expression of gene, presence of orthologs in other malaria parasites, and an assigned metabolic function. For the detection of SNPs in putative housekeeping genes, both exons and introns from each gene were selected. PCR primers were manually designed and the location of each primer is shown in Figure 1 .

Figure 1. Schematic representation of Plasmodium vivax housekeeping genes and location of primers.

Red box, exon; gray box, intron; green arrow, forward primer; black arrow, reverse primer; number indicates start and end of respective gene. Abbreviations: L35e, Ribosomal protein l35e; ACP, Acyl carrier protein; Rpol, RNA polymerase-II; Dg, DNA gyrase; L34a, Ribosomal protein l34a; Stpk, Serine threonine protein kinase; Cdpk, Calcium dependent protein kinase; Ed, Exonuclease domain and Ac, Adenylate cyclase.

Plasmodium vivax isolates and DNA extraction

We analyzed 100 P. vivax field isolates collected between 2003–2006 from Delhi, Nadiad (Gujarat), Panna (Madhya Pradesh), Chennai (Tamil Nadu), and Kamrup (Assam), a total of twenty samples from each site (Figure S1). Human populations at these study sites do not have the Duffy negative trait [27]. Other details about the study sites such as parasite and vector species prevalence and disease transmission patterns are given in the Text S1 and reported elsewhere [28], [29]. DNA extraction was as described in reference [28], [29].

Ethics statement

The ethics committee of the National Institute of Malaria Research approved the study protocol. All subjects provided informed consent, with children providing consent via a parent or guardian.

PCR amplification, sequencing, and sequence analysis

PCR amplification reactions were carried out in a final volume of 20.0 µl that included 1–2 µl (∼3–5 ng) template DNA, 10 pM for each primer, and 2× Master Mix (Promega). PCR primers and the protocols used for amplification of the housekeeping genes are given in Table S1. PCR products were purified and sequenced commercially (Macrogen Inc, Seoul, Korea, http://dna.macrogen.com). For each gene, both forward and reverse primers were used in DNA sequencing. DNA Lasergene software (DNA Star Inc., USA) was used for editing raw DNA sequences (EditSeq Module), and sequences alignment (Clustal W module). Each mutation observed in a sample was confirmed by both forward and reverse sequences.

Single clone infection typing

As multi-clone isolates could hamper correct genotyping and lead to over-estimating genetic diversity in a multi-locus genotyping study, Pvmsp-3α PCR-RFLP analysis was used to identify single- and multi-clone infections [30]; only single clone samples (n = 100) were used for genotyping.

Tandem repeat genotyping

Tandem Repeat Finder version 4.00 [31] was used to identify microsatellites from the P. vivax genome. The characteristics of microsatellites are listed in Table S2. Each forward primer was modified with fluorescence dye, 6FAM, TET and HEX for accurate microsatellite allele sizing. Amplified PCR products were multiplexed with two different dyes and run on a DNA sequencer (ABI 3730: Applied Biosystems Inc. USA). Peak Scanner (Applied Biosystems, Foster City, CA) was used for microsatellite allele sizing.

Measures of genetic diversity and neutrality

Genetic diversity was measured in the P. vivax population using parameters including nucleotide diversity (π), haplotype diversity (Hd) and average number of nucleotide differences (K) using DnaSP version 4.10 [32]. Microsatellite genetic diversity was measured by calculating expected heterozygosity (He) for each locus using MicroSatellite Analyzer (MSA) version 4.00 [33]. Expected heterozygosity (He) was defined as [n/(n−1)] [1−Σp_i ²], where n is the number of isolates analyzed and pi is the frequency of the i^th allele in the population.

Genetic differentiation test

We estimated genetic differentiation between five geographical populations of P. vivax in the Indian subcontinent using DnaSP version 4.10 [32]. This software calculated chi-square (χ²) statistics of housekeeping gene haplotype frequencies between populations [34]. The significant P-value (<0.05) of χ² statistics rejects null hypothesis. The null hypothesis assumes that all populations are genetically undifferentiated.

Test of neutrality

We calculated D statistics [35], [36] and ratio of d_N/d_S to detect signature of selection at putative housekeeping genes using DnaSP version 4.10 [32]. The number of segregating sites was used for inferring D test statistics. To establish the nature of selection at codons of putative housekeeping genes, we assessed the ratio of the rates of non-synonymous and synonymous substitutions.

Estimation of divergence, TMRCA, and effective population size

The divergence time of human and monkey has been deduced as 30–35 million years ago (mya) [37], [38] which is consistent with 11–41 mya divergence time between P. vivax and nonhuman primate malarias [8]. We presumed a 23–30 mya divergence time between P. vivax and P. knowlesi that is coincident with their host divergence time [37], [38]; this divergence time was used in the estimation of mutation rate and synonymous divergence rate by comparing orthologous putative housekeeping genes of P. vivax and P. knowlesi. In addition, the recent divergence estimates between P. vivax and P. knowlesi (2 to 3 mya and 3.8 to 6.3 mya) was assumed on the basis of radiation of Asian macaques [13], [39]. These divergence estimates were also used for the calculation of the above molecular rates.

We estimated the Time to Most Recent Common Ancestor (TMRCA) and effective population size using SNPs present in putatively selectively neutral housekeeping genes. The TMRCA of P. vivax was determined by the equation d_S = 2 μ _s×Tw, where d_S is synonymous substitution rate at synonymous site, μ _s is synonymous mutation rate per site per year and Tw is TMRCA [18]. Synonymous mutation rate was determined by the equation Ks = 2 μ _s×Tb+d_S [18], where Ks is the divergence at synonymous sites between species (P. vivax and P. knowlesi), d_S is the nucleotide diversity (polymorphism) within species (P. vivax), μ _s is synonymous mutation rate per generation and Tb is time of the divergence between species (P. vivax and P. knowlesi). Effective population size of extant P. vivax was determined by the equation θ = 4Ne μ (for diploid organisms) and θ = 2Ne μ (for haploid and mitochondrial genomes), where θ (theta) is the mutation parameter, Ne the effective population size, and μ is the mutation rate per site per year.

Bottleneck/stable population detection

Heterozygosity deficiency and mode shift analyses were used to detect evidence of a recent population bottleneck using BOTTLENECK software 1.2.02 [40]. In brief, a recently bottlenecked population would show higher observed gene diversity than the expected equilibrium gene diversity (Heq) which was computed from the observed number of alleles (k), under the assumption of a constant-size (equilibrium) population [41]. A two-phase mutation model (TPM) was used for heterozygosity deficiency analysis at mini- and microsatellite loci. TPM is an intermediate between the stepwise mutation model (SMM) and the infinite allele model (IAM), mostly consisting of one-step mutations having a small percentage (5–10%) of multi-step changes, as per BOTTLENECK software [41]. The allele frequency distribution analysis (mode shift analysis) showed whether it was approximately L-shaped (as expected under mutation-drift equilibrium) or not (recent bottlenecks provoke a mode shift). Bottleneck analysis can be performed using tandem repeat polymorphism data; the minisatellite polymorphism data being used in this study has been taken from earlier published work [28]. We also used network analysis of tandem repeat polymorphisms to detect possible signatures of bottlenecked or stable populations [42]. Two minisatellites located on a single chromosome (Chr 6), were used to construct reduced-median (RM) network of haplotypes using Network software [42]. In brief, a star-like network indicates a recent population expansion, whereas the absence of a star-like network indicates an ancient population expansion.

Estimation of expected and observed pairwise differences

The estimation of expected and observed frequencies of pairwise differences at nucleotide sites provides a signature of whether a population is stable or has recently experienced a population bottleneck [36]. In summary, an L-shaped curve between observed and expected allele frequencies spectrum indicates a stable population whereas a non L-shaped curve suggests a population bottleneck. The pairwise nucleotide difference at individual housekeeping genes was estimated using DnaSP version 4.10 [32].

Accession numbers

Accession numbers for alleles of all housekeeping genes are: HM047879–HM047972 (ACPex), HM047973–HM048020 (ACPin), HM048021–HM048117 (DNA gyrase), HM048118–HM048217 (Exonuclease domain), HM048118–HM048217 (Enolase), HM048318–HM048418 (L34a), HM048419–HM048518 (L35e), HM048619–HM048711 (RNA polymerase-II), HM048712–HM048811 (Stpk), and HM048812–HM048829 (Ac).

Results

Screening the genome for SNPs and tandem repeats

We screened the P. vivax Salvador 1 reference genome and identified ten putative housekeeping genes, and ten minisatellites and eight microsatellites, to infer the evolutionary history of this parasite in the Indian subcontinent. The selected housekeeping genes are exonuclease domain (ed), adenylate cyclase (ac), serine/threonine protein kinase (stpk), acyl carrier protein (acp), ribosomal protein l35e (l35e), 60S ribosomal protein l34a (l34 a), DNA gyrase (dg), calcium-dependent protein kinase (cdpk), enolase and RNA polymerase-II (Rpol). The structure of the housekeeping genes (arrangement of introns and exons), gene identifier and fragments used for SNP identification are given in Figure 1 and Table 1 . Approximately 400 to 600 bp of intron and exon sequence were used to identify SNPs. However, introns were not present in two housekeeping genes (ac and ed), therefore, partial exon sequence of these were used. The selected minisatellites and microsatellites are located at six different chromosomes and their features are listed in Table S2. Among the eight microsatellites, a single microsatellite (Gomez_1) was reported earlier by Gomez et al [43].

Table 1. Mutations in housekeeping genes from 100 Indian Plasmodium vivax isolates.

Housekeeping gene	Gene ID	Fragment size (bp)	Coding sites (bp)	Non-coding sites (bp)	Segregating sites	Synonymous substitution	Non-Synonymous substitution	Non-coding substitution	Total changes	Haplotype diversity (Hd)	Nucleotide diversity (π)
Ribosomal protein l35e	PVX_091865	518	170	348	12	2	5	5	13	0.665	0.00188
Exonuclease Domain	PVX_003660	300	300	0	1	1	0	0	1	0.366	0.00119
Adenylate Cyclase	PVX_092535	496	496	0	3	2	1	0	3	0.614	0.00146
Acyl Carrier Protein	PVX_114420	1336	706	630	10	3	3	4	10	0.494	0.00083
Serine threonine protein kinase	PVX_113435	1103	619	484	4	0	2	2	4	0.169	0.00016
Ribosomal protein l34a	PVX_088065	1134	586	548	7	0	0	7	7	0.864	0.00132
RNA Polymerase-II	PVX_122080	984	532	452	9	0	1	8	9	0.677	0.00106
Enolase	PVX_095015	1160	557	603	20	2	5	13	20	0.837	0.00147
DNA Gyrase	PVX_123795	1162	507	655	7	3	3	1	7	0.741	0.00092
Calcium dependent protein kinase	PVX_119610	1105	802	302	2	0	0	2	2	ND	ND
Total		9298	5275	4022	75	13	20	42	76

ND: not determined.

Putative housekeeping gene polymorphisms

Ten housekeeping genes were successfully amplified and sequenced to at least two-fold coverage. Analysis of the sequences revealed size polymorphisms in four of the housekeeping genes and two to six size variants were observed. These size variants were due to indels (l35e) or tandem repeat variation (l34a, DNA gyrase) in the gene's repeat region (Figure S2). Analyzing 9,298 nucleotide sites revealed a substantial number of SNPs (n = 75) in both coding and non-coding regions (Table 1). The number of synonymous, non-synonymous and non-coding SNPs observed, are listed in Table 1 . On average, putative housekeeping genes had a low level of nucleotide (π = 0.002076±0.00059) and haplotype diversity (Hd = 0.5894±0.108) in P. vivax field isolates. Of the 75 SNPs identified, 55 were putatively selectively neutral (13 synonymous and 42 non-coding) and 20 were non-synonymous ( Table 1 ). Sequencing of the Pvcdpk gene revealed presence of tandem repeats in the central region of gene, which caused difficulty in aligning the sequences correctly, and was therefore excluded from further analysis.

Putative housekeeping genes are selectively neutral

The neutrality of housekeeping genes was inferred from the results of three tests. 1) The distribution of SNPs among exons (n = 33) and introns (n = 42) of putative housekeeping genes seems to be random (χ² = 0.572, p = 0.449) suggesting a lack of functional constraint on exons. 2) By Tajima's D test, none of the putative housekeeping genes showed signs of significant deviation from neutrality ( Table 2 ); however, Fu and Li's D test showed biased singleton mutation distribution in two of the nine putative housekeeping genes; these two genes were enolase (D = −2.920 p = <0.004) and l35e (D = −3.617, p = <0.004). 3) The d_N/d_S ratio showed a signature of purifying selection for two putative housekeeping genes (l35e and dg), whereas mutations in the remaining genes were selectively neutral ( Table 2 ). Further, none of the housekeeping genes showed significant departure from neutrality by the above three tests conducted together. Thus, these tests suggest that these housekeeping genes are primarily evolving in a neutral fashion and therefore can be employed as genetic markers for inferring population and evolutionary history of P. vivax.

Table 2. Neutrality test and mutation parameter of Plasmodium vivax housekeeping genes on the Indian subcontinent.

Gene	Tajima's D	Fu & Li's D	dN±SE (10−3)	dS±SE (10−3)	dN = / = dS	Theta (θ) per site	Nucleotide substitutions rates in Pv		Divergence rates between Pv & Pk
							dS	dN	Ks	Ka
ed	1.027	0.491	0.00	2.0±2.0	1.005	0.00064*	0.00	0.002±0.002	0.4334	0.1181
ac	−0.421	−0.804	7.0±5.0	0.00	−1.151	0.00173	0.00	0.001±0.001	0.3399	0.0410
acp-in	−0.434	1.006	-	-	-	0.00126	0.00	0.000	0.2907	0.0257
acp-ex	−1.36	−1.726	2.0±2.0	0.00	−0.955	0.00166	0.00	0.001±0.001	0.4202	0.1423
l35e	−1.543	−2.92	0.00	1.0±1.0	2.074	0.00448	0.004±0.003	0.000	0.3798	0.0134
l34a	0.231	−0.557	0.00	0.000	-	0.0012	0.00	0.0025±0.002	0.2332	0.0068
stpk	−1.487	−1.437	0.00	0.000	1.418	0.0007*	0.002±0.002	0.000	0.2575	0.0320
enolase	−1.624	−3.617	4.0±3.0	0.000	−1.035	0.00332	0.000	0.000	0.6643	0.5624
RNA pol	−1.031	−1.651	0.00	2.5±2.0	0.992	0.00179	0.007±0.005	0.000	0.5496	0.0867
dg	−0.501	−0.547	0.00	1.0±1.0	2.061	0.00117	-	-	0.6966	0.7130
Mean						0.002076±0.00059	0.004±0.001	0.0016±0.0003	0.3965	0.1142

Boldface values are statistically significant (p<0.05), *excluded in averaging θ, Pv: Plasmodium vivax, Pk: P. knowlesi, d_S: synonymous substitution rate, d_N: non-synonymous substitution rate, Ks: synonymous divergence rate, Ka: non synonymous divergence rate.

Lack of geographical structuring between populations

To understand whether P. vivax isolates are structured in populations, we undertook a genetic differentiation test using individual housekeeping genes. Our null hypothesis is that populations of P. vivax in the Indian subcontinent are genetically un-differentiated. Analysis of seven of the eight housekeeping genes accepted this hypothesis, while only DNA gyrase rejected the null hypothesis ( Table 3 ). Since DNA gyrase does not appear to be neutral by neutrality tests ( Table 2 ), it may not be ideal for measuring genetic differentiation between P. vivax populations. We confirmed the suitability of using chi-square statistics for genetic differentiation by determining the critical value of haplotype diversity (<0.95) [34]. The haplotype diversity measured at each housekeeping gene was lesser than the critical value (Hd = 0.169–0.864) ( Table 3 ), confirming suitability of the use of chi-square statistics for genetic differentiation. Based on the seven selectively neutral housekeeping genes, it appears that different populations of P. vivax are not geographically structured in India. Thus, P. vivax isolates collected from different geographical regions of the Indian subcontinent will not have an adverse impact on the pooled analyses of TMRCA, effective population size, and population bottleneck.

Table 3. Genetic differentiation test between Plasmodium vivax populations in India.

Housekeeping genes	Sample size (N)	No of Haplotypes	Haplotype diversity (Hd = <0.95)	Chi square (χ2)	Degree of freedom	P value
acpex	95	7	0.425	25.241	24	0.392
dg	98	11	0.741	68.888	40	0.003
ed	100	2	0.366	4.291	4	0.368
enolase	100	22	0.837	104.361	84	0.065
l34a	100	10	0.864	51	36	0.053
l35e	100	14	0.665	68.006	52	0.067
RNA pol-II	94	12	0.677	48.65	44	0.291
stpk	100	5	0.169	12.709	12	0.39

Boldface values indicate significant genetic differentiation.

Estimation of synonymous divergence rate and mutation rate

Since P. vivax is a close relative of P. knowlesi and the genome sequence of the latter has been determined [44], orthologous genes from P. knowlesi could be used to determine the genetic distance (divergence) between P. knowlesi and P. vivax and the pattern of evolutionary pressure (positive or negative selection) on these putative housekeeping genes. An approximately tenfold higher synonymous divergence rate over the non-synonymous divergence rate was observed between P. vivax and P. knowlesi ( Table 2 ), suggesting that the putative housekeeping genes are evolving strictly under purifying selection. The average synonymous divergence and mutation rate for P. vivax was determined under various divergence time scenarios between the P. knowlesi and P. vivax. The estimated rates of synonymous divergence and mutation are given in Table 4 . Based on this range, the synonymous divergence rate (per site per year) for the putative housekeeping genes was calculated as 8.61×10⁻⁹ (μ_sa) and 6.60×10⁻⁹ (μ_sb) under 23 mya and 30 mya divergence scenarios, respectively. Similarly, the mutation rates (per site per year) under the 23 mya and 30 mya divergence scenarios were determined to be 6.51×10⁻⁹ (μ_a) and 4.99×10⁻⁹ (μ_b), respectively. In contrast, few studies suggested relatively recent divergence time of P. vivax viz 2–3 mya [10] and 3.8–7 mya [13] and based on these divergence time mutation rates were also estimated. Under recent divergence time scenario, synonymous divergence rate (μ _s) and mutation rate (μ) are calculated as above, and listed in Table 4 .

Table 4. Estimation of mutation and synonymous divergence rates in Plasmodium vivax.

Divergence time scenario	Average mutation rate per site	Lower limits of mutation rate/site/year (μa)	Upper limits of mutation rate/site/year (μb)	Average synonymous divergence rate per site	Lower limits of synonymous divergence rate/site/year (μsa)	Upper limits of synonymous divergence rate/site/year (μsb)
[37] 23–30 mya	0.14985	6.51×10−9	4.99×10−9	0.3965	8.61×10−9	6.60×10−9
[39] 2–3 mya		7.49×10−8	4.99×10−8		9.90×10−8	6.60×10−8
[13] 3.8–6.3 mya		3.94×10−8	2.37×10−8		5.21×10−8	3.14×10−8

TMRCA and effective population size (Ne) estimates

We determined a range of TMRCA for extant P. vivax in India that indicate for recent (20,202 to 30,303 years) or ancient (232,288 to 303,030 years) existence, based upon assumptions of recent or ancient divergence ( Table 5 ). Similarly, on the basis of higher and lower mutation rate estimates, the effective population size estimate of extant P. vivax was obtained as recent (Ne = 6,929 to 10,400) and long-term (Ne = 79,235 to 104,008), respectively ( Table 4 ).

Table 5. Time to Most Recent Common Ancestor (TMRCA) estimate of Plasmodium vivax on the Indian subcontinent.

Divergence time scenario	Synonymous substitutions rate (dS)	TMRCA lower limits (yrs)	TMRCA upper limits (yrs)	Theta (θ)	Ne lower limits	Ne upper limits	TMRCA estimates of P. vivax in India based on mt genome (yrs)
							*Jongwutiwes et al. [14]	*Mu et al. [15]	#Cornejo et al. [50]
23–30 mya	0.004±0.001	232288±58072	303030±75757	0.002076±0.00059	79235±22657	104008±29559	13,000–17,000	122,700–164,900	143 400–192 600
3.8–6.3 mya		38387±9596	63897±15923		13172±3747	21898±6223
2–3 mya		20202±5050	30303±7575		6929±1969	10400±2933

^*: The TMRCA of Indian P. vivax is estimated by Cornejo et al, #: TMRCA estimates analyzed by joining data of Jongwutiwe et al 2005, and Mu et al 2005.

Plasmodium vivax populations are stable

We tested the housekeeping gene polymorphism data to see if there were detectable differences between the observed and expected allele frequency, which might indicate an unstable population structure of P. vivax in India. Assuming constant population equilibrium, we determined that the observed allele frequency spectrum was similar to the expected one ( Figure 2 ). In addition, we calculated the pairwise difference analysis for all samples and individual populations (Figure S3), and also found the observed allele frequency spectrum followed the expected frequency. Thus this analysis indicates the stable nature of P. vivax populations in the Indian subcontinent.

Figure 2. Expected and observed pairwise differences at seven Plasmodium vivax housekeeping genes.

Tandem repeat variability and population bottleneck

Seven microsatellites, three from one chromosome (Chr 6), one each from four chromosomes (Chr 2, Chr 5, Chr 7 and Chr10), were identified from the P. vivax genome sequence, and a subset of isolates (n = 40) was tested by microsatellite analysis. A substantial number of alleles (range 6–13, AE = 8.62±1.16) and high expected heterozygosity (He = 0.65 to 0.90, AE = 0.789±0.039) were observed for each locus. Using data that we had previously generated for ten minisatellites on the same sample set used here [28], bottleneck analysis (heterozygote deficiency and allele frequency mode shift tests) was undertaken to detect whether the extant P. vivax population in the Indian subcontinent reflects a signature of a recent population bottleneck or of a more ancient population. A majority of loci (80%) showed heterozygosity deficiency ( Table 6 ), suggesting that they are in expected genetic diversity equilibrium. Similarly, mode shift analysis revealed a strictly L-shaped allele frequency distribution ( Figure 3 ). The high heterozygosity deficiency and L-shaped allele frequency distribution at minisatellites suggests that the Indian P. vivax population has not undergone a recent population bottleneck. This supports our ancient age estimates of P. vivax inferred from putative housekeeping genes.

Table 6. Observed and expected heterozygosity at mini and microsatellite loci of Plasmodium vivax on the Indian subcontinent.

Locus	Observed (He)			Calculated by TPM (Heq)
	N	K	He	Heq	SD	DH/sd
PvCDPK	95	22	0.916	0.932	0.013	−1.254
MiniSat 1	95	18	0.826	0.911	0.017	−4.994
MiniSat 2	92	11	0.842	0.84	0.038	0.074
MiniSat 5	93	16	0.912	0.898	0.023	0.616
MiniSat 6	95	16	0.888	0.897	0.021	−0.426
MiniSat 8	55	7	0.698	0.757	0.067	−0.876
MiniSat 11	94	18	0.924	0.91	0.02	0.7
MiniSat 13	91	14	0.887	0.88	0.025	0.279
MiniSat 14	96	14	0.873	0.878	0.027	−0.161
MiniSat 16	95	11	0.815	0.838	0.038	−0.582
MS_38	36	6	0.656	0.735	0.073	−1.088
MS_40	40	7	0.786	0.772	0.062	0.223
MS_50	39	9	0.779	0.833	0.041	−1.327
MS_21	39	8	0.734	0.808	0.050	−1.497
MS_73	40	7	0.836	0.772	0.060	1.061
MS_92	37	11	0.862	0.876	0.031	−0.472
MS_128	38	13	0.905	0.900	0.035	0.150
Gomez_1	40	8	0.760	0.808	0.052	−0.922

N: number of samples, K: number of alleles observed, He: observed gene diversity and Heq: expected gene diversity equilibrium. Boldface values indicate heterozygosity deficiency.

Figure 3. Allele frequency distribution curve based on Plasmodium vivax minisatellite and microsatellite polymorphism in the Indian subcontinent.

Network analysis of tandem repeat loci

We constructed a reduced-median (RM) network of tandem repeat-based haplotypes to understand whether P. vivax populations in India expanded recently (which would produce a star-like network). A RM haplotype network derived from more than two tandem repeat loci produces a highly complex network, therefore, we limited our analysis to two tandem repeat loci on P. vivax Chr 6. No star- like network of haplotypes was produced ( Figure 4 ), suggesting an ancient population expansion of P. vivax has occurred in the Indian subcontinent.

Figure 4. Reduced-median haplotype network derived from Plasmodium vivax tandem repeat loci.

Discussion

This is the first study concerning P. vivax evolutionary history on the Indian subcontinent using SNPs in putative housekeeping genes and minisatellite and microsatellite markers. In this study we identified 1) polymorphisms in Indian P. vivax populations at neutral genetic loci; 2) neutral housekeeping genes suitable for inferring the evolutionary history of P. vivax in India; 3) no geographical structuring of P. vivax populations; and 4) an ancient and stable population of P. vivax on the Indian subcontinent.

The high degree of genetic polymorphism observed in tandem repeat loci agrees with earlier studies which revealed tremendous genetic polymorphism among global P. vivax isolates [22], [43], [45], [46], [47], [48]. This study successfully identified neutral genetic variation in several genetic loci, and this renders them highly useful as molecular markers for population structure studies. The high density of putatively neutral SNPs observed in housekeeping genes among Indian P. vivax isolates is in accordance with observations of Feng et al. [22], suggesting SNPs in P. vivax isolates are comparatively more common than in P. falciparum [17], [22]. Recently this was confirmed by deep sequencing that showed a higher genetic variability in P. vivax than P. falciparum [49]. Our neutrality test results imply that most of the housekeeping genes are free from directed selection pressure. Neutral evolution of the housekeeping genes described here argues for their utility as molecular markers for understanding demographic events and population history of P. vivax. We also tested whether pooling the P. vivax isolates collected from five geographically disparate populations might have adversely impacted the analyses of TMRCA and effective population size estimations, due to geographic structuring of subpopulations. However, we found no evidence for significant divergence between the populations, suggest that pooling of samples will not have an adverse impact on the analyses of TMRCA and effective population size. The absence of population structure between these five populations was also confirmed in an earlier study on the basis of genetic distance data derived from ten minisatellite loci [28].

Using the neutral polymorphisms of several housekeeping genes, we deduced that the MRCA of extant P. vivax was present on the Indian subcontinent about 232,228 to 303,030 years ago. This ancient TMRCA is strongly supported by long-term effective P. vivax population size (Ne) estimates and stable population indexes. The stable population index of P. vivax in Indian populations was established earlier using other neutral genetic loci [26] that also supports our older age estimate of this species. This ancient evolutionary history of extant P. vivax in India is similar to the molecular age inferred from mitochondrial genome diversity, i.e., 162,400–464,600 years [14], [15], [50]. Our TMRCA estimate strongly supports the hypothesis that P. vivax was a hominoid primate parasite before it became a human parasite by means of a host switch [12], [15], [50] and that it has evolved in Southeast Asia. The alternative hypothesis claiming an African origin for P. vivax is based on the fixation of the Duffy negative trait in the black African population. However, this alternate hypothesis is fraught with inconsistencies. For example, the Duffy negative trait arose around 100,000 years ago [51]; this time scale is shorter than the P. vivax TMRCA estimated in the present study and others [14], [15], [50]. The Duffy receptor is used for invasion by many pathogens including bacteria [52] and viruses [53], [54], [55]; thus, P. vivax is not necessarily the only evolutionary force for the fixation of this trait in the West African native population. Finally, P. vivax infection of Duffy negative people [56], [57], [58] suggests the existence of alternate invasion mechanisms, such as occur in P. falciparum [59], [60], [61].

In contrast, a much younger age estimate of P. vivax was determined under a recent divergence model of P. vivax and P. cynomolgi [10] coincident with the radiation of Asian macaques 2–3 mya [39]. This assumption implies that the MRCA of extant P. vivax dates to just 20,202–30,303 years ago. It is of interest to mention that under this recent divergence model [10], P. vivax shows a ten-fold higher mutation rate than P. falciparum [17], and it is unlikely that such a high mutation rate difference exists between related species. The radiation of Asian macaques was inferred from analysis of a mitochondrial gene, which may be evolving at a different rate than nuclear genes. Combined, our population genetic analyses such as pairwise difference, allele frequency, reduced-median network of haplotypes, and heterozygote deficiency conducted in the present study do not reflect the signature of a recent population expansion or bottlenecked population of P. vivax in the Indian subcontinent. Therefore, an ancient divergence time (23–30 mya) of P. vivax and P. knowlesi, seems more plausible.

In conclusion, our findings reveal that P. vivax isolates have an ancient evolutionary history in the Indian subcontinent. For the first time we report that neutral nuclear genome markers (housekeeping genes) displayed an evolutionary history of P. vivax similar to that inferred from mitochondrial genome diversity.

Supporting Information

Figure S1

Map of India showing location of Plasmodium vivax sampling sites. 1: Delhi; 2: Panna, Madhya Pradesh; 3: Nadiad, Gujarat; 4: Chennai, Tamil Nadu; and 5: Kamrup, Assam.

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Figure S2

Tandem repeat variation in housekeeping genes from Plasmodium vivax field isolates. A) DNA gyrase and B) Ribosomal protein l34a. Tandem repeat unit is underlined. Dash (–) represents deleted nucleotides.

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Figure S3

Expected and observed pairwise differences at seven Plasmodium vivax housekeeping genes.

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Table S1

Primers and amplification conditions.

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Table S2

Characteristic features of Plasmodium vivax mini and microsatellite markers.

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Text S1

Details of study sites.

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Funding Statement

This work was supported by the Department of Biotechnology and Indian Council of Medical Research, New Delhi, and with funds from a National Institutes of Health/Fogarty International Center, Global Infectious Disease training grant (D43 TW007884). The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.