The Irish potato famine pathogen Phytophthora infestans originated in
central Mexico rather than the Andes
Goss, E. M., Tabima, J. F., Cooke, D. E. L., Restrepo, S., Fry, W. E., Forbes, G.
A., ... & Grünwald, N. J. (2014). The Irish potato famine pathogen Phytophthora
infestans originated in central Mexico rather than the Andes. Proceedings of the
National Academy of Sciences, 111(24). doi:10.1073/pnas.1401884111
10.1073/pnas.1401884111
National Academy of Sciences
Version of Record
http://cdss.library.oregonstate.edu/sa-termsofuse
The Irish potato famine pathogen Phytophthora
infestans originated in central Mexico rather than
the Andes
Erica M. Gossa, Javier F. Tabimab, David E. L. Cookec, Silvia Restrepod, William E. Frye, Gregory A. Forbesf,
Valerie J. Fielandb, Martha Cardenasd, and Niklaus J. Grünwaldg,h,1
a
Department of Plant Pathology and Emerging Pathogens Institute, University of Florida, Gainesville, FL 32611; bDepartment of Botany and Plant Pathology,
Oregon State University, Corvallis, OR 97331; cThe James Hutton Institute, Invergowrie, Dundee DD2 5DA, Scotland; dDepartment of Biological Sciences,
University of the Andes, 110321 Bogota, Colombia; eDepartment of Plant Pathology and Plant-Microbe Biology, Cornell University, Ithaca, NY 14853; fCIP
China Center for Asia and the Pacific, International Potato Center, Beijing 100081, China; gHorticultural Crops Research Laboratory, US Department of
Agriculture Agricultural Research Service, Corvallis, OR 97330; and hDepartment of Botany and Plant Pathology and Center for Genome Biology and
Biocomputing, Oregon State University, Corvallis, OR 97331
Phytophthora infestans is a destructive plant pathogen best known
for causing the disease that triggered the Irish potato famine and
remains the most costly potato pathogen to manage worldwide.
Identification of P. infestan’s elusive center of origin is critical to
understanding the mechanisms of repeated global emergence of
this pathogen. There are two competing theories, placing the origin
in either South America or in central Mexico, both of which are
centers of diversity of Solanum host plants. To test these competing
hypotheses, we conducted detailed phylogeographic and approximate Bayesian computation analyses, which are suitable approaches
to unraveling complex demographic histories. Our analyses used
microsatellite markers and sequences of four nuclear genes sampled
from populations in the Andes, Mexico, and elsewhere. To infer the
ancestral state, we included the closest known relatives Phytophthora phaseoli, Phytophthora mirabilis, and Phytophthora ipomoeae, as well as the interspecific hybrid Phytophthora andina. We
did not find support for an Andean origin of P. infestans; rather, the
sequence data suggest a Mexican origin. Our findings support the
hypothesis that populations found in the Andes are descendants
of the Mexican populations and reconcile previous findings of ancestral variation in the Andes. Although centers of origin are well
documented as centers of evolution and diversity for numerous crop
plants, the number of plant pathogens with a known geographic
origin are limited. This work has important implications for our understanding of the coevolution of hosts and pathogens, as well as
the harnessing of plant disease resistance to manage late blight.
biological invasion
stramenopile
distribution for Phytophthora andina, a phylogenetic relative of P.
infestans (6).
Evidence supporting a Mexican center of origin is substantial,
but inconclusive (4). Two close relatives of P. infestans, Phytophthora ipomoeae and Phytophthora mirabilis, are endemic to
central Mexico (7, 8). P. ipomoeae and P. mirabilis cause disease
on two endemic plant host groups, Ipomoea spp. and Mirabilis
jalapa, respectively. Populations of P. infestans in the Toluca
Valley, southwest of Mexico City, are genetically diverse, are in
Hardy–Weinberg equilibrium, and contain mating types A1 and
A2 in the expected 1:1 ratio for sexual populations (9, 10). Before a migration event from Mexico to Europe in the 1970s (11,
12), only A1 mating types of P. infestans were found worldwide
outside of central Mexico, limiting other populations to asexual
reproduction (13). Tuber-bearing native Solanum species occur
throughout the Toluca Valley (14). Of the R genes that have
been used to confer resistance to strains of P. infestans in potato,
the majority described to date originated from Solanum demissum or Solanum edinense in the Toluca Valley, with some discovered in South America (15).
Significance
The potato late blight pathogen was introduced to Europe in
the 1840s and caused the devastating loss of a staple crop,
resulting in the Irish potato famine and subsequent diaspora.
Research on this disease has engendered much debate, which
in recent years has focused on whether the geographic origin
of the pathogen is South America or central Mexico. Different
lines of evidence support each hypothesis. We sequenced four
nuclear genes in representative samples from Mexico and the
South American Andes. An Andean origin of P. infestans does
not receive support from detailed analyses of Andean and
Mexican populations. This is one of a few examples of a pathogen with a known origin that is secondary to its current
major host.
| coalescent analysis | oomycete | population genetics |
T
he potato pathogen Phytophthora infestans, the causal agent
of potato late blight, is the plant pathogen that has most
greatly impacted humanity to date. This pathogen is best known
for its causal involvement in the Irish potato famine after introduction of the HERB-1 strain to Ireland from the Americas
in the 19th century (1). To this day, potato late blight remains
a major threat to food security and carries a global cost conservatively estimated at more than $6 billion per year (2). In
the 1980s, a single asexual lineage named US-1, possibly derived
from the same metapopulation as HERB-1 (1), dominated global populations, whereas a genetically diverse and sexual population of P. infestans in central Mexico led to formulation of the hypothesis identifying Mexico as this pathogen’s center of origin (3,
4). A competing hypothesis argues that the center of origin of the
potato, the South American Andes, is the center of origin of
P. infestans (5). This hypothesis recently gained prominence after
an analysis demonstrated ancestral variation in Andean lineages
of P. infestans (5). Other evidence supporting this hypothesis
includes infection of native Solanum hosts and an Andean
www.pnas.org/cgi/doi/10.1073/pnas.1401884111
Author contributions: E.M.G., D.E.L.C., S.R., G.A.F., and N.J.G. designed research; E.M.G.,
J.F.T., D.E.L.C., S.R., W.E.F., G.A.F., V.J.F., M.C., and N.J.G. performed research; D.E.L.C., S.R.,
W.E.F., G.A.F., and N.J.G. contributed new reagents/analytic tools; E.M.G., J.F.T., D.E.L.C.,
V.J.F., M.C., and N.J.G. analyzed data; and E.M.G., J.F.T., D.E.L.C., S.R., W.E.F., G.A.F., M.C.,
and N.J.G. wrote the paper.
The authors declare no conflict of interest.
This article is a PNAS Direct Submission.
Data deposition: The sequences reported in this paper have been deposited in the GenBank
database (accession nos. KF979339–KF980878).
1
To whom correspondence should be addressed. E-mail: grunwaln@science.oregonstate.
edu.
This article contains supporting information online at www.pnas.org/lookup/suppl/doi:10.
1073/pnas.1401884111/-/DCSupplemental.
PNAS | June 17, 2014 | vol. 111 | no. 24 | 8791–8796
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SCIENCES
Edited by Detlef Weigel, Max Planck Institute for Developmental Biology, Tübingen, Germany, and approved May 6, 2014 (received for review
January 30, 2014)
Results
Population Structure and Mode of Reproduction. Our sample of
P. infestans included 40 isolates from Colombia, Ecuador, and
Peru and 48 isolates from Toluca Valley and Tlaxcala State in
central Mexico (SI Appendix, Table S1). We found 30 multilocus
simple sequence repeat (SSR) genotypes in the Andes sample
and 43 in the Mexico sample. The Mexico sample had slightly
higher mean allelic richness per locus compared with the Andes
sample (6.7 vs. 5.2) after correction for sample size by rarefaction. The mean number of private alleles per locus for the Mexico
sample was more than twice that for the Andes sample (2.1 vs.
0.8). In the Mexico sample, clonality was detected in isolates
sampled from single patches of the indigenous host S. demissum.
The index of association, IA, calculated for clone-corrected data
for the Mexico isolates accepted the hypothesis of sexual reproduction (P = 0.25). In contrast, the hypothesis of no linkage
among markers was rejected for the Andes sample (P < 0.001),
supporting a clonal mode of reproduction.
We inferred population structure based on SSR genotypes
separately for the Mexico and Andes samples of P. infestans,
based on a priori knowledge of their sexual and clonal reproduction, respectively, using structure (32). The Mexico sample
consisted of admixed subpopulations with at least K = 4 underlying groups (Fig. 1A and SI Appendix, Figs. S1 and S2), whereas
the Andes sample consisted of two distinct clusters with very
little admixture (Fig. 1B and SI Appendix, Figs. S1 and S2).
Phylogeographic Root of P. infestans. We used Bayesian multilocus
phylogeographic analysis to infer the geographic location of the
8792 | www.pnas.org/cgi/doi/10.1073/pnas.1401884111
A
Mexico
Observed
IA = 0.08
P = 0.25
Count
150
100
PiMX29
PiMX65
PiMX21
PiMX22
PiMX02
PiMX15
PiMX23
PiMX04
PiMX20
PiMX03
PiMX12
PiMX41
PiMX61
PiMX62
PiMX27
PiMX40
PiMX14
PiMX16
PiMX10
PiMX42
PiMX06
PiMX26
PiMX18
PiMX30
PiMX19
PiMX11
PiMX24
PiMX25
PiMX28
PiMX01
PiMX64
PiMX67
PiMX63
PiMX66
PiMX13
PiMX17
PiMX72
PiMX71
PiMX05
PiMX07
PiMX50
PiMX48
PiMX49
PiMX43
PiMX44
PiMX45
PiMX46
PiMX47
50
0
0.2 0.4
Index of association
Observed
IA = 2.63
P < 0.001
200
Count
B
-0.4 -0.2
Andes
150
100
50
PiPE01
PiCO01
PiCO02
PiCO03
PiCO04
PiEC03
PiPE11
PiPE12
PiPE14
PiPE05
PiPE09
PiEC01
PiPE04
PiPE02
PiPE08
PiPE13
PiPE07
PiPE26
PiEC02
PiPE10
PiPE03
PiPE06
PiCO05
PiPE21
PiEC06
PiEC04
PiPE20
PiEC11
PiEC12
PiEC07
PiEC08
PiEC10
PiEC13
PiEC14
PiPE27
PiEC05
PiPE22
PiPE23
PiPE25
PiPE24
Support for the alternate hypothesis that P. infestans originated in the Andes is based on a coalescent analysis conducted
by Gómez-Alpizar et al. (5). This analysis used the nuclear RAS
locus and the mitochondrial P3 and P4 regions to infer rooted
gene genealogies that showed ancestral lineages rooted in the
Andes. Furthermore, the Mexico sample harbored less nucleotide diversity than the Andean population. P. andina was identified as the ancestral lineage for the mitochondrial genealogy;
however, P. mirabilis and P. ipomoeae were not included in that
study. P. andina has since been shown to be a hybrid species derived
from P. infestans and a Phytophthora sp. unknown to science (16).
Surprisingly, populations of P. infestans and P. andina are clonal in
South America and are not in Hardy–Weinberg equilibrium (6, 17–
19). Thus, the question of whether P. infestans originated in the
Andes or central Mexico remained unresolved.
Powerful approaches for determining the demographic and
evolutionary history of organisms are now available (20). Many
of these approaches rely on the power of coalescent theory for
inferring the genealogical history of a species based on a representative population sample (21–23). Bayesian phylogeography
uses geographic information in light of phylogenetic uncertainty
to provide model-based inference of geographic locations of
ancestral strains (24). The isolation with migration (IM) model
and associated software uses likelihood-based inference to infer
divergence time between evolutionary lineages (25). Approximate
Bayesian computation (ABC) makes use of coalescent simulations
and likelihood-free inference to contrast complex demographic
scenarios. Each of these methods has proven useful in reconstructing the demography of pests and pathogens (24, 26–29).
The objective of the present study was to reconcile the two
competing hypotheses on the origin of P. infestans using Bayesian
phylogenetics and ABC. We sampled key populations of P. infestans
from central Mexico and the Andes and expanded on the analysis of Gómez-Alpizar et al. (5) by sequencing additional nuclear
loci to assess support for the center of origin across multiple loci.
To determine ancestral state, we added sequences from the sister
taxa P. andina, P. mirabilis, P. ipomoeae, and Phytophthora phaseoli,
all of which belong to Phytophthora clade 1c (30, 31). Finally, we
aimed to reconcile the biology of P. infestans in Mexico with the
findings of Gómez-Alpizar et al. (5) of ancestral variation in
the Andes.
EC1
PE7 PE3
US8
US1
0
1
2
Index of association
Fig. 1. Population structure of Mexico and Andes samples of P. infestans
inferred using structure (32). (A) The Mexico sample shows admixed individuals assigned to K = 4 clusters. Isolates collected from patches of
S. demissum are in bold type. Based on the index of association, IA, there is
no evidence of linkage disequilibrium among loci (P = 0.25), consistent with
a sexually recombining population. (B) The Andes sample clusters into K = 2
distinct clades with little or no admixture. The hypothesis of no linkage
among markers is rejected (P < 0.001), indicating a clonal population.
root (“root state”) of P. infestans and the Phytophthora clade 1c
species using BEAST (24, 33). For this analysis, we included
a representative global sample including isolates from the nowdiverse populations in Europe (SI Appendix, Table S1). Comparison of different molecular clocks for each sequenced nuclear
locus showed that three of four loci fit a strict clock, in which the
standard deviation of the uncorrelated lognormal relaxed molecular clock indicated no variation in rates among branches. In
contrast, the RAS locus (intron Ras and Ras fragments) showed
high variation in rates among branches and required a relaxed
lognormal molecular clock (SI Appendix, Table S2). The PITG_11126
locus had the highest rate of evolution, whereas β-tubulin (b-tub)
had the lowest substitution rate.
Root state reconstruction produced the highest posterior probabilities for Mexico as the root state of both the P. infestans and
clade 1c datasets (Fig. 2). For each locus independently, posterior
probabilities of a Mexico root were >0.8 for clade 1c (SI Appendix,
Fig. S3). In nearly all of the P. infestans clades, there was an
inferred ancestral connection to Mexico (SI Appendix, Figs. S4–
S8). All of the species in Clade 1c were monophyletic with high
support, except for the hybrid species P. andina as previously
demonstrated (16, 34).
Evolution of P. infestans in the Andes. We found that three out of
four loci had either greater nucleotide diversity or Watterson’s
theta for the Andes sample compared with the Mexico sample
(SI Appendix, Table S3). To better understand the evolution of
the Andes lineages and the relationship between P. infestans in
Mexico and the Andes, we estimated pairwise times since divergence using combined SSR genotypes and nuclear sequence
data using the IMa program (25). Divergence times were estimated between each of the clonal lineages in the Andes sample
(US-1, EC-1, PE-3, and PE-7) and one another and the Mexico
sample (Fig. 3). EC-1, PE-3, and PE-7 produced recent pairwise
divergence times. EC-1 showed the most recent divergence from
US-1 and the Mexico population. The time since divergence of
PE-3 and US-1 was less than that of PE-3 and Mexico. The time
since divergence between PE-7 and Mexico was greater than for
EC-1 or PE-3 from Mexico. The marginal posterior probability
distribution for the divergence time between PE-7 and US-1 was
flat, indicating uncertainty in the history of PE-7.
We further explored scenarios for the evolution of the Andes
lineages by testing a series of alternative models using ABC as
implemented in the DIYABC program (35). We first examined
Goss et al.
P. ipomoeae
MX
0.9
MX
MX
1.0
1.0
P. mirabilis
EC
1.0
P. andina
MX
0.8
Location
Mexico
MX P. infestans
Ecuador
1.0 P. andina
Root state posterior probabiliy
C
Clade 1c
0.5
0.4
0.3
0.2
0.1
0.0
CO EC ES HU MX NL PE SA SW UK US VT
P. infestans
0.20
0.15
0.10
0.05
0.00
CO EC ES HU MX NL PE PO SA SW UK US VT
Fig. 2. Root state probabilities by country inferred using BEAST (33). (A)
Summarized maximum clade credibility phylogeny of Phytophthora clade 1c
species. Colors of branches indicate the most probable geographic origin of
each lineage. Posterior probabilities of major branches supporting the tree
topology are shown below each branch. Root state posterior probabilities indicate that Mexico is the most probable origin of clade 1c (B) and
P. infestans (C ).
the relationships among the lineages EC-1, PE-3, and PE-7.
Model comparison indicated that the PE-3 and PE-7 lineages
have more recent shared ancestry compared with the more
widespread EC-1 lineage (SI Appendix, Fig. S9). We next tested
the relationships of each of these lineages to the Toluca population in Mexico and the US-1 lineage in the Andes (SI Appendix, Fig. S10). Here we used only isolates from the Toluca
Valley, because we know that this population is panmictic (4).
Preliminary analyses showed support for the PE-3 and PE-7
lineages being both closely related and distantly related to the
other lineages.
To better understand this pattern, we included scenarios
containing all possible pairwise admixture events among populations as well as an admixture with an unsampled population
(36) (SI Appendix, Fig. S10). There was relatively strong support
for PE-3 as an admixed lineage. The scenario in which PE-3 is
derived from an admixture event between US-1 and an unsampled population had a posterior probability of 0.67 (Fig. 4A and
SI Appendix, Table S4). All other scenarios had posterior probabilities <0.14, most <0.01. The equivalent scenario for PE-7
also had the highest posterior probability of the tested models
at 0.37, but there was also support for PE-7 emerging from
an admixture event between the Toluca population and the
unsampled population (Fig. 4 B and C and SI Appendix, Table S4).
The relationship of EC-1 to US-1 and the Toluca population was
uncertain as well, with nearly equal support for two scenarios (Fig.
4 D and E and SI Appendix, Table S4). In one scenario, the EC-1
lineage recently diverged from the Toluca population (P = 0.25),
and in the other, EC-1 was an admixture of the Toluca population
and an unsampled population (P = 0.31). Our Andes samples were
highly clonal; thus, we interpret these results as indicating that the
PE-3, PE-7, and perhaps EC-1 lineages formed after a sexual event
between two distinct lineages or populations.
We used the most highly supported scenarios to test more
complex scenarios including all four Andean lineages and
Toluca. Testing all possible admixture events proved to be too
complex with support split among scenarios with various combinations of admixture events. Furthermore, the PE-7 results
from both IMa and DIYABC analyses suggest that this lineage
has a complex ancestry. Therefore, the final scenarios tested
admixture in the evolution of EC-1 and PE-3, and excluded PE-7
(Fig. 5). We found that scenario B, in which EC-1 split from the
Toluca population and PE-3 originated from an admixture event,
had the highest posterior probability of 0.74 (Fig. 4). Notably,
there was minimal support for scenario C, with simple ancestral
divergence of PE-3 (Fig. 5).
Goss et al.
We estimated type I and type II errors for scenario B and
found that 65% of the datasets simulated under scenario B
produced the highest posterior probability for scenario B (type I
error, 0.352). Pseudo-observed datasets generated under scenarios
A and C were wrongly assigned to scenario B at frequencies of
0.210 and 0.096, respectively (type II error). Posterior distributions
for parameters were wide, indicating limited confidence in the
parameter estimates.
Discussion
We found multilocus support for a Mexican origin of P. infestans.
Bayesian phylogeographic analysis rooted both P. infestans and
Phytophthora clade 1c in Mexico for each of four nuclear loci. Our
results are consistent with the population biology of P. infestans in
central Mexico and, taken together, point to Mexico as the origin
of this pathogen. These results are supported by the previously
noted pathogen and host characteristics. Specifically, Toluca
populations are sexual, whereas South American populations
of P. infestans are clonal (6, 9, 10, 17–19). Both mating types of
P. infestans are known to have been present since at least the
1960s in central Mexico (37, 38).
The genealogical connections between continents that we
observed in our phylogeographic analysis are consistent with the
movement of P. infestans among widespread potato growing
regions. Migration estimates using microsatellite variation also
support our sequence analysis by showing migration from Mexico
to the Andes, but not from the Andes to Mexico (SI Appendix).
The commercial potato seed trade can explain much of the
current global population structure of P. infestans; however, the
early movements of P. infestans have not been fully reconstructed
(1), and examination of the processes underlying the emergence
of new, highly successful strains is ongoing (3, 39). The diverse
population in central Mexico may be the ultimate source for the
appearance of new strains worldwide (3, 40), although seed potatoes from Europe are behind recent migrations of virulent strains
(41, 42). Detailed genetic reconstruction of global migrations of
P. infestans may be feasible using population genomic data.
We explored the evolution of the Andean lineages and the
relationship between P. infestans in Mexico and the Andes by
testing a series of alternative models using the ABC technique.
Our intention was to determine the timing of divergence of the
Andean lineages and their relationship to the Toluca population
in Mexico. Surprisingly, we found evidence for diversification of
the Andes population as a result of admixture or hybridization.
Because of our limited power to discriminate between models,
we view this analysis as hypothesis-generating. Nevertheless,
even moderate support for hybridization generating novel
50
EC-1
PE-3
PE-7
US-1
PE-3
PE-7
US-1
0
50
0
50
0
50
Mexico
0
0
0.2 0
0.2
0
0.2
0
0.2
Scaled time since divergence
Fig. 3. Estimated marginal posterior probabilities of relative divergence
times in pairwise comparisons among Andes clonal lineages (EC-1, PE-3, PE-7,
and US-1) and the Mexico population estimated using IMa (64). Smaller
means and modes of the scaled time since divergence indicate more recent
divergence of lineages. Lineages EC-1, PE-3, and PE-7 show more recent divergence from one another than from US-1 and Mexico.
PNAS | June 17, 2014 | vol. 111 | no. 24 | 8793
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1.0
B
Estimated marginal posterior probability
MX
Root state posterior probabiliy
A
A
P = 0.67
Toluca US-1 PE-3
B
P = 0.37
Toluca US-1 PE-7
C
P = 0.29
US-1 Toluca PE-7
DP = 0.25
Toluca EC-1
E
P = 0.31
Time
US-1 US-1 Toluca EC-1
Fig. 4. Scenarios for the evolution of P. infestans in the Andes tested using
ABC in DIYABC (35). Shown are the scenarios with the highest posterior
probabilities out of 15 scenarios testing the relationships of PE-3, PE-7, and
EC-1 lineages, in turn, to the US-1 lineage and Toluca Valley population (SI
Appendix, Fig. S10). Present-day populations are at the base of the tree
schematic. Ancestral relationships among these populations are represented
by lines intersecting in the past, with the vertex of the schematic representing the most recent common ancestor of all samples. Horizontal lines
indicate admixture events between the ancestral populations connected by
the horizontal line. Potential changes in population size over time are indicated by changes in line thickness, but line thickness is not proportional to
population size. The dashed line represents an unsampled population that
has contributed to the genetic variation observed in sampled populations.
(A) For PE-3, the most probable scenario includes an admixture of US-1 and
an unsampled population, leading to the PE-3 lineage. (B and C) For PE-7,
support is split between two scenarios containing an admixture event with
an unsampled population. (D and E) For EC-1, the scenarios with the greatest
support showed a simple divergence from the Toluca population or an admixture between Toluca and an unsampled population. Posterior probabilities for all tested scenarios and their 95% confidence intervals are given in SI
Appendix, Table S4.
explicit treatment of geography in our BEAST analysis did not
require us to make assumptions about population structure, but
rather incorporated the divergent origins of our isolates into
the analysis.
Resolving the origin of P. infestans is important to our understanding of the emergence and reemergence of damaging
pathogens. P. infestans is one of a limited number of agricultural
plant pathogens with a well-characterized center of origin (45).
An expectation of long-term coevolution between a crop and its
host-specific pathogen can mislead one into thinking that the
pathogen originates from the crop’s center of origin; however,
there are other well-documented and suspected instances of
host-jumping by crop pathogens (45–47). P. infestans appears to
be an example of a pathogen originating from wild relatives in
a secondary center of host diversity. Identification of the center
of origin also advances our understanding of pathogen evolution
outside of this region, that is, how the pathogen has changed
after introduction to new environments.
Global populations of P. infestans have undergone rapid
changes owing to both migration and evolution after migration
(39, 48). Knowledge of pathogen diversity and evolution both
within and outside of the center of origin is critical to crop
breeding efforts (49). The long-term success of efforts to breed
late blight-resistant potatoes will require breeders to account
for geographic and evolutionary sources of novel variation in
P. infestans and its hosts.
Materials and Methods
lineages of P. infestans is compelling, given that a new pathogen
of Solanum hosts, P. andina, has been generated via hybridization (16), and that infrequent hybridization among lineages of
P. infestans is suspected to be responsible for novel genotypes
elsewhere (43).
Considering the diversity of Solanum hosts in the Andes, there
is great potential for clonal diversification of P. infestans as
available niches are colonized and rare events contribute to
generation or recombination of variation. There is no evidence
of genetic variation among P. infestans isolates from potatoes in
Peru as recently as the mid-1980s (44). If there were diversity in
P. infestans or clade 1c in the Andes, it must have been limited to
other unsampled hosts. Based on our analyses, we hypothesize
that the Andean diversity in P. infestans has been driven by global
migration together with hybridization among populations established via independent migration events.
Given our results, why did Gómez-Alpizar et al. (5) infer an
Andean origin? First, their mitochondrial coalescent gene tree
included the Andean endemic P. andina, but not the Mexican sister
species, and thus species selection rooted the tree in the Andes. At
the time that the work was conducted, P. andina was not recognized as a hybrid species with two haplotypes derived from two
distinct parental species (16). When we removed P. andina from
their dataset, the location of the root was ambiguous (SI Appendix);
therefore, the mitochondrial loci used in the analysis were not
phylogeographically informative. The root of the P. infestans mitochondrial genome was recently dated to 460 y ago (95% highestprobability density, 300–643), around the time of the Spanish
conquest of the Americas (1). Thus, the two major mitochondrial
haplotypes may be the product of movement of the pathogen
by humans, resulting in the formation of a new population of
P. infestans and the evolution of diverged mtDNA haplotypes
before global expansion of the pathogen some 200 y later.
Second, the coalescent root of the single nuclear locus used by
Gómez-Alpizar et al. is dependent on migration rate (SI Appendix),
which was estimated using the same locus. The RAS gene in
P. infestans has two diverged haplotypes in the first intron. This
creates two diverged clades of haplotypes, one of which is not found
in the Mexican sample. This might have biased the migration rate
estimates for this gene and affected the outcome of the coalescent
analysis. Our analysis of this locus required a relaxed molecular
clock and took an exceptionally long time to converge. Finally,
8794 | www.pnas.org/cgi/doi/10.1073/pnas.1401884111
Sampling Individuals. A sampling of the known global diversity in P. infestans
was obtained from several collaborators (SI Appendix, Table S1). We focused
on assembling two large samples from Mexico (n = 48) and the South
American Andes (n = 40) representing the known diversity from each of
these regions, and included a more moderate global sample of P. infestans
for context (SI Appendix, Table S1).
SSR Typing. Isolates were genotyped using 11 SSR markers as described
previously (39, 50). Given that the individuals varied in ploidy, analysis was
restricted to approaches that can accommodate nondiploid genetics (51).
Population Structure (SSR). Allelic richness was calculated using the ADZE
program (52). Population composition was inferred using structure 2.3 (32)
by testing the number of population clusters (K) between 1 and 20 using
the admixture model for the Mexico and Andes samples (53) and the noadmixture model for the Andes sample. The no-admixture model may be
more appropriate for the Andean population (i.e., Ecuador, Colombia, and
Peru) given a priori knowledge of its clonality (17). Analysis was performed
separately for the two different populations. A total of 10 independent
runs each of 1,000,000 iterations with a burn-in period of 20,000 Markov
chain Monte Carlo (MCMC) iterations were conducted. The results from
structure were postprocessed using Structure Harvester (54). The ΔK
method was used to evaluate the rate of change in the log probability of
data between successive K values, to infer the number of clusters (55).
AP = 0.02
BP = 0.74
[0.016, 0.028]
CP = 0.24
[0.686, 0.791]
[0.187, 0.292]
Time
Toluca EC-1 US-1
PE-3
Toluca EC-1 US-1
PE-3
Toluca EC-1 US-1
PE-3
Fig. 5. Final three scenarios used to examine the relationships between the
Toluca Valley population and EC-1, PE-3, and US-1 lineages in the Andes by
ABC. Tree schematics are drawn as in Fig. 4. The three scenarios are simple
divergence of populations such that PE-3 is an ancestral lineage (A); emergence of the PE-3 lineage after an admixture of US-1 and an unsampled
population (B); and scenario B plus emergence of the EC-1 by an admixture
between the Toluca population and an unsampled population (C). Scenario
B was the most likely of the three, with a posterior probability of 0.74. The
95% confidence intervals for the posterior probabilities are in brackets.
Goss et al.
DNA Amplification and Sequencing. Nuclear loci were amplified and directly
sequenced as described by Goss et al. (16). A larger fragment of the b-tub gene
was sequenced than that sequenced by Gómez-Alpizar et al. (5). Haplotype
phases of nuclear gene sequences with multiple heterozygous sites were
inferred using PHASE software (51). Inferred haplotypes were confirmed by
cloning PCR products for a subset of genotypes and sequencing inserts. In
several instances, three distinct alleles were recovered from a given individual;
these were the only times when the PHASE-inferred haplotypes were not
validated. In some instances, isolates with three alleles at one locus were
cloned at another locus, and only two alleles were found; thus, it was not
assumed that these isolates had three distinct alleles at other loci.
For the phylogenetic and coalescent-based analyses, we removed indels and
recombinant alleles from the datasets. We used the four-gamete test to detect
signals of recombination, and found recombination in the b-tub, PITG_11126,
and RAS alignments. For PITG_11126, the last 65 nucleotides were excluded
owing to recombination in this region relative to the remainder of the fragment. For b-tub, the signal of recombination was removed when an indel was
deleted from the alignment and isolate PiEC01 was excluded. For the RAS locus,
PiEC07, PiUS11, and PiUS17 were excluded.
The sequences generated have been deposited in GenBank (accession nos.
KF979339–KF980878).
Demographic and Phylogeographic History. We adopted a Bayesian coalescent
approach to investigate divergence and phylogeographic history using BEAST
1.7.4 (33, 60). BEAST implements a method for sampling all trees that have
a reasonable probability given the data. The analysis is based on haplotypes,
and two haplotypes in a given individual may or may not share a most
common recent ancestor. Furthermore, genealogies obtained from BEAST
necessarily estimate how old the common ancestor of these haplotypes
might be for each haplotype (even when haplotype sequences are identical),
resulting in slight branch length variation among identical haplotypes. This
is an expected outcome of coalescent analysis in which identical sequences
at a given locus are expected to show divergence at the genome level. Note
that although branch length variation is observed among identical haplotypes, there is no support for nodes at this level until different haplotype
sequences coalesce to their common recent ancestors, and this branch
length variation should not be interpreted.
To initialize BEAST, we obtained the most likely models of nucleotide
substitution for each alignment using jModelTest 2.1 (61) and ModelGenerator
0.57 (62), and selected the consensus model from these programs (SI Appendix,
Table S5). To ensure adequate sampling of parameters, we conducted the
BEAST analyses with independent MCMC simulations of 200 million iterations for each locus both for P. infestans only and with the other clade 1c
species. Analyses were conducted at least twice to ensure repeatability. For
each MCMC run, we sampled every 10,000 generations and discarded nonstationary samples after 25% burn-in. Effective sample size estimates were
typically greater than 200, and parameter trace plots supported MCMC
convergence and good mixing in each independent run. Multilocus analyses
were also run for P. infestans only and also for all Phytophthora clade 1c
species. For each dataset, models of nucleotide substitution, constant coalescent priors (for the P. infestans dataset) or Yule speciation models (for
the clade 1c dataset) were used as specified priors to improve the calculation
of clock rates, geographic ancestral states, and phylogenetic relationships.
To infer the most likely geographic origin for each clade, we used the discrete
phylogeographic approach as implemented by Lemey et al. (24). This method
uses the geographic locations of the samples to reconstruct the ancestral states
of tree nodes, including estimation of the root state posterior probability.
Maximum clade credibility (MCC) trees were obtained using TreeAnnotator and
visualized in FigTree 1.3.1. The bar plots for the posterior probability of the
root state were created with the ggplot2 package (63) using R statistical
computing and graphic language (59). Maximum clade credibility trees were
obtained for each locus as well as for multigene analyses.
Divergence Times Under Isolation with Migration. IMa version 2.0 was used to
estimate divergence times for each pair of Andean lineages and between
Andean lineages and the Mexican population (64). The data used were the 4
nuclear loci and 8 of the 11 SSR loci. Two SSR loci that did not conform to the
stepwise mutation model (D13 and G11) and one SSR locus that was nearly
Goss et al.
monomorphic (Pi33) were excluded. The infinite sites model was used for all
nuclear loci. Initial maxima for uniform prior distributions of the parameters
were as follows: population size (q), 15.0; divergence time (t), 0.5; migration
rate (m), 1.0. Runs including the Mexican sample were also performed using
larger priors for q (20.0) and t (1.0), and similar results were obtained. The
option of running the burn-in and recording periods for indefinite durations
was chosen to ensure stabilization of likelihoods before the end of the burnin and adequate sampling of the posterior distribution. Metropolis coupling
was implemented using the geometric increment model and 80 chains with
geometrical increment parameters of 0.97 and 0.3.
ABC. We evaluated alternative scenarios for the evolution of the Andean
P. infestans lineages in a systematic stepwise manner using ABC with
DIYABC version 1.0.4.45 (35). ABC has been used to estimate parameters
for complex evolutionary models for which likelihoods are difficult or
practically impossible to compute (65, 66). The DIYABC program simulates
coalescent genealogies under user-specified evolutionary models using
parameters drawn from prior distributions and compares statistics summarizing various aspects of the simulated data with those of the observed
data. The similarity of summary statistics between observed and simulated
datasets is used to calculate posterior probabilities of competing evolutionary models and posterior distributions of parameters. In effect, models
that generate datasets with summary statistics close to the observed data
have higher probability. We used this method to evaluate posterior probabilities for alternate scenarios representing different possible evolutionary
relationships among P. infestans populations in Mexico and the Andes. The use
of ABC to evaluate alternate scenarios has been questioned owing to potential
problems with using summary statistics, but DIYABC incorporates tests that
address many of these concerns (67, 68). In particular, confidence in model
choice can be evaluated empirically by calculating type I and II errors using
pseudo-observed datasets.
To narrow the number of evolutionary scenarios tested against one another, we used four sets of scenarios to inform a final fifth set of scenarios. We
grouped the Andes isolates by clonal lineage to tease apart the evolutionary
history of each lineage. Isolates were assigned to a clonal lineage based on
a previously determined RG-57 fingerprint (3) and confirmed with SSR
genotypes grouped using structure and k-means clustering (69). We first
simulated the three different possible relationships among the Andean
lineages EC-1, PE-3, and PE-7 (SI Appendix, Fig. S9) using the settings in
SI Appendix, Table S6A. We next examined 15 alternative relationships for
the US-1 lineage, the Toluca population, and each of the Andean lineages in
turn (SI Appendix, Fig. S10 and Table S6B). Although the US-1 lineage has
had a global distribution, for these analyses we used only US-1 isolates
collected in the Andes, because our focus was on the genetic variation and
evolution history of the Andes population. Based on the results of preliminary analyses, these scenarios included admixture events between lineages as well as admixture with an unsampled population.
Finally, we used the scenarios with the highest posterior probabilities to
construct three final scenarios (Fig. 4 and SI Appendix, Table S6C). This final
set tested admixture events generating the EC-1 and PE-3 lineages relative
to a scenario with no admixture. We removed the PE-7 lineage from this
final analysis, because there were too many plausible admixture events
behind the emergence of this lineage.
We tested prior distribution settings with small numbers of simulations
by running a principal components analysis on the summary statistics and
comparing the overlap of the simulated and observed data. Posterior
probabilities and 95% confidence intervals were estimated by polychotomic
weighted logistic regression on 1% of the simulations, as implemented in
DIYABC. Model checking was conducted for the final three scenarios by estimating type I and type II errors. In short, 500 pseudo-observed datasets (pods)
were generated according to each evolutionary scenario using parameters
drawn from the same prior distributions as used for the simulated genealogies.
The posterior probability of each scenario was calculated for each pod. Type I
error was estimated as the proportion of pods for which the correct scenario
did not receive the highest posterior probability. Type II error was calculated as
the proportion of pods erroneously assigned to a given scenario.
ACKNOWLEDGMENTS. We are grateful to the many colleagues who provided isolates for this study. We thank Karan Fairchild, Kevin Myers, Caroline
Press, and Naomi Williams for maintenance of the cultures and general
technical support. This research is supported in part by US Department of
Agriculture (USDA) Agricultural Research Service Grant 5358-22000-039-00D,
USDA National Institute of Food and Agriculture Grant 2011-68004-30154
(to N.J.G.), and the Scottish Government (D.E.L.C.).
PNAS | June 17, 2014 | vol. 111 | no. 24 | 8795
AGRICULTURAL
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The mode of reproduction was assessed by evaluating observed linkage
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(57). IA was calculated using the poppr package (58) in R (59) separately for
the Mexico and Andes samples and evaluated with 2,000 permutations using
clone-corrected data.
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Supporting Information
Supporting*Methods*............................................................................................................................*1!
Supporting*Results*..............................................................................................................................*2!
References*Cited*...................................................................................................................................*3!
Supporting*Tables*................................................................................................................................*4!
Supporting*Figures*............................................................................................................................*19!
Supporting Methods
Genetree analysis. We revisited the coalescent analysis of Gómez-Alpizar et al. (1) using
their data and ours to investigate the sensitivity of root inference to estimates of migration rates.
Our concern was that there is little power to estimate migration rates with only a single locus, yet
these rates were used to infer the rooting of structured coalescent trees in the program Genetree
(2). Furthermore, Gómez-Alpizar et al. considered migration to and from South America, which
confounds migration from Mexico and other global populations. P. infestans is transported
transcontinentally and intercontinentally via infected seed tubers, and there is a vibrant
commercial seed tuber trade from Northwest Europe with known pathways of migration from
Europe to South America.
We revised the Genetree analysis of the P3 and P4 mtDNA regions using sequences from
Gómez-Alpizar et al. (1) for isolates from Mexico and the Andes but removing the haplotypes
representing the P. andina isolates (haplotype 1c). The topology and rooting of the coalescent
tree for the P. infestans haplotypes remained the same. We inferred the maximum likelihood
value of theta and a symmetric migration rate for the revised data set. We then used 1×107
simulations to examine the inferred subpopulation of the most common recent ancestor (MRCA)
of the sample while varying theta and symmetric migration rates using three sets of runs, each set
using a different starting seed.
For the RAS nuclear gene, we repeated the Gómez-Alpizar et al. (1) analysis while
varying migration rates. We used their data set and value of theta. We conducted two runs of
1×107 simulations for each set of migration rates. We varied migration rates from low and
symmetric to the values used by Gómez-Alpizar et al. We also examined the coalescent history
of the RAS locus using our sequences from Mexico and the Andes. The tree was rooted using
ancestral states obtained from P. ipomoeae, P. mirabilis, and P. phaseoli. We used four runs of
1×106 or 1×107 simulations and three symmetric migration rates using two different values of
theta (1.5 and 2.0) and four starting seeds.
Migration scenarios from SSR genotypes. The program Migrate version 3.3 was used to
examine recent migration between the Andes and Mexico, using SSR genotypes. Three
migration models were compared (3): bidirectional migration, migration from Mexico to the
Andes only, and migration from the Andes to Mexico only. The runs used Brownian motion
approximation for the stepwise mutation model, initial parameter values from FST, and mutation
rates per locus estimated from the data. Bayesian inference across 10 replicates used slice
sampling, uniform prior distributions from 0 to 1000 for both theta and M parameters, and four
chains (temperatures: 1,000,000, 3.0, 1.5, 1.0) in which the cold chain was sampled at 10,000
!
1!
steps at 200 step increments after a burnin of 500,000 steps. Models were evaluated using Bezier
approximation of log marginal maximum likelihoods.
Supporting Results
Dependence of Genetree results on migration rates. When we removed P. andina from
the Gómez-Alpizar et al. mitochondrial data set and included only the Mexican and South
American isolates, the root location was uncertain such that there was equal probability of
rooting in Mexico or South America when migration rates were symmetric (Table S7A).
Asymmetric migration rates increased the probability of the root in the population that was the
source of migration to around 0.95, irrespective of which population was assigned the higher
emigration rate.
For the RAS locus, the location of the coalescent root was dependent on migration rates
as well (Table S7B). When we used the Gómez-Alpizar et al. data under low symmetric
migration rates the rooting was uncertain, and asymmetric migration rates affected the inferred
population of origin. The migration rates used by Gómez-Alpizar et al. produced a high
probability for a South American root, which replicates their result. The opposite condition
produced a similarly high probability for a non-South American root. Therefore, both
mitochondrial and RAS analyses were highly dependent on choice of migration parameters.
We used our data set to examine the root location of RAS for Mexican and Andean
isolates only. Using RAS sequences from P. andina, P. mirabilis, P. ipomoeae, and P. phaseoli,
we were able to unambiguously assign ancestral states to each segregating site and these
ancestral states were used to root the P. infestans RAS tree. The coalescent history of the gene
was simulated on the rooted topology to infer the location of the root in Mexico or the Andes.
Moderate and inconclusive probabilities for root location were observed under nearly all
conditions examined, including three symmetric migration rates and two values of theta (Table
S8).
Key to the Gómez-Alpizar et al. analysis was their finding of a higher migration rate
from South America to non-South American populations (i.e. Mexico, USA, and Ireland) than
vice-versa using the nuclear RAS locus. Given this result, we used our SSR data to test among
models of migration between the Andes and Mexico using the program Migrate (3). Multiple
loci are expected to provide more robust estimates of migration rates for the nuclear genome than
can be obtained from a single locus. This analysis revealed a higher migration rate from Mexico
to the Andes than from the Andes to Mexico (M = 11.7 vs. 0.3, respectively). Bayesian
comparison of migration models strongly supported unidirectional migration from Mexico to the
Andes (Bezier approximation of the log marginal likelihood = -11,055) compared to the opposite
scenario of migration from the Andes to Mexico (-12,243) or bidirectional migration (-52,357).
This result is consistent with the known directions of trade in commercial seed tubers.
!
!
2!
References Cited
1.
2.
3.
4.
5.
6.
7.
!
Gómez-Alpizar L, Carbone I, & Ristaino JB (2007) An Andean origin of Phytophthora
infestans inferred from mitochondrial and nuclear gene genealogies. Proc Natl Acad Sci
U S A 104(9):3306-3311.
Griffiths RC & Tavaré S (1994) Ancestral inference in population genetics. Statistical
science 9(3):307-319.
Beerli P & Palczewski M (2010) Unified framework to evaluate panmixia and migration
direction among multiple sampling locations. Genetics 185(1):313-U463.
Nei M (1987) Molecular Evolutionary Genetics (Columbia University Press, New York)
p 512
Watterson GA (1975) On the number of segregating sites in genetic models without
recombination. Theoretical Population Biology 7:256-276.
Tajima F (1989) Statistical method for testing the neutral mutation hypothesis by DNA
polymorphism. Genetics 123(3):585-595.
Fu Y-X & Li W-H (1993) Statistical tests of neutrality of mutations. Genetics
133(3):693-709.
3!
Supporting Tables
Table S1. Isolates used in the study.
ID
Original name
Year
sampled
Country
State
Host
Source1
Lineage
P. infestans
EC-1
PiCO01
PiCO02
1011
1063
Colombia
Colombia
Cundinamarca
Cundinamarca
S. tuberosum
S. tuberosum
Restrepo
Restrepo
PiCO03
1064
Colombia
Cundinamarca
S. tuberosum
Restrepo
EC-1
EC-1
PiCO04
1068
Colombia
Cundinamarca
S. tuberosum
Restrepo
EC-1
PiCO05
4084
Colombia
Cundinamarca
Physalis peruviana
Restrepo
US-8
PiEC01
EC_3843
2004
PiEC02
EC_3527
2002
Ecuador
S. andreanum
Forbes
EC-1
PiEC03
EC_3626
2003
Ecuador
potato
Forbes
EC-1
PiEC06
EC_3841
2004
Ecuador
S. habrochaites
Forbes
US-1
PiEC07
EC_3921
2006
Ecuador
S. jugandifolium
Forbes
US-1
PiEC08
EC_3774
2004
Ecuador
S. ochanthum
Forbes
US-1
PiEC10
EC_3378
2001
Ecuador
S. lycopersicum
Forbes
US-1
PiEC11
EC_3381
2001
Ecuador
S. lycopersicum
Forbes
US-1
PiEC12
EC_3150
1997
Ecuador
S. muricatum
Forbes
US-1
PiEC13
EC_3520
2002
Ecuador
S. muricatum
Forbes
US-1
PiEC14
EC_3809
2004
Ecuador
S. caripense
Forbes
US-1
2005_10
2005
Estonia
potato
Fry
2005_17
2005
Estonia
potato
Fry
2005_19
2004
Estonia
potato
Fry
PiES04
2004_4
2004
Estonia
potato
Fry
PiES05
2004_16
2004
Estonia
potato
Fry
PiHU02
Josze_S32
Hungary
potato
Bakonyi
PiMX01
MX010006
Mexico
potato
Fry
PiES01
PiES02
PiES03
Ecuador
potato
Forbes
EC-1
MX980211
1998
Mexico
potato
Fry
PiMX04
MX980230
1998
Mexico
potato
Fry
PiMX05
MX980317
1998
Mexico
potato
Fry
MX980352
1998
Mexico
potato
Fry
MX980400
1998
Mexico
potato
Fry
PiMX10
PIC97008
1997
Mexico
Toluca
potato
Flier/Grünwald/PRI
PiMX11
PIC97066
1997
Mexico
Toluca
potato
Flier/Grünwald/PRI
PIC97106
1997
Mexico
Toluca
potato
Flier/Grünwald/PRI
PIC97111
1997
Mexico
Toluca
potato
Flier/Grünwald/PRI
PiMX03
PiMX06
PiMX07
PiMX12
PiMX13
PiMX14
PIC97130
1997
Mexico
Toluca
potato
Flier/Grünwald/PRI
PiMX15
PIC97136
1997
Mexico
Toluca
potato
Flier/Grünwald/PRI
PiMX16
PIC97146
1997
Mexico
Toluca
potato
Flier/Grünwald/PRI
PIC97149
1997
Mexico
Toluca
potato
Flier/Grünwald/PRI
PIC97153
1997
Mexico
Toluca
potato
Flier/Grünwald/PRI
PiMX19
PIC97159
1997
Mexico
Toluca
potato
Flier/Grünwald/PRI
PiMX20
PIC97187
1997
Mexico
Toluca
potato
Flier/Grünwald/PRI
PIC97310
1997
Mexico
Toluca
potato
Flier/Grünwald/PRI
PIC97318
1997
Mexico
Toluca
potato
Flier/Grünwald/PRI
PiMX23
PIC97335
1997
Mexico
Toluca
potato
Flier/Grünwald/PRI
PiMX24
PIC97340
1997
Mexico
Toluca
potato
Flier/Grünwald/PRI
PIC97389
1997
Mexico
Toluca
potato
Flier/Grünwald/PRI
PIC97392
1997
Mexico
Toluca
potato
Flier/Grünwald/PRI
PiMX27
PIC97423
1997
Mexico
Toluca
potato
Flier/Grünwald/PRI
PiMX28
PIC97432
1997
Mexico
Toluca
potato
Flier/Grünwald/PRI
PIC97438
1997
Mexico
Toluca
potato
Flier/Grünwald/PRI
PIC97442
1997
Mexico
Toluca
potato
Flier/Grünwald/PRI
PiMX40
PIC97716
1997
Mexico
Toluca
S. demissum
Flier/Grünwald/PRI
PiMX41
PIC97724
1997
Mexico
Toluca
S. demissum
Flier/Grünwald/PRI
PIC97727
1997
Mexico
Toluca
S. demissum
Flier/Grünwald/PRI
PIC97744
1997
Mexico
Toluca
S. demissum
Flier/Grünwald/PRI
PIC97748
1997
Mexico
Toluca
S. demissum
Flier/Grünwald/PRI
PiMX17
PiMX18
PiMX21
PiMX22
PiMX25
PiMX26
PiMX29
PiMX30
PiMX42
PiMX43
PiMX44
!
5!
PIC97749
1997
Mexico
Toluca
S. demissum
Flier/Grünwald/PRI
PiMX46
PIC97750
1997
Mexico
Toluca
S. demissum
Flier/Grünwald/PRI
PiMX47
PIC97751
1997
Mexico
Toluca
S. demissum
Flier/Grünwald/PRI
PIC97785
1997
Mexico
Toluca
S. demissum
Flier/Grünwald/PRI
PIC97791
1997
Mexico
Toluca
S. demissum
Flier/Grünwald/PRI
PiMX50
PIC97793
1997
Mexico
Toluca
S. demissum
Flier/Grünwald/PRI
PiMX61
Tlax 701
2007
Mexico
Tlaxcala
potato
Fernández Pavia
Tlax 715
2007
Mexico
Tlaxcala
potato
Fernández Pavia
Tlax 722
2007
Mexico
Tlaxcala
potato
Fernández Pavia
PiMX64
Tlax 728
2007
Mexico
Tlaxcala
potato
Fernández Pavia
PiMX65
Tlax 740
2007
Mexico
Tlaxcala
potato
Fernández Pavia
Tlax 748
2007
Mexico
Tlaxcala
potato
Fernández Pavia
Tlax 756
2007
Mexico
Tlaxcala
potato
Fernández Pavia
PiMX71
T48
2003
Mexico
Tlaxcala
potato
Fernández Pavia
PiMX72
T68
2003
Mexico
Tlaxcala
potato
Fernández Pavia
NL_01096
2001
Netherlands
potato
Kessel
NL_96259
1996
Netherlands
potato
Kessel
BTLM 004
1997
Peru
Lima
NA
Forbes
PE-7
PiPE02
PHU 076
2003
Peru
Huánuco
potato
Forbes
EC-1
PiPE03
PHU 079
2003
Peru
Huánuco
potato
Forbes
EC-1
PiPE04
PPI 015
2000
Peru
Piura
S. huancabambense
Forbes
EC-1
PiPE05
PTS 031
Peru
Cajamarca
S. caripense
Forbes
PiPE06
1696
1995
Peru
Arequipa
potato
Forbes
PE-3
PiPE07
PCA 004
1999
Peru
Cajamarca
potato
Forbes
PE-3
PiPE08
PCZ 024
1997
Peru
Cuzco
potato
Forbes
EC-1
PiPE09
PCZ 080
1997
Peru
Cuzco
potato
Forbes
EC-1
PiPE10
PSR 001
2005
Peru
Junín
NA
Forbes
EC-1
PiPE11
PCA 020
1999
Peru
Cajamarca
NA
Forbes
PE-7
PiPE12
PLI 003
1999
Peru
Lima
NA
Forbes
PE-7
PLI 036
2000
Peru
Lima
S. wittmackii
Forbes
PE-7
PiMX45
PiMX48
PiMX49
PiMX62
PiMX63
PiMX66
PiMX67
PiNL01
PiNL02
PiPE01
PiPE13
!
1998
6!
EC-1
PiPE14
POX 100
2003
Peru
Pasco
potato
Forbes
PE-7
PiPE20
PCA 025
1999
Peru
Cajamarca
NA
Forbes
US-1
PiPE21
PPI 009
2000
Peru
Piura
S. caripense
Forbes
US-1
PiPE22
PPI 013
2000
Peru
Piura
S. caripense
Forbes
US-1
PiPE23
PPI 014
2000
Peru
Piura
S. caripense
Forbes
US-1
PiPE24
PPI 023
2000
Peru
Piura
S. caripense
Forbes
US-1
PiPE25
PPI 028
2000
Peru
Piura
S. caripense
Forbes
US-1
PiPE26
PPU 048
1997
Peru
Puno
potato
Forbes
PE-3
PiPE27
PPU 097
1997
Peru
Puno
potato
Forbes
US-1
PiPE28
PCA 006
1999
Peru
Cajamarca
potato
Forbes
PE-3
PiPE29
PCA 010
1999
Peru
Cajamarca
potato
Forbes
PE-3
PiPO01
MP_618
2005
Poland
potato
Lebecka
MP_622
2005
Poland
potato
Lebecka
SA960008
1996
South Africa
potato
Fry
SE_03058
2003
Sweden
potato
Andersson
SE_03087
2003
Sweden
potato
Andersson
PiUK01
2006_3984C
2006
UK
potato
Cooke
EU_1_A1
PiUK02
2006_4012F
2006
UK
potato
Cooke
EU_3_A2
PiUK03
2006_3928A
2006
UK
potato
Cooke
EU_13_A2
PiUK04
2006_4132B
2006
UK
potato
Cooke
EU_13_A2
PiUK05
2006_3888A
2006
UK
potato
Cooke
EU_2_A1
PiUK06
2007_5866B
2007
UK
potato
Cooke
EU_5_A1
PiUK07
2006_4388D
2006
UK
potato
Cooke
EU_17_A2
PiUK08
2006_4100A
2006
UK
potato
Cooke
EU_6_A1
PiUK09
2006_4440C
2006
UK
potato
Cooke
EU_10_A2
PiUK10
2006_4232E
2006
UK
potato
Cooke
EU_8_A1
PiUS08
US040009
2004
USA
potato
Fry
US-8
PiUS11
US050007
2005
USA
tomato
Fry
US-11
PiUS12
US940494
1994
USA
tomato
Fry
US-12
PiUS17
US970001
1997
USA
tomato
Fry
US-17
Vn02-076
2002
Vietnam
tomato
Le
US-1
PiPO02
PiSA01
PiSW01
PiSW02
PiVT01
!
7!
US-1
PiVT02
Vn02-106
2002
Vietnam
tomato
Le
US-1
PiVT03
Vn03-416
2003
Vietnam
potato
Le
US-1
Vn03-590
2003
Vietnam
potato
Le
US-1
PiVT04
P. mirabilis
PmMX01
CBS 136.86
Mexico
NA
CBS
PmMX02
CBS 678.85
Mexico
NA
CBS
PmMX03
DF 409
Mexico
NA
Fernández Pavia
PmMX04
G 11-3
1998
Mexico
NA
Flier/Grünwald/PRI
PmMX05
00M 410
2000
Mexico
NA
Fernández Pavia
PmMX06
P 3001
Mexico
NA
Flier/Grünwald/PRI
PmMX07
P 3006
Mexico
NA
Flier/Grünwald/PRI
PmMX08
P mirabilis DF 07
2007
Mexico
NA
Fernández Pavia
P. mirabilis Mich
2003
Mexico
NA
Fernández Pavia
WF014/PIC99114
1999
Mexico
NA
Flier/Grünwald/PRI
WF035/PIC99135
1999
Mexico
NA
Flier/Grünwald/PRI
00Ip5
2000
Mexico
NA
Fernández Pavia
Ipom1-2
1999
Mexico
NA
Flier/Grünwald/PRI
Ipom2-1
1999
Mexico
NA
Flier/Grünwald/PRI
PoMX04
Ipom2-4
1999
Mexico
NA
Flier/Grünwald/PRI
PoMX05
Ipom3-3
1999
Mexico
NA
Flier/Grünwald/PRI
Ipom6
1999
Mexico
NA
Flier/Grünwald/PRI
P. ipomoeae
1999
Mexico
NA
Fernández Pavia
PaEC01
EC_3189
1998
Ecuador
Anarrichomenum
Forbes
PaEC02
EC_3399
2001
Ecuador
Anarrichomenum
Cooke
EC_3818
2004
Ecuador
Anarrichomenum
Cooke
EC_3821
2004
Ecuador
Anarrichomenum
Forbes
PaEC05
EC_3780
2004
Ecuador
S. hispidum
Forbes
PaEC06
EC_3655
2003
Ecuador
S. hispidum
Forbes
PmMX09
PmMX10
PmMX11
P. ipomoeae
PoMX01
PoMX02
PoMX03
PoMX06
PoMX07
P. andina
PaEC03
PaEC04
!
8!
EC_3163
1998
Ecuador
Anarrichomenum
Forbes
PaEC08
EC_3510
2002
Ecuador
S. betaceum
Forbes
PaEC09
EC_3540
2002
Ecuador
Anarrichomenum
Forbes
EC_3561
2002
Ecuador
S. quitoense
Forbes
EC_3563
2002
Ecuador
S. quitoense
Forbes
PaEC12
EC_3678
2003
Ecuador
Anarrichomenum
Forbes
PaEC13
EC_3836
2004
Ecuador
S. betaceum
Forbes
EC_3860
2005
Ecuador
Torva
Forbes
EC_3864
2005
Ecuador
Torva
Forbes
PaEC16
EC_3865
2005
Ecuador
S. jugandifolium
Forbes
PaEC17
EC_3936
2006
Ecuador
S. ochanthum
Forbes
POX 102
2003
Peru
S. betaceum
Forbes
POX 103
2003
Peru
S. betaceum
Forbes
PaEC07
PaEC10
PaEC11
PaEC14
PaEC15
PaPE01
PaPE02
P. phaseoli
PpUS01
CBS 556.88
CBS
PpUS02
P10150
USA
Delaware
Coffey
1
Isolates were contributed by the authors and the following colleagues: Sampled by W. G. Flier and N. J. Grünwald and curated by Geert Kessel, Plant Research
International (PRI), Netherlands; Geert Kessel, Plant Research International (PRI), Netherlands; Silvia Fernández Pavia, Universidad Michoacana de San Nicolás
de Hidalgo, Mexico; Michael Coffey, University of California Riverside, USA; Vihn Hong Le and Arne Hermansen, Norwegian Institute for Agricultural and
Environmental Research, Norway; Björn Andersson, Swedish University of Agricultural Sciences, Sweden; Renata Lebecka Młochow Research Centre, Poland;
Jozsef Bakonyi, Academy of Agricultural Sciences, Hungary.
!
9!
Table S2. Molecular clock and mutation rates obtained in this study for each locus for (A) Clade
1c and (B) P. infestans datasets. See Table S3 for indices of nucleotide variation at each locus.
A. Clade 1c
Locus
β-tubulin
RAS
Trp1
PITG_11126
Clock
Strict
Log Normal
Strict
Strict
Clock Rate
0.824
1.839
1.73
4.09
UCLD stdev
0.04
2.2
0.03
0.02
B. P. infestans
Locus
β-tubulin
RAS
Trp1
PITG_11126
Clock
Strict
Log Normal
Strict
Strict
Clock Rate
0.54
2.25
1.73
3.03
UCLD stdev
0.02
1.94
0.012
0.01
10 Table S3. Nucleotide variation by locus, species, and sampling location. Statistics given are
number of individuals (Nind), number of sequences (Nseq), length of alignment excluding gaps
(L), segregating sites (S), number of heterozygous sites (Het), number of haplotypes (Hap),
average pairwise nucleotide diversity (π), Watterson’s theta (θw), Tajima’s D, and Fu and Li’s
D* and F* (4-7).
Locus
Species/Popn
Nind
Nseq
L
S
Het
Hap
π
θW
Tajima’s
D
Fu &
Li’s
D*
Fu &
Li’s F*
P. infestans
Europe
Mexico
S. America
United States
Africa/Asia
P. andina
P. ipomoeae
P. mirabilis
P. phaseoli
119
22
48
40
4
5
19
7
11
2
242
46
96
82
8
10
38
14
22
4
764
764
764
764
779
779
748
787
778
779
13
7
9
11
2
3
16
2
11
0
13#
7#
9#
11#
2
3
16#
1
11
0
10
5
6
8
2
2
3
3
3
1
0.00286
0.00294
0.00154
0.00394
0.00138
0.00214
0.01040
0.00052
0.00593
0
2.144
1.593
1.752
2.210
0.771
1.060
3.808
0.629
4.610
0
0.04
1.10
-0.82
0.97
1.45
2.06*
3.39***
-0.96
1.83
NA
0.79
1.25
-0.17
0.79
1.11
1.15
1.58**
-0.45
1.44*
NA
0.61
1.41
-0.47
1.01
1.30
1.53
2.56**
-0.66
1.80**
NA
P. infestans
Europe
Mexico
S. America
United States
Africa/Asia
P. andina
P. ipomoeae
P. mirabilis
P. phaseoli
118
22
48
39
4
5
19
7
11
2
238
44
96
80
8
10
38
14
22
4
1590
1590
1590
1590
1590
1590
1590
1590
1590
1590
9
6
7
9
5
0
23
2
16
0
9#
6#
7#
9#
5#
0
23
2
15#
0
8
3
3
7
3
1
2
2
6
1
0.00138
0.00061
0.00185
0.00113
0.00124
0
0.00743
0.00018
0.00469
0
1.488
1.379
1.363
1.817
1.928
0
5.474
0.629
4.389
0
1.06
-0.79
2.75**
-0.03
0.08
NA
3.92***
-1.48
2.54**
NA
-0.43
1.18
1.20
-0.84
0.75
NA
1.70**
-1.83
1.54**
NA
0.13
0.67
2.03**
-0.67
0.65
NA
2.89**
-1.97
2.14**
NA
P. infestans
Europe
Mexico
S. America
United States
Africa/Asia
P. andina
P. ipomoeae
P. mirabilis
P. phaseoli
117
22
48
38
4
5
19
7
11
2
234
44
96
76
8
10
38
14
22
4
813
813
813
813
813
813
813
812
813
813
9
4
6
6
4
3
10
0
1
0
7
3
4
6
4
3
10
0
1
0
9
4
5
6
4
2
3
1
2
1
0.00183
0.00185
0.00144
0.00211
0.00180
0.00205
0.00293
0
0.00011
0
1.492
0.920
1.168
1.224
1.543
1.060
2.380
0
0.274
0
-0.004
1.48
-0.20
0.95
-0.22
2.06*
3.48***
NA
-1.16
NA
0.42
-0.06
1.12
0.22
-0.18
1.15
1.40*
NA
-1.57
NA
0.32
0.47
0.81
0.54
-0.21
1.53
2.42**
NA
-1.68
NA
P. infestans
Europe
Mexico
S. America
United States
Africa/Asia
P. andina
P. ipomoeae
P. mirabilis
P. phaseoli
117
21
47
40
4
5
17
7
10
1
234
42
94
80
8
10
34
14
20
2
762
766
766
762
766
766
765
768
766
764
15
10
11
10
11
1
23
3
6
0
15#
10
11#
10
11
1
23#
0
6#
0
13
6
8
5
4
2
4
2
3
1
0.00364
0.00569
0.00164
0.00377
0.00643
0.00205
0.01433
0.00103
0.00091
0
2.487
2.324
2.150
2.019
4.242
1.060
5.625
0.943
1.973
0
0.290
2.585*
-1.09
1.12
0.808
2.06*
3.28***
-0.49
-2.13*
NA
0.311
1.40
-2.51*
1.38
1.52**
1.15
1.39
1.07
-3.08**
NA
0.364
2.096**
-2.39*
1.53
1.50
1.53
2.37**
0.76
-3.25**
NA
PITG_11126
β-tubulin
Trp1
RAS
!
11!
#
Also heterozygous for one or more indel.
* P < 0.05
** P < 0.02
*** P < 0.001
!
12!
Table S4. Results from testing relationships among Toluca population, US1 and Andean
lineages as illustrated in Figure S10.
Andean lineage
PE3
PE7
EC1
!
Scenario
1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
Admixed population
PE3
Toluca
US1
PE3
PE3
US1
US1
Toluca
Toluca
PE3
US1
Toluca
PE7
Toluca
US1
PE7
PE7
US1
US1
Toluca
Toluca
PE7
US1
Toluca
EC1
Toluca
US1
EC1
EC1
US1
US1
Toluca
Toluca
EC1
US1
Toluca
Probability
0.0040
0.0071
0.0066
0.0014
0.0062
0.0009
0.6709
0.1094
0.0023
0.0052
0.0020
0.1302
0.0474
0.0011
0.0053
0.0089
0.0327
0.0141
0.0038
0.0093
0.0191
0.3656
0.2893
0.0016
0.0248
0.0121
0.0880
0.1242
0.0012
0.0050
0.2524
0.0293
0.0575
0.0908
0.0843
0.0216
0.0320
0.3060
0.0071
0.0234
0.0177
0.0140
0.0088
0.0517
0.0035
13!
95% CI
[0.0028,0.0052]
[0.0058,0.0084]
[0.0055,0.0077]
[0.0010,0.0017]
[0.0051,0.0073]
[0.0008,0.0011]
[0.6478,0.6939]
[0.0994,0.1194]
[0.0011,0.0034]
[0.0034,0.0070]
[0.0009,0.0032]
[0.1093,0.1511]
[0.0410,0.0537]
[0.0004,0.0017]
[0.0034,0.0073]
[0.0055,0.0124]
[0.0265,0.0389]
[0.0107,0.0176]
[0.0025,0.0051]
[0.0073,0.0112]
[0.0148,0.0234]
[0.3393,0.3919]
[0.2656,0.3131]
[0.0003,0.0030]
[0.0145,0.0350]
[0.0032,0.0211]
[0.0673,0.1087]
[0.1069,0.1416]
[0.0003,0.0022]
[0.0021,0.0079]
[0.2335,0.2713]
[0.0260,0.0326]
[0.0519,0.0631]
[0.0830,0.0987]
[0.0773,0.0913]
[0.0192,0.0239]
[0.0276,0.0364]
[0.2811,0.3309]
[0.0053,0.0088]
[0.0188,0.0280]
[0.0144,0.0210]
[0.0116,0.0163]
[0.0069,0.0106]
[0.0420,0.0614]
[0.0026,0.0043]
Table S5. Nucleotide substitution model for each locus as inferred from jModelTest and
ModelGenerator. The appropriate most similar model available in BEAST was used for each
analysis.
A. Clade 1c
Locus
β-tubulin
RAS
Trp1
PITG_11126
jModelTest
HKY
JC
K80
HKY
ModelGenerator
HKY
JC
HKY
HKY
Model Used
HKY
JC
HKY
HKY
B. P. infestans
Locus
β-tubulin
RAS
Trp1
PITG_11126
jModelTest
HKY
F81
HKY
HKY
ModelGenerator
HKY
JC
HKY
HKY
Model Used
HKY
JC
HKY
HKY
!
14!
Table S6. Settings used for DIYABC analyses. All runs used the same summary statistics:
within population statistics were number of segregating sites, mean of pairwise differences,
variance of pairwise differences, and number of private segregating sites; between population
statistics were number of segregating sites, mean of pairwise differences, and FST. Posterior
probabilities of scenarios were calculated using the closest 1% of simulated datasets using
logistic regression.
A. Prior distributions for scenarios in Figure S9.
Parameter
Population size
EC-1
PE-3
PE-7
Ancestor of two lineages
Ancestor of three lineages
Shape
Min.–Max.
Increment
Uniform
Uniform
Uniform
Uniform
Uniform
1–200000
1–200000
1–200000
1–500000
1–1000000
1
1
1
1
1
Time since divergence1
t1: two lineages
t2: all three lineages
Uniform
Uniform
1–300000
1–500000
1
1
Nucleotide sequence evolution2
Mean mutation rate
Uniform
1.00×10-10 –
1.00×10-8
Gamma distribution
Uniform
1.00×10-11 –
2.00
1.00×10-7
1
An additional condition was put on the prior distributions such that t2>t1.
2
The Kimura 2-parameter nucleotide substitution model was used with invariant sites=90 and gamma rate variation
parameter α=0.050.
B. Prior distributions for scenarios in Figure S10.
Parameter
Population size
Toluca
EC-1
PE-3
PE-7
US-1
Unsampled population
Ancestor of two lineages
Time since divergence3
t1: two populations (scenarios 1-3)
t2: two or three populations
t3: sampled & unsampled populations
(scenarios 7-15)
Admixture events
Proportion from parent population
ta1: timing since admixture event
(scenarios 4-12)
ta2: timing since admixture event
(scenarios 13-15)
!
Shape
Min.–Max.
Increment
Uniform
Uniform
Uniform
Uniform
Uniform
Uniform
Uniform
1–1000000
1–300000
1–200000
1–200000
1–500000
1–2000000
1–2000000
1
1
1
1
1
1
1
Uniform
Uniform
Uniform
1–200000
1–500000
1–10000000
1
1
1
Uniform
Uniform
0.001–0.999
1–300000
0.001
1
Uniform
1–1000000
1
15!
Nucleotide sequence evolution4
Mean mutation rate
1.00×10-10 –
1.00×10-8
Gamma distribution
Uniform
1.00×10-11 –
2.00
1.00×10-7
3
Additional conditions were put on the prior distributions to force the timing of events into the tree structure shown
in Figure S9, including placing admixture events before or after population splits and ordering of the population
splits such that t2>t1, t2>ta1, t3>ta1, ta2>t2, and t3>ta2.
4
The Kimura 2-parameter nucleotide substitution model was used with invariant sites=90 and gamma rate variation
parameter α=0.050.
Uniform
C. Prior distributions for scenarios in Figure 5.
Parameter
Population size
Toluca
EC-1
PE-3
US-1
Unsampled population
Ancestor to Toluca & EC-1
Ancestor to Toluca & US-1
Shape
Min.–Max.
Increment
Uniform
Uniform
Uniform
Uniform
Uniform
Uniform
Uniform
1–1000000
1–400000
1–200000
1–400000
1–1000000
10–1000000
10–1000000
1
1
1
1
1
1
1
Time since divergence5
t1: Toluca–EC-1
t2: Toluca–US-1
t3: All populations
Uniform
Uniform
Uniform
1–200000
1–600000
1–1000000
1
1
1
Admixture events
Proportion from parent population
Timing since admixture event
Uniform
Uniform
0.001–0.999
1–200000
0.001
1
Nucleotide sequence evolution6
Mean mutation rate
Uniform
1.00×10-10 –
1.00×10-8
Gamma distribution
Uniform
1.00×10-11 –
2.00
1.00×10-7
5
Additional conditions were put on the prior distributions to force the timing of events into the tree structure shown
in Figure 5, including placing admixture events before or after population splits and ordering of the population splits
such that t3>t1, t3>t2.
6
The Kimura 2-parameter nucleotide substitution model was used with invariant sites=90 and gamma rate variation
parameter α=0.050.
!
16!
Table S7. Inferred root subpopulation using three starting seeds for (A) the mitochondrial P3 and
P4 regions using only isolates from Mexico and the Andes, and (B) the nuclear RAS locus, using
the data from Gómez-Alpizar et al. (1).
A. P3 and P4
Theta
Migration
1.8
0.3, 0.3
1.0, 1.0
5.0, 5.0
10.0, 10.0
1.0, 1.0
5.0, 5.0
10.0, 10.0
2.0
Seed 1
Root
location
Mexico
Andes
Mexico
Mexico
Andes
Andes
Andes
Seed 2
Prob. Root
location
0.505 Mexico
0.501 Andes
0.559 Mexico
0.587 Mexico
0.504 Andes
0.513 Andes
0.689 Mexico
Prob.
0.500
0.505
0.556
0.577
0.501
0.531
0.727
Seed 3
Root
location
Andes
Mexico
Mexico
Andes
Mexico
Andes
Andes
Prob.
0.501
0.508
0.510
0.669
0.503
0.562
0.549
B. RAS
Seed 1
Seed 2
Root
Prob. Root
location
location
2.0
0.5, 0.5
SA
0.515 NSA
5.0, 5.0
SA
0.514 SA
10.0, 10.0
NSA
0.889 NSA
5.0, 10.0
SA
0.916 SA
10.0, 5.0
NSA
0.679 NSA
4.3, 14.6 * SA
0.965 SA
14.6, 4.3
NSA
0.939 NSA
* Migration rates used by Gómez-Alpizar et al. (1)
Theta
!
Migration
17!
Prob.
0.537
0.582
0.875
0.949
0.902
0.992
0.996
Seed 3
Root
location
SA
SA
SA
SA
SA
SA
NSA
Prob.
0.535
0.847
0.686
0.985
0.935
0.970
0.979
Table S8. Root population inferred using RAS sequences from Mexico and Andean samples
from this study. Migration rates were symmetric for all runs.
Simulations
θ
M
1.5
0.5
5.0
10.0
2.0
0.5
5.0
10.0
!
Seed 1
1×106
Root
Mexico
Mexico
Andes
Andes
Mexico
Mexico
Prob.
0.541
0.638
0.723
0.676
0.883
0.714
Seed 2
1×106
Root
Mexico
Mexico
Mexico
Andes
Andes
Andes
Prob.
0.584
0.703
0.975
0.638
0.614
0.688
18!
Seed 3
1×107
Root
Andes
Mexico
Mexico
Mexico
Mexico
Mexico
Prob.
0.510
0.564
0.612
0.513
0.590
0.663
Seed 4
1×107
Root
Mexico
Mexico
Andes
Mexico
Andes
Mexico
Prob.
0.521
0.583
0.794
0.514
0.794
0.939
Supporting Figures
Figure S1. Structure plots for K from 2 to 10 for the Andes (with and without admixture) and
Mexico samples of P. infestans.
Figure S2. Delta K values obtained from Structure Harvester for (A) Mexico and (B) Andes
(with admixture) samples of P. infestans. Note the highest delta K value corresponds to K=4 for
Mexico and K=2 for the Andes.
Figure S3. Root state posterior probabilities for each location for (A) Clade 1c and (B) P.
infestans. Independent analysis of each locus produced high probabilities for the root of both
Clade 1c and P. infestans in Mexico (green bar).
Figure S4. Maximum clade credibility genealogy for the β-tubulin locus. Colors of branches
indicate the most probable geographic origin of each lineage.
Figure S5. Maximum clade credibility genealogy for the PITG_11126 locus. Colors of branches
indicate the most probable geographic origin of each lineage.
Figure S6. Maximum clade credibility genealogy for the RAS locus. Colors of branches indicate
the most probable geographic origin of each lineage.
Figure S7. Maximum clade credibility genealogy for the Trp1 locus. Colors of branches
indicate the most probable geographic origin of each lineage.
Figure S8. Maximum clade credibility phylogeny of Phytophthora Clade 1c from all four loci.
Colors of branches indicate the most probable geographic origin of each lineage and taxon colors
represent species (purple: P. phaseoli; blue: P. ipomoeae; green: P. mirabilis; red: P. andina;
black: P. infestans).
Figure S9. Scenarios used to test evolutionary relationships among Andes lineages EC-1, PE-3,
and PE-7 using DIYABC. Present day populations are at the base of the tree schematic.
Ancestral relationships among these populations are represented by lines intersecting in the past,
with the vertex of the schematic representing the most recent common ancestor of all samples.
Horizontal lines indicate admixture events between the ancestral populations connected by the
horizontal line. Change in line thickness indicates a potential change in population size, such that
all branches in scenarios D, E, and F had independently estimated population sizes. The
scenarios in which PE-3 and PE-7 diverged more recently from each other than from EC-1
produced high posterior probabilities.
Figure S10. Scenarios used to test evolutionary relationships of EC-1, PE-3, and PE-7 lineages
to US-1 in the Andes and to the Toluca, Mexico population. The 15 scenarios were compared
against each other, using three independent sets of scenarios with EC-1, PE-3, and PE-7, in turn,
substituted for population ‘X’. Present day populations are at the base of the tree schematic.
Ancestral relationships among these populations are represented by lines intersecting in the past,
with the vertex of the schematic representing the most recent common ancestor of all samples.
!
19!
Horizontal lines indicate admixture events between the ancestral populations connected by the
horizontal line. Potential changes in population size over time are indicated by changes in line
thickness, but line thickness is not proportional to population size. The dashed line represents an
unsampled population that has contributed to the genetic variation observed in sampled
populations.
!
20!
A. Andes (No admixture model)
B. Andes (Admixture model)
C. Mexico (Admixture model)
A. Mexico
B. Andes
Posterior Probability of Root State
A) Clade 1c
B-tubulin
Trp1
PITG_11126
RAS/iRAS
CO EC ES HU MX NL PE PO SA SW UK USA VT
CO EC ES HU MX NL PE PO SA SW UK USA VT
CO EC ES HU MX NL PE PO SA SW UK USA VT
CO EC ES HU MX NL PE PO SA SW UK USA VT
B-tubulin
Trp1
PITG_11126
RAS/iRAS
CO EC ES HU MX NL PE PO SA SW UK USA VT
CO EC ES HU MX NL PE PO SA SW UK USA VT
CO EC ES HU MX NL PE PO SA SW UK USA VT
CO EC ES HU MX NL PE PO SA SW UK USA VT
0.8
0.6
0.4
0.2
0.0
Posterior Probability of Root State
B) P. infestans
0.8
0.6
0.4
0.2
0.0
Location (Country)
Figure S3. Root state posterior probability values for each location after 300 millions MCMC generations
by locus for (A) Clade 1c species and (B) P. infestans. The posterior probability for a Mexico root (green
bar) is higher than for any of the other countries for each locus independently and both datasets.
Figure S4. Maximum clade credibility genealogy for the β-tubulin locus. Colors of
branches indicate the most probable geographic origin of each lineage.
location.states
Colombia
Ecuador
Estonia
Hungary
Mexico
Netherlands
South Africa
Sweden
United Kingdom
United States
Vietnam
9a b
E2 50
PiP iMX 01b b
P iES 16 b
P iMX 64 b
P iMX 02
P iMX 18b
P iMX 72b
P iMX 42a
P X 1b
PiM X1 0b
PiM X4 1b
PiM X4 9b
PiM X2 8b
PiM X4 b
PiM X19
PiM E02b
PiP E09b
PiP E08b
PiP E05b
PiP E04b
PiP O01b
PiC O03b
PiC 02b
PiCO 04b
PiCO 03b
PiEC 02b
PiEC 07b
PiMX 2b
4
PiMX 1b
PiMX7 b
X
iM
P 06 b
PiMX15
PiMX10b
PiMX49b
PiUK10b
PiMX19a
M
X
US
MX
PpUS01b
PpUS02a
PpUS01a
PpUS02b
PmMX02b
PmMX02a
PmMX03b
PmMX06b
PmMX0
9a
PmMX01
PmMX b
PmMX 09b
PmM 01a
X
PaPE 06a
PaPE 02b
PaEC 01b
PaE 09b
PaE C15b
EC
PaE C13b
PaE C08b
PaE C02b
PaE C16b
PaE C12b
Pa C04b
PaEEC11b
Pa C14
Pa EC01 b
Pa EC03 b
E
Pa C0 b
Pa EC1 6b
Pa EC0 7b
M
Pa EC 7b
P EC 05b
X
P mM 10b
PmmM X04
P M X1 b
P mM X1 0b
P mM X1 1b
Pm mM X0 0a
Pm M X0 4a
M X12 5b
X0 a
5a
MX
P
Pi iMX
P MX 16
PiMiMX 26b a
P X 23a
PiMiMX 25a
PiM X4 03a
PiM X4 3a
PiM X4 0a
PiM X0 3b
PiM X0 5a
PiM X4 4a
5
PiM X44 a
PiM X44 b
PiM X17b a
PiM X29a
PiM X10a
PiM X47b
PiM X12a
X
PiES 15a
PiES 05a
0
PiES 2b
PiES 03a
PiES 01a
0
PiES 4b
0
PiES 4a
PiMX 02a
6
PiMX 7b
61
PiEC0 a
6b
PiEC11
a
PiEC12a
PaEC03a
PaEC15a
PiES05b
PiES03b
PiPO01b
PiUK01b
P iU K 0 8 b
P iU K 0 9 b
0.04 substitutions per site
MX
2b
X1 a
M X11 3a
Pm M X0 b
Pm mM X03 a
P oM X03 a
P oM X04 a
P M 01
Po oMX 06a
P oMX 06b
P MX 04b
Po MX 2a
Po MX0 02b
Po MX 5b
Po X0 1b
M
Po MX0 8a
Po M X0 a
Po X05 8b
PoMM X0
Po S11b
PiU O05c
PiC X01b
PiM X06a
PiM X30b
PiM X71a
PiM 24b
PiMX 05b
PiCO 63b
PiMX 8b
0
PiUS 3a
6
PiMX 1b
PiMX6 a
PiMX30 a
PiMX66
PiMX62a
PiMX72a
PiMX62b
PiMX21b
PiMX66b
PiMX18a
PiMX65b
P iM X 0 2 a
PiCO01c
P
Pa iEC
Pi EC 11b
PiN NL0 09a
P L 1b
P iNL 02a
PiM iNL 01a
PiM X2 02b
PiM X0 8b
PiM X4 4b
PiM X6 7a
5
PiU X28 a
PiU K05 a
PiU K03 b
a
PiU K07b
PiU K10a
PiU K09a
PiU K01a
PiU K08a
PiU K05a
K
PiU 02b
K
PiUK 06a
0
PiUK 7a
PiUK 02a
PiUK 04b
0
PiUK 3b
0
PiUK 4a
06b
PiPO0
1
PiPO0 a
2
PiPO02 a
b
PiUS08
a
PiUS17a
PiUS17b
PiUS12a
PiUS11a
PiUS12b
PiCO05a
PiCO01a
PiCO03a
PiCO02a
PiCO04a
PiMX07a
PiMX26a
PiMX27a
PiMX13a
PiMX25b
PiMX01a
PiMX13b
b
PiMX12 a
PiVT03
4b
PiVT0 b
3
PiVT0 2a
PiVT0 1a
0
T
iV
P
01b
PiVT 04a
PiVT 02b
iV
P T 20b
X
PiM X41a
PiM X22a
PiM X23b
PiM X46a
PiM X05b
PiM X46b
PiM X03b a
PiM X14 a
PiM X20 b
PiM X45 a
1
PiM X1 4a
PiM X2 7b
PiM X2 4b
PiMMX1 17a
Pi iMX 21a
P X 67a
PiM X 50a
PiMiMX 22b a
P MX 49 a
Pi iMX 48
P iMX
P
PiPE29b
P iP E 1 0 a
P iP E 1 1 a
PiPE28b
PiPE24a
PiPE20b
PiPE14b
PiPE22a
PiPE23a
PiSW02
PiSW02 b
PiSW0 a
PiPE1 1b
PiPE2 3b
PiPE 5a
2
PiPE 7a
PiPE 04a
PiPE 10b
PiPE 12b
PiSW14a
PaP 01a
PiP E01a
PiP E28a
PiP E20a
PiP E09a
PiM E23b
PiP X64
PiP E24 a
PiP E12 b
Pa E01 a
PiP PE0 a
PiP E2 2a
P E0 6b
PiPiPE2 5a
P E 6a
P iPE 25b
P iPE 27b
PiP iPE0 11b
P E 7
Pi iPE0 06b a
PE 2
01 a
b
Poland
P iP E 2 1 a
P iP E 2 1 b
PiPE22b
PiPE08a
PiSA01b
PiSA01a
PiPE06a
PiPE13a
b
PiPE07
a
PiEC02
0b
PiEC1 a
17
PaEC 6a
1
PaEC 08a
PiEC 2a
0
PaEC 02a
PiHU 02b
PiHU 06a
C a
PaE
C01
PaE C10a
PiE 13a
C
PiE 12a
C
PaE C05a
PaE C13b
PiE C04a
b
PaE C14 a
PiE C07
PiE C07a a
E
Pa EC10 4a
Pa C1 a
PiE C08 3a
E
Pa iEC0 7b
P C0 8b
PiE C0 3a
PiE EC1 06a
Pa C 1a
PiE EC1 14a
Pa aEC 12b
P iEC
P
Peru
Figure S5. Maximum clade credibility genealogy for the PITG_11126 locus. Colors of
branches indicate the most probable geographic origin of each lineage.
location.states
Colombia
Ecuador
Estonia
Hungary
Mexico
Netherlands
Peru
MX
3a
X0 2a
M X0 4a
o
M
P o X0 3b
P oM X0 6a
P oM X0 5b
P oM X0 2b
P oM X0 1b
P oM X0 b
P oM X 0 8 8a
0 a
P oM
P MX X05 b
Po mM X05 a
P M 03
m
P MX 07a
Pm MX 01a
Pm MX 06a
Pm MX 3b
Pm MX0 4a
Pm MX0 6b
Pm MX0 2b
Pm MX1 b
Pm MX07 a
Pm MX12
Pm MX02a
Pm X11a
M
Pm X01b
PmM X09b
PmM X10a
PmM X04b
PmM 11b
X
PmM 10b
X
PmM 09a
M
Pm X 2b
0
PmMX
Pp US 01 b
a
S02
PpU
PpUS 02b
PpUS01 a
US
PaEC04b
PaEC07b
PaEC06b
PaEC02b
PaEC11b
PaEC01b
PaEC16b
PaEC17
b
PaPE02
PaEC12 b
b
PaEC
1
PaEC 0b
PaEC 15b
PaEC 09b
PaE 05b
C
PaE 14b
PaP C03b
PaE E01b
PaE C08b
PiP C13b
PiP E12b
PiP E09b
PiP E04b
PiP E01b
PiP E08
PiP E13 b
PiP E03 b
P i E0 b
P i E C 0 2b
Pi EC0 1b
P i EC0 3b
P U K 2b
P iCO 09b
Pi iUK 01b
0
U
P
K 5
P iCO 01 b
Pi iCO 04 b
b
C
0
P
O 3
P iS 0 b
P iS W0 2b
Pi iES W 0 1 b
ES 0 2 b
02 2a
b
EC
MX
b
14 1b
PE 1 b
Pi E 05 b
P
Pi iPE X 2 7 2 b
P iM X6 b
P
49 b
M
Pi iMX 05 b
P iCO 02
P O 04b
P
Pi i U K 08c
P UK 03b
Pi UK 0b
Pi UK1 7b
Pi US1 1b
Pi US1 2b
Pi S1 a
PiUN L 0 2 b
Pi L02 b
PiN U02 b
PiH X42
PiM X26a
P iM X 2 6 b
P iM X 1 1 b
P iM X 4 8 b
P iM X 2 5 b
P iM X 1 1 a
P iM X 1 7 a
P iM 4 0 b
P iM X 1 7 b
P iM X 2 3 b
P iM X
61b
P iM X 4 b
P iM X 6 a
P iM X 28
b
P iM X 41
Pi M X1 6b
Pi MX 25 a
PiM X1 3b
PiM X20 b
PiM X65 b
PiMX18b
PiMX14b
P
P iM
P iM X3
Pi iMX X50 0a
M
P
X 04 a
P iMX 21 a
Pi iMX 41 a
a
M
Pi X 4 6 2 a
P i PE 2 a
P i M X 22a
0
M
5
Pi X6 a
Pi MX1 5a
Pi MX1 2b
M
PiM X0 5b
PiM X4 4b
PiM X40 4a
PiM X66 a
PiM X63 a
a
PiE X 2 0 a
PiE C10b
PiE C11b
P iV C06b
P iV T 0 2 b
T
P iV 0 3 b
T
P iS 0 1 b
A01
b
P iV T
PiPE 0 4 b
P iM X 23b
64a
PiPE
2
PiPE2 2b
1
PiPE2 b
4
PiEC14 b
b
PiEC12
b
PiEC13b
PiPE25b
PiPE20b
PiPE27b
PiM X50 b
PiMX16a
PiMX19b
PiMX28b
P
P iEC
P i V T 07
Pi iVT 02 a
P VT 01 a
P iPE 0 4 a
P iPE 14 a
Pa iPE 21a a
2
Pi PE0 3a
Pi PE1 2a
P i PE2 4c
P i U K 0 0a
U
PiP K 1 6 c
PiP E27 0 a
P i U E24 a
PiU K05 a
PiU K04 a
PiE K02 a
a
PiU S01b
P iS K 0 3 a
W
P iN 0 1 a
P iN L 0 1 a
PiU L 0 1 b
S
PiU 08 a
S
PiU 12 a
S
PiU S 17 a
P iU S 11 a
0
PiES 8 b
0
P iU K 1a
0
PiPO 8 a
0
P iC O 0 1b
4
P iC O 03 a
a
P iC O 02
a
Pi CO 01 a
Pi SW 02 a
PiES05b
PiPE03a
PiPE10a
PiPE09a
PiPE26a
PiPE04a
PiPE07a
PiPE28a
PiPE02a
PiPE06a
PiEC02a
PiEC01a
Pi UK 06 a
a
P iU K 09
a
PiPE29 a
5
PiPE0 a
8
0
E
PiP 6 a
0
P iM X 0 6 b
P iM X 0 7 b
P iM X 0 7 a
X
P iM 0 5 b
X
P iM 2 4 b
X
P iM X 7 1 b
P iM X 2 2 b
a
iM
P
X46
P iM X 2 4 a
P iM X 1 3 a
a
PiM X45 b
PiM X47 a
PiM X43 a
PiM X49 3a
PiM X2 2b
PiM X7 3b
M
Pi MX4 1a
Pi MX7 7b
Pi MX6 14a
Pi MX 27a
Pi MX 21b b
Pi MX 10 a
Pi iMX 15 b
P iMX 29 b
P iMX 03 9a
P iMX X1 2a
P iM X1
P iM
P
X
Vietnam
M
United States
PiEC10a
PaEC03a
PiPE11a
PiPE25a
PiS A01 a
PaEC07a
Pi VT 03 a
PiES04a
PiES03
a
PiES05
P iC O 0 a
5
a
PiPO
0
PiPO 1a
PiEC 02a
PiEC 13a
PaP 0 6 a
E
P iM 01a
P iM X 6 7 a
P iM X 0 3 a
P iM X 0 2 a
P iM X 3 0 b
P iM X 4 4 b
PiM X22a
PiM X10
PiM X18 a
PiM X46 a
Pi X4 b
P i MM X 6 8 a
Pi X0 3b
Pi MX2 1b
Pi M X 9 a
Pi PE1 4 5 b
P PE 3a
P iPE 12a
P i M X 01a
Pi iMX 01
P M 72 a
P iM X6 a
P oM X4 6b
Po oM X0 7a
Po M X0 6b
M X0 5a
X0 4
1a b
United Kingdom
X
Sweden
M
South Africa
PaEC06a
PaEC16a
PaEC10a
PaEC04a
PiEC14a
PaEC01a
PiEC03a
a
PaEC11 a
PaEC02 a
15
PaEC 1a
1
PiEC 8b
0
PiEC 8a
0
PiEC 7b
0
PiEC 17a
C
PaE 12a
C
PaE C09a
PaE C13a
PaE 05a
C
PaE C12a
PiE C14a
a
E
Pa C08 c
E
Pa EC02 b
Pi X 0 2 a
PiM X61 b
P i M PE06 0b
Pi E1 b
PiP 29 6b
E
PiP PE2 3b
Pi S0 7 b
E 0 a
Pi
UK 7
P i UK0 04b
Pi iES 0 2 a
P U 02b
H
a
Pi iUK 01 b
P iUK 08 b
P UK 06 b
P i i U K 28 7b
P iPE E0
P iP
P
Poland
2.0E-4 substitutions per site
Figure S6. Maximum clade credibility genealogy for the RAS locus. Colors of
branches indicate the most probable geographic origin of each lineage.
location.states
Colombia
Ecuador
Estonia
Hungary
Mexico
United States
Vietnam
PiPE25a
PiPE12a
PiPE27a
PiUK01a
PiPE22a
PiPE23a
PiPE14
a
PiMX02
a
PiMX28
a
PiMX
15a
PiMX
41a
PiMX
24
PiMX a
06a
PiPE
24
PiPE a
03
PiPE a
05a
PiP
E0
PiP 2a
E0
PiM 9a
X43
PiM
b
X
PiM 66b
X
PiM 44a
X4
PiM
5b
PiM X44b
PiM X14b
PiM X42a
PiM X45
a
PiM X43
a
PiM X41
PiM X04 b
PiM X1 b
2
PiM X4 b
PiM X2 2b
PiM X0 5a
3
X4 b
6a
United Kingdom
PiPE21a
Sweden
PiPE01a
South Africa
PiVT01a
PiVT02a
PiVT03a
PiVT04a
Poland
PiNL02a
PiEC10a
7a
PiMX1
a
PiMX21
a
PiMX01
a
PiES01
06a
PiEC
13a
PiEC
11a
PiEC
14a
PiEC a
X64
PiM 2a
X1
PiM
b
X06
PiM 19a
X
PiM 03a
X
PiM 48a
X
PiM 61a
X
PiM 28b
X
PiM 11a
X
PiM 20b
X
PiM X62a
PiM X07b
a
PiM X13
a
PiM X40
b
PiM X19 b
1
PiM O0 a
PiP O01 b
PiP C13 a
7
PiE C0 a
E
3
Pa C0
PiE
Peru
PiPE13a
PiPE11a
PiPE20a
Netherlands
6b
X4 9b
PiM X4 a
2
PiM S1 5b
PiU X6 a
2
PiM W0
a
PiS E08
b
PiP E04
b
PiP X18
a
PiM X47
b
PiM X25
PiM X11b
PiM X48b
PiM 08b
C
PiE 11a
C
PaE 03a
C
PaE 02a
C
PaE 10a
C
PaE 01a
C
PaE 3b
0
PiEC 4a
C0
PaE
02a
PiPO b
03
PiCO
02b
PiEC
01b
PiEC
02a
PiCO
1a
PiNL0
a
PiUK05
a
PiCO04
b
01
PiCO
PiMX16b
Pa
Pa EC1
3
E
PiE C1 a
2
C
PiE 06 a
Pa C01 b
EC
a
Pa
E 06
PiM C09 a
a
PiM X05
a
X
PiM 67
b
PiM X07a
X
PiE 22a
C0
Pa
EC 2a
PiM 05a
X
PiM 16a
X1
3b
PiM
X
PiM 21b
X2
PaE 6b
C15
PiEC a
1
PiEC 2a
11
PiEC b
08a
PaE
C14
PiEC a
12b
PiMX
30a
PiUS
08a
PiUS
12b
PiMX0
2b
PiMX14
a
PiMX2
0a
PiMX29a
PiMX01b
PiUK09a
PiUK07a
PiUK02a
PiMX63b
PiMX29b
PiMX27a
PiMX40b
PiMX47b
PiUK10b
PiEC14b
PiEC10b
US
MX
PaEC08a
PiPE06a
PiPE20b
PiPE07a
PoMX07a
PoMX01a
PoMX04a
PoMX05a
PoMX01
b
PoMX0
3a
PoMX0
4b
PoMX
06b
PoMX
03b
PoMX
05b
PoM
X06a
PoM
X02b
PoM
X02a
PaE
C12
b
PaE
C0
PaE 8b
C11
b
PaE
C07
b
PaE
C
PaE 06b
C
PaE 13b
C
PaE 01b
C0
4b
Pa
E
Pa C10b
EC
02b
Pa
E
Pa C15b
E
Pa C05
b
E
Pa C09
b
E
Pa C14
E
b
Pa C03
P
Pa E02 b
Pm PE01 a
Pm MX a
0
M
4
Pm
a
X
Pm MX 03a
M 03
X0 b
1a
MX
M
EC
M
PiUK09b
PiUK01b
PiUK06b
PiES05b
PiV
PiM T0
PiM X6 4b
PiM X2 3a
6
PiM X2 a
2
PiM X1 b
7
PiM X05 b
b
PiM X66
a
PiM X64
b
PiM X30b
PiM X72a
PiM X50a
X
PiM 61b
X2
4b
PiM
X
PiM 71b
X04
a
PiS
A01
a
PiS
A01
b
PiC
O01
a
PiC
O05
a
PiC
O04
PiCO b
02
PiCO b
03a
PiUK
10a
PiUK
04a
PiES03
a
PiES01
b
PiES05
a
PiES04
a
PiES02a
PiUK05b
PiCO05b
PiUK04b
PiUK02b
X
1b
X0 b
M 11
Pm MX 11a
Pm MX 07b
Pm MX 08b
Pm MX 6a
0
Pm MX 4b
X0
Pm
a
M
0
Pm MX1 b
5
Pm MX0 b
0
Pm MX1
a
Pm X05
M
08a
Pm
MX
a
Pm X07
M
Pm X09a
M
Pm
06b
MX
Pm X09b
M
Pm 02b
O
PiP
b
E11
PiP 3b
1
PiPE b
01
PiPE
26b
PiPE
14b
PiPE
28b
PiPE
07b
PiPE
b
PiPE12
b
PiPE10
b
PiPE29
b
PiPE06
b
PiNL01
PiUK07b
PiUS08b
PiSW01b
PiSW02b
PiES04b
PiES03b
PiES02b
PiPE10a
PiPE29a
PiPE08b
b
PiPE22
a
PiSW01
a
PiPE26
b
24
PiPE
27b
PiPE
8a
2
E
PiP
09b
PiPE
04a
E
PiP
21b
PiPE b
25
iP
P E 2b
X7
PiM
a
X71
iM
P
b
E02
PiP
b
E01
PaP 23b
E
iP
P
5b
E0
PiP 03b
T
PiV 02b
L
b
iN
P
02
PE
Pa X67a
a
PiM X49
b
PiM X27
b
PiM X15 a
PiM X65 b
2
PiM X6 a
8
PiM X1 2b
PiM T0 1b
PiV T0
PiV
X
PiPE03b
PiUK06a
2.0E-4 substitutions per site
PiMX50b
PpUS01a
PpUS01b
PoMX07b
location.states
Figure S7. Maximum clade credibility genealogy for the Trp1 locus. Colors of
branches indicate the most probable geographic origin of each lineage.
Colombia
Ecuador
Estonia
Hungary
Mexico
Poland
South Africa
Sweden
United Kingdom
United States
Vietnam
b
03 4b
PE 0 b
Pi iPE 07 1 b
P iPE 0 b
P iPO 02 b
P iPO 04 b
P iCO 02
P iCO 11b
P iUS 09b
P iUK 08b
P UK 6b
Pi UK0 0b
Pi UK1 1b
P i U K 0 7b
P i C0 b
PiE C01 b
PiE C08 b
PiE C03
PiE C02b
PiE K 0 5 b
PiU K04b
P iU K 0 7 b
P iU X 0 2 b
PoM X02a
PoM X06b
PoM X05a
PoM X01a
PoM 03a
X
PoM X 0 8 b
P m M 06a
PoMX 4a
0
PoMX 4b
0
PoMX b
P oM X 01
5b
X0
M
Po
Po MX 03 b
Po MX 08 a
MX
MX
MX
PpU S02 a
PpU S01 b
PpUS 02b
PpUS01a
PmMX07a
PmMX02a
PmMX 12b
PmM X04 a
Pm MX 03b
Pm MX 10 a
Pm M X0 5a
Pm M X1
2a
PmMX
06
PmMX b
0
PmMX 1a
PmM 05b
X
PmM 04b
PmM X01b
X
PmM 06a
PmM X07b
Pm X11b
M
Pm X09b
M
Pm X11a
Pm MX10
b
Pm MX02
Pm MX09 b
Pa M X 0 a
Pa EC0 3 a
Pa EC1 8b
Pa EC0 3b
Pa EC0 1b
Pa EC 9b
Pa EC 11b
Pa EC 14b
P EC 07b
P aEC 03
Pa aEC 02 b
P E 15 b
P aE C1 b
Pa aEC C05 7b
P E 0 b
Pa aE C 1 6 b
PE C0 0 b
02 4b
b
US
MX
M
X
b
01 6b
PE 1 2 b
C
Pa aE C 1
a
P aE
01 a
P
SW 02
Pi iSW 02b
P i S W 11b
P EC 10b
Pi C 4b
E
Pi EC1 3b
Pi EC1 6b
Pi C0 b
PiE C12 b
PiE A01 b
PiS T02 b
PiV T03
PiV T01b
PiV T04b
P i V E24b
PiP E22b
PiP E25b
PiP 27b
E
PiP 20b
E
PiP 4 1 a
X
P iM 2 7 b
X
P iM 4 1 b
P iM X 0 6 b
P iM X 5 b
1
P iM X 8 b
2
P iM X
7b
P iU S 1
a
P iM X 14
Pi N L0 1a
PiES02a
PiES05a
PiES04a
PiM X22 a
PiMX23a
PiMX05a
PiMX21a
P
Pa aE
C
P EC 01
Pi iEC 03 a
Pa EC 07 a
a
E
1
P i C 0a
P i V T 06a
P VT 01
Pa i V T 0 2 a a
0
P EC 3 a
Pa iEC 14a
EC 06a
P
1
Pa iEC0 2a
Pa EC1 2a
Pa EC0 0a
7
E
Pi C02 a
Pa EC03 a
E
a
PiE C09a
PiE C01a
PiE S03b
PiE S03a
S
PiE 02b
PaP S01a
E
PiP 02a
E
PaP 22a
E
PiPE 01a
P iH U 11a
0
PiPE 2 a
1
PiPE2 0a
6
PiPE0 a
1
PiPE04 a
a
PiPE01
b
PiPE03a
PiPE06a
PiPO01a
PiPE23a
PiES04b
PiPE21a
PiUK03a
P
P iPE
P iP 0
P i iPE E29 5a
P M X 09 a
Pi iMX 67 a
Pi MX 21 a
M
Pi X 66a b
Pi MX 29a
Pi MX6 28a
Pi MX6 1b
Pi MX0 3a
M
Pi X2 6a
MX 9b
PiM 4
PiM X07 3b
PiM X03 b
PiN X30 b
a
PiN L02a
PiM L01b
P iM X 4 8 b
P iM X 4 4 a
P iM X 1 1 a
P iM X 2 5 a
X
P iM 1 1 b
X
P iM 4 7 a
X
P iM 5 0 a
X
P iM X 0 4 b
2
P iM X 7 a
1
P iM X 6 b
42b
P iM X
66
PiPE20 b
a
P iM X 16
a
Pi M X5 0b
Pi MX 42 a
PiM X6 5b
PiM X46 b
PiM X19 a
PiMX6 4b
PiMX61a
PiSW01b
PiPO02a
PiMX1 2a
PiM X72 a
PiM X01 a
PiM X2 0b
Pi MX 01 b
Pi M X0 2a
a
P iM X 24
5b
P iM X 0 b
47
P iM X 6 a
4
P iM X 4 b
4
P iM X 2 b
0
P iM X 4 9 a
X
P iM 2 4 b
X
P iM 2 6 a
X
P iM 0 7 a
X
P iM X 6 5 a
P iM K 0 4 a
P iU X 7 1 a
P iM X 6 2 a
PiM X45a
a
P i M A01 a
PiS K08 a
PiU K05 a
P i U C05 a
8
E
Pa EC0 2a
Pa iEC1 4 a
P V T 0 5a
P i EC1 4a
0
Pa EC 13a
Pa iEC 14a a
P EC 17
Pi EC 13a a
Pa aEC 11 a
P iEC C11 8a
P E 0 a
6
Pa iEC C1
P E
Pa
PiUS11a
PiUS17a
PiUK0 9a
PiUK 02a
PiU K06 a
PiU K1 0a
Pi UK 07 a
Pi U K0 1a
P iU K 03
b
P iM X 1
3
P iM X a
4
P iM X 3 a
3
P iM X 0 b
P iM X 2 2 b
PiU S 4 9 b
P iM 12 a
X
P iM 1 8 b
P iC X 1 8 a
P iC O 0 3 b
P iM O 0 1 b
P iM X 6 3 b
PiM X67b
PiM X10
PiM X62 b
PiM X13 b
Pi X7 b
Pi MX2 1b
Pi MX1 6b
Pi MX7 2b
Pi U K 0 2 b
P i ES0 2 b
H
Pi U 5b
P ES 0 2 b
Pi iPE0 0 1b
P
P E 5b
P iPE 09
P iPE 26 b
Pi iPE 06 b
P PE 28 b
Pi iPE 10 b
PE 0 b
29 2b
b
Peru
PiUS08a
PiCO0 4a
PiCO 01a
PiC O0 2a
PiC O0 3a
Pi CO 05 a
Pi M X4 5b
b
P iM X 14
9b
P iM X 1 b
17
P iM X
04a
P iM X 0 b
4
P iM X 1b
2
PiPE 27a
PiPE 2 0 a
X
P iM 2 3 b
X
P iM 2 5 b
X
P iM X 1 0 a
P iM X 1 5 a
P iM X 1 7 a
P iM X 6 4 a
PiM S08b
b
PiU S12
a
PiU X03 a
PiM X48 a
0
P i M X 4 4a
P i M PE2 5a
Pi E2 2a
PiP E1 5 b
P 0 a
Pi
CO 3
P i iPE1 12b
P PE 1b
Pi PE1 3b
Pi PE1 0 2 b
Pi N L 23b a
P i E 28 a
P
Pi iPE 02 a
P iPE 07
P iPE
P
Netherlands
4.0E-5 substitutions per site
location.states
Colombia
Ecuador
Estonia
Hungary
Mexico
Netherlands
South Africa
Sweden
United Kingdom
United States
Vietnam
P iMX 43b
P iMX47a
PiMX46b
PiMX45b
PiMX44a
PiMX04b
PiMX10a
PaEC17a
PiMX45a
PaEC04a
a
PaEC02 a
PaEC03 a
1
PaEC0 0a
PaEC1 1a
PaEC102a
PiPO 46a
PiMX 6c
0
PiUK 05a
PiUK 27a
X
PiM X44b
PiM X47b
PiM E24a
PiP C02c
PiE 07a
PiEC S12a
PiU C06a
PiE 11a
PiEC C14a
PiE C13a a
PiE C10 a
PiE T04 a
PiV VT01 a
Pi T03 a
PiV VT02 4a
Pi X2 5a
PiM X1 1a
PiM iES0 13a
P PE 1a
Pi iPE0
P
Poland
PiMX43a
P iMX 03b
PiCO04a
PiCO02a
PiPE05a
PiPE03a
PiPE08a
PiPE02a
PiPE09a
PiUS08a
PiUS17a
PiMX49
PiMX4 a
PiMX 0a
PiCO065a
PiEC1 5a
PiUS1 2a
PaEC 1a
PiSA 12a
PiUK 01a
PaE 02a
PaE C13a
PaECC07a
PaE 15a
PiE C06a
PaE C03a
Pa C14a
PiE EC05a
PaE C08a
Pa C08
Pa EC09 a
PiMEC16 a
Pi X2 a
P MX 5b
PiNiMX2 14b
P L0 5a
P iMX 2a
P iMX 17a
PiMiMX 23b
P X 28
PiMiMX 26a a
X1 20b
6a
Peru
MX
MX
MX
MX
MX
2b
L0 11a
PiN iMX X17b
P iM 03b
P iUK 12b
P iUS 4a
P iPE0 1a
P CO0 3a
Pi CO0 a
Pi E26 a
PiP E29 a
PiP E28 a
PiP C02
PiE C01a
PiE E10a
PiP E07a
PiP E06a
PiP K09a
PiU K06a
PiU K08a
PiU X05b
PiM X07a
PiM X29a
PiM X64a
PiM 21b
PiPE 3b
PiPE2 61a
PiMX 7a
PiUK0 2a
PiHU00a
PiUK1 a
PiUK04 a
PiMX04
PiES03a
PiMX13a
PiMX48a
PiMX20a
PiMX67a
PiMX22b
PiMX12a
PiMX03a
PiMX50a
PpUS02a
PpUS02b
PpUS01a
PpUS01b
PoMX07b
PoMX07a
PoMX02b
PoMX04a
PoMX06a
PoMX03
MX
PoMX0 b
PoMX0 5a
PoMX 1b
PoMX 03a
PoMX 01a
PoM 04b
PoM X05b
PoM X06b
PoM X02a
PoM X08 b
Pm X08a
PmMMX01a
Pm X06
Pm MX07 a
Pm MX02 a
Pm MX0 a
Pm MX0 2b
Pm MX0 6b
Pm MX 1b
Pm MX 03b
Pm MX0 09b
Pm MX 9a
Pm M 03a
Pm MX X05b
P M 05
P mM X11 a
P mM X0 a
PmmMX X12 7b
P M 1 b
P mM X1 2a
Pm mM X0 0a
M X04 4a
X1 b
0b
1b
X1 8b
M EC0 3b
Pm Pa aEC1 02b
P PE 1b
Pa aPE0 04b
P EC 0b
Pa EC1 b
Pa EC01 6b
Pa EC0 5b
Pa C1 b
PaE EC17 b
Pa EC11 b
Pa C16
PaE EC03b
Pa EC09b
Pa C12b
PaE C05b
EC
PaE C07b
PaE C02b
PaE C14b
PaE
14c
PiPE E01a
PaP 02a
PaPE 01b
PiNL 3b
PiES0 8b
PiUS005b
PiCO 7b
PiUK0 b
PiUK02b
PiES05 b
PiUK08
PiPE28b
PiES04b
PiPE26b
PiUK06b
PiPE07b
PiPE10b
PiPE29b
P iP E 06b
P iUK 04b
P
Pi iEC0
PiE UK1 1b
P S 0
Pi iMX 01b b
Pi MX 10b
PiMMX7 72b
Pi X0 1b
PiMMX3 1b
PiM X24 0a
PiM X6 b
PiM X71 3a
PiM X66 a
PiM X62 a
PiM X21 a
PiM X30bb
PiM X72a
PiM X66b
PiM X06a
PiM X02a
PiM X61b
PiMXX65b
PiUS 18a
PiCO 11b
PiMX 05c
PiMX 62b
6
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PiCO0 1b
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PiPE13b
PiPE14b
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PiSW01b
PiSW02b
PiUK01b
P iUK 09b
PiUK05b
P iP O02b
PiUK08c
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P
Pi iPE1
Pi UK0 4a
PiP PE12 1a
Pi E1 a
Pi PE2 1a
PiP PE25 2a
P E2 a
PiM iPE2 7a
PiM X01 0a
X
PiM 1 a
PiM X05 4a
PiM X23 a
PiM X22 a
a
PiES X67b
PiE 05a
PiPOS04a
PiS 01a
PiM W01a
PiM X13b
PiH X26b
PiM U02b
X
PiUS 28b
PiMX 17b
27b
PiES0
PiPE2 2a
PiPE2 7b
2
PiPE25 b
PiPE20 b
PiSA01 b
b
PiPE24b
PiVT01b
PiVT03b
PiVT02b
PiVT04b
PiEC06b
PiEC11b
PiEC10b
PiEC12b
PiEC13b
PiEC14b
PiEC07b
PiEC08b
PiMX12b
PiNL01a
PiUK03a
PiSW02a
PiPE21a
PiPE23a
PiMX41a
a
PiMX21 b
0
PiMX5 0b
4
X
PiM 8b
PiMX4 1b
1
PiMX 42b
PiMX 49b
PiMX 16b
PiMX 18b
PiMXX41b
PiM X64b
PiM X19b
PiM X42a
PiM X29b
PiM X19a
PiM X02b
PiM X07bb
PiM X06 b
PiM X15 b
PiM O04 b
PiC O02 b
PiC iPE03 b
P E09 b
PiP PE05 b
Pi PE02 8b
Pi PE0 3b
Pi O0 1b
PiC CO0 04b
Pi iPE 03b
P EC 2b
Pi iEC0
P
3.0E-4
A.
EC1
B.
PE7
PE3
PE3
0.9 [0.7, 1.1]
PE7
EC1
1.4 [1.1, 1.7]
PE3
PE3
PE3
PE7
0.9 [0.7, 1.2]
E.
PE7
EC1
21.9 [19.7, 24.0]
D.
EC1
C.
F.
PE7
73.5 [71.1, 75.8]
EC1
EC1
PE3
1.4 [1.1, 1.7]
PE7
1.
2.
Toluca
X
US1
4.
Toluca
3.
US1
X
5.
Toluca
X
US1
7.
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X
X
Toluca
X
Toluca US1
13.
Toluca
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Toluca
X
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Toluca
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Toluca
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12.
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X
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15.
14.
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9.
11.
10.
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8.
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X
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US1 Toluca