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BMC Genetics
BioMed Central
Open Access
Research article
Reconstructing recent human phylogenies with forensic STR loci: A
statistical approach
Suraksha Agrawal*1 and Faisal Khan1,2
Address: 1Department of Medical Genetics, Sanjay Gandhi Post Graduate Institute of Medical Sciences, Raebareli Road, Lucknow (UP) 226014
India and 2Department of Biotechnology, Bundelkhand University, Jhansi (UP), India
Email: Suraksha Agrawal* - [email protected]; Faisal Khan - [email protected]
* Corresponding author
Published: 28 September 2005
BMC Genetics 2005, 6:47
doi:10.1186/1471-2156-6-47
Received: 29 May 2005
Accepted: 28 September 2005
This article is available from: http://www.biomedcentral.com/1471-2156/6/47
© 2005 Agrawal and Khan; licensee BioMed Central Ltd.
This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/2.0),
which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.
Short tandem repeatsForensicPhylogenyNeighbor-joiningMaximum likelihoodPC plot
Abstract
Background: Forensic Short Tandem Repeat (STR) loci are effective for the purpose of individual
identification, and other forensic applications. Most of these markers have high allelic variability and
mutation rate because of which they have limited use in the phylogenetic reconstruction. In the
present study, we have carried out a meta-analysis to explore the possibility of using only five STR
loci (TPOX, FES, vWA, F13A and Tho1) to carry out phylogenetic assessment based on the allele
frequency profile of 20 world population and north Indian Hindus analyzed in the present study.
Results: Phylogenetic analysis based on two different approaches – genetic distance and maximum
likelihood along with statistical bootstrapping procedure involving 1000 replicates was carried out.
The ensuing tree topologies and PC plots were further compared with those obtained in earlier
phylogenetic investigations. The compiled database of 21 populations got segregated and finely
resolved into three basal clusters with very high bootstrap values corresponding to three geoethnic groups of African, Orientals, and Caucasians.
Conclusion: Based on this study we conclude that if appropriate and logistic statistical approaches
are followed then even lesser number of forensic STR loci are powerful enough to reconstruct the
recent human phylogenies despite of their relatively high mutation rates.
Background
Short Tandem Repeats (STR), with a repetitive sequence
ranging from 2–6 base pairs are amongst the most polymorphic markers reported till date. They exhibit substantial allelic variability due to high rate of germline
mutations [1]. The STR loci have a uniform and dense distribution throughout the genome and exhibit high level of
relatively stable polymorphism [2]. All these features
makes them an ideal candidate for diverse applications
including forensic applications [3], individual identification, paternity/maternity detection [2], fine scale genetic
mapping [4] and inter and intra group phylogenetic
reconstruction [5].
However, a specific set of STR can be employed for specific
applications and this specificity is solely based on the
properties of STR loci involved and their suitability to the
particular application. STR loci used for forensic purposes
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Table 1: Population compiled for database of five forensic STR loci
S.No.
Populations
No. of samples analyzed *
TPOX
1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
Basque
Poland
Germany
Italy
Portugal
Spain
Canadian Caucasians
Middle Eastern Arabs
US Caucasian
Slovenia
Austria
China
Japan
Philippine
Taiwan
Sharawasi Africans
Cameroon
Moroccan Arabs
Lisongo Africans
US Afro-Americans
North Indian Hindus **
FES
vWA
F13A
Tho1
768
703
2876
11388
1239
1782
435
165
562
235
153
658
1491
498
716
59
65
127
32
580
1000
627
643
7683
4827
2091
2325
321
132
597
235
153
435
397
103
100
59
65
199
60
679
1000
615
572
13667
7135
4720
3361
428
149
759
779
1946
1146
1743
376
600
99
65
193
30
797
1000
208
334
3438
1677
1158
1864
435
127
587
236
1056
137
668
133
149
59
65
75
30
691
1000
859
488
7373
4900
4639
4037
435
173
765
560
1816
2503
2905
528
764
59
65
271
30
793
1000
Source of data:* http://www.uni-duesseldorf.de/WWW/MedFak/Serology/database.html [9]
** Present study
are the one that possess numerous observed alleles, high
level of heterozygosity, high polymorphism information
content and high power of exclusion. On the contrary,
STR loci preferred for the phylogenetic analysis of the
human populations are those which have substantial
lower allelic counts and carries signature alleles for specific populations [6,7]. Still, there are few studies in which
there is some overlap between the sets of forensic STRs
and those exclusively studied for phylogenetic investigation. However, this overlap is not extensive and is without
any definitive rationale or design.
There are two school of thoughts regarding the use of
forensic STR in phylogenetic studies. According to one
view, the requirement of extremely high level of intra
group variation along with high mutation rates in forensic
systems indicates a rapid diffusion of genetic variation
and thus, confers a greater risk of failure in detection of
convergent evolution among some populations [8]. Other
perception is that random noise generated by allelic variability in forensic systems is not strong enough to veil the
evolutionary signals generated by these STR loci. Furthermore, fine scale resolution of forensic STR may prove
handful in delineating genetic difference and affinities
between closely related ethnic groups [6].
In the present study, we have made an attempt to explore
the utility of forensic STR loci in inferring phylogenetic
relationships. To approach this goal, we have compiled a
geographically targeted and racially diverse set of 21-population database from forensic literature obtained from
Wolfgang Huckenbeck and Hans-Georg Scheil's website
"The Distribution of the Human DNA-PCR Polymorphisms" [9] while the north Indian Hindus from the state
of Uttar Pradesh were genotyped in our own lab. Forensic
STR loci for which the allele frequency data was compiled
were Tho1, vWA, FES. F13 and TPOX. They all carries
tetrameric core repeat sequence and reside on different
chromosomes and are amongst the most reputed one in
forensic system. The choice of these loci is exclusively on
the basis that these markers have been studied in all the 21
populations hence a precise phylogenetic analysis could
be performed [Table 1].
Phylogenetic assessment was carried out through two different approaches – genetic distance and maximum likelihood along with a statistical Bootstrapping procedure
involving 1000 replicates. The ensuing tree topologies and
PC plots were then compared with those obtained in earlier phylogenetic investigations. The main question that
we have tried to address in this meta-analysis is whether a
limited number of forensic STR can predict accurate
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Table 2: Different statistical analysis done on allele frequency data of five STR loci which are important criterion for a good forensic
loci
Tho1
Allele3
Allele 4
Allele 5
Allele 6
Allele 7
Allele 8
Allele 9
Allele 9.3
Allele 10
Allele 11
Allele 12
Allele 13
Allele 14
Allele 15
Allele 16
Allele 17
Allele 18
Allele 19
Allele 20
Observed Heterozygosity
PIC
Power of exclusion
Average heterozygosity
Mean PIC
Total exclusionary power
VWA
0.01
0.28
0.16
0.08
0.17
0.30
0.06
0.680
0.738
0.381
FES
0.04
0.01
0.08
0.14
0.04
0.34
0.14
0.30
0.02
0.02
0.760
0.714
0.354
human phylogenies, if the data is evaluated using proper
statistical approaches.
F13
0.06
0.06
0.20
0.40
0.26
0.02
0.27
0.36
0.18
0.02
0.04
0.760
0.725
0.371
0.734
0.700
0.875
TPOX
0.02
0.40
0.12
0.08
0.32
0.04
0.02
0.740
0.660
0.283
0.730
0.669
0.308
branch. The scores next to the nodes characterize the
number of bootstrap replicates (out of 1000) exhibiting
these specific bifurcations.
Results
Allele frequency distribution
Analysis of five STR loci- Tho1, vWA, FES, F13 and TPOX
has revealed high level of diversity among North Indian
Hindus. Total 7–8 alleles were found (7 each for Tho1,
vWA, F13 and TPOX and 8 for FES). All the loci were in
Hardy-Weinberg equilibrium. Table 2 shows allele frequency distribution at all the five loci among North
Indian Hindus. High allelic variability was further
depicted by high-observed Heterozygosity (0.68 at Tho10.76 at vWA), high PIC (0.66 at F13-0.74 at Tho1) and
high power of exclusion (0.28 at F13-0.38 at Tho1). All
these criterions are indicative of the fact that these STR loci
are useful and informative tools for all types of forensic
applications.
Phylogenetic assessment
Phylogenetic analysis carried out in 21 populations is
depicted by two enrooted radial phylograms (NJ and ML)
as shown in Figure 1a and 1b and a PC plot was plotted
based on the allele frequency variation [Figure 1c]. The
edge lengths displayed in these phylograms indicated that
the amount of evolutionary change occurred along each
NJ phylogenetic tree depicts three different basal groups
corresponding to three ethnic groups- African, Caucasian
and Orientals. The Caucasian cluster has three monophyletic units- Austria/German, Basque/Portuguese and
USA/Canadian Caucasians. Total 8 out of the 14 nodes
have bootstrap values more than 50%, most important
among them is (i) division between Africans and other
two groups of Caucasians and Orientals-863, (ii) the division between Caucasian and other two groups-960 and
(iii) the division between Orientals and other two groups995.
ML phylograms also displayed comparable topology to
that of NJ tree. It has also depicted three basal nodes with
clear demarcation of Africans, Caucasians and Orientals.
Similar to NJ tree, all the three basal monophyletic topologies in ML tree have bootstrap values more than 50% i.e.
931, 790 and 995 respectively for Africans, Caucasians
and Orientals. In both the phylogenies, NJ and ML, North
Indian Hindus clustered with the Caucasians albeit with
low bootstrap value of 456.
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Figure 1
(ML) tree with 1000 bootstrap replicates and PC plot analysis based on allele frequency differences (b) Maximum Likelihood
Phylogenetic reconstruction based on (a) Neighbor-joining (NJ) tree with 1000 bootstrap replicates;
Phylogenetic reconstruction based on (a) Neighbor-joining (NJ) tree with 1000 bootstrap replicates; (b) Maximum Likelihood
(ML) tree with 1000 bootstrap replicates and PC plot analysis based on allele frequency differences.
First and second Principal component that together constitutes 70.4% of the total variability (PC1-39.3% and
PC2-31.1%) were plotted and presented in Figure 1c.
There is a significant separation of the Orientals from
Caucasians on Y-axis (PC2) and with that of Africans on
X-axis (PC1). While Caucasians and Africans reveal relatively clear division along both X-axis (PC1) and Y-axis
(PC2), with Middle Eastern Arabs and Moroccan Arabs
positioning near to each other. Furthermore, the African
populations have clustered into two sub-groups corresponding to the Central and North Africans. North Indian
Hindus have clustered with Caucasians.
Discussion
Five forensic STR loci are found highly successful in providing fine resolution for the reconstruction of recent
human evolutionary histories. All three approaches used
for phylogenetic reconstruction (NJ and ML tree topologies and PC-plot analysis) have depicted strong racial par-
titioning and deciphering the accurate phylogenetic
information about North Indian Hindus which is in
accordance with those derived from other more
renounced phylogenetic markers as well as historical evidences [10-12].
The phylograms (NJ and ML) generated from present data
set were calculated from CONTML and NJ algorithms,
where CONTML works upon the conjecture that random
action of genetic drift is the solitary basis of the differences
between allele frequencies in different population groups
[13]. On the contrary, the NJ algorithm construct a
branching array from a matrix of genetic distances calculated from Nei's formula assuming that both genetic drift
and mutation causes allele frequency differences [14].
Both phylograms, NJ and ML have more or less similar
basal cluster patterns among the three geo-ethnic groups
indicating that component of genetic drift instead of
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BMC Genetics 2005, 6:47
mutation is the major player in these distant estimates.
Both the trees have longer African branch than any other
group. Such a patristic separation is also visible in PC-plot
analysis [Figure 1c]. The African populations have been
clustered into central (Cameroon and Lisongo) and North
African (Moroccan Arabs and Saharawasi Africans)
groups. Such clustering has also been reported by CavalliSforza et al, 2003 based Fst genetic distance based on polymorphisms of 120 protein-coding genes [15] and Ychromosome binary haplogroup [16,17]. This sub clustering further strengthens the utility of the 5 STR loci in deciphering the accurate phylogenies even within the same
geographical region. Middle Eastern Arabs display a
branch nearer to Caucasians and to some extent near to
Moroccan Arabs suggesting strong Caucasian element
along with African admixtures suggestive of the Demic
expansion of the middle east genes, agriculture innovations and languages into north west Africa [16,17], which
is further supported by the near medial position of Arabs
in the PC-plot. Recently, Y-chromosome SNP analysis by
Al-Zahery et al. 2003 [18] has also revealed similar pattern
in other Middle Eastern populations. European branching
pattern differs slightly between the two trees, but still both
are resolving completely with Basque, Spaniards and Portuguese having a separate cluster from that of German/
Austrian branch. North Indian Hindus clustered with
Caucasians in both the phylograms, which is in agreement with the findings of earlier studies. Bamshad et al.
2001[12] based on mtDNA HVR-I and HVR-II sequencing
and Y-chromosome haplotypes has shown that North
Indian populations reveal high frequency of west Eurasian
haplogroups. North Indian Hindus are basically IndoAryan speakers, who invaded from the steppes of central
Asia and then settled in the Indus valley, in northwestern
India [10].
The major finding of the present study is the productivity
of a limited set of 5 forensic STR loci in resolving the
human phylogenies in a similar manner as reported elsewhere on a much higher number of loci. Further, the
study also highlights the utility of combined use of varied
statistical approaches in reaching a definitive conclusion.
Our study scores a point over some of the successful
reports like that of Bowcock et al., 1997[19] which has
shown substantial phylogenies but with much larger sets
of STR – 30 STR loci. Similarly, Perez-lezaun et al. 1999
[20] has used 20 STR loci and computed Fst based distances depicting similar separation of inter and intra ethnic groups. Even though, in the same study, phylogenetic
tree based on DSW distance exhibited a defused picture
having trifurcation two Caucasoid and one African group.
http://www.biomedcentral.com/1471-2156/6/47
13 CODIS loci, but their phylogenetic assessment was
confined to simple NJ and UPGMA trees and distance
measures which yields single output tree. To overcome
this, we have incorporated both the phylogenetic
approaches i.e. distance and optimal criterion along with
statistical bootstrapping which yields 1000 trees and then
built a consensus tree. In this regard, a successful attempt
was made by Rowold et al. 2003 [6], by compiling 10 geographically and racially different populations on five
forensic STR loci. However, incorporating different set of
STR loci, we have been able to compile larger population
database of 21 populations.
Overall, the analysis of five forensic STR loci have
depicted a strong racial phylogeny indicating that high
heterozygosity and/or numerous observed alleles do not
necessarily interfere with the phylogenetic information
content of the locus, provided that frequency distribution
of the populations is significantly different. Significantly,
larger number of alleles increases the chances of the presence of signature alleles in segregating populations.
Despite all the potential problems associated with forensic STR loci including that of high mutation rates, successfully resolution the genetic difference between inter and
intra geo-ethnic groups suggesting that if well-defined statistical approaches are followed, then even a smaller
number of forensic STR loci are powerful enough in
reconstructing human phylogenies.
Methods
Populations (North Indian Hindus)
A total of 1000 unrelated individuals were randomly
selected. Regional addresses and detailed computerized
lists were prepared before sample collection. Random
numbers were generated with the help of computer and
samples were collected from the different collection sites
of Uttar Pradesh- Lucknow, Kanpur, Faizabad, Basti,
Gonda and Agra. Whole blood was obtained by venipuncture and collected in EDTA vacutainer tubes. Three-generation pedigree charts were prepared to assure unrelatedness in all the samples. The ethical committee of
the institute approved the study and blood samples were
taken after obtaining informed consent from the subjects.
DNA extraction and STR genotyping
DNA was extracted by phenol chloroform method as
described by Comey et al. 1993 [22] and purified by ethanol precipitation. All the five STR loci were detected by
PCR. PCR amplification was performed using flanking
primers described elsewhere [20]. The amplified product
was separated and detected on 9% PAGE using silver
staining.
Various attempts of phylogenetic reconstruction using
forensic STR loci have also been done in recent past like
that of Budowle and Chakraborty, 2001[21] who studied
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Population database
20 geographically targeted populations were selected
from forensic literature [9], while the data of north Indian
Hindus was generated from our lab (Agrawal et al.,
unpublished data). The criterion of selection was to cover
the major geographical and geo-ethnic groups i.e. African,
Caucasoid and Orientals. All the populations selected
have allele frequency data for five STR loci. In order to
embrace a large sample size and to overcome the predicament of some studies focusing only on 2 or 3 STR loci,
allele frequency profile of different STR loci analyzed in
different populations samples but of the same geographic
or ethnic origin has also been included. However, wherever possible, a care has been taken to include the allele
frequency profile of the same set of sample for different
markers. For example, same 65 samples of Cameroon
population has been used for allele frequency data of 5
STR, whereas a large pooled sample size has been used for
other groups like Germany, Portugal, Italy, China, Japan
etc. In order to avoid the discrepancies, number of samples for each population genotyped for different STR loci
and source of allele frequency data is shown in Table 1.
Maximum of the populations compiled in the database
are pooled samples from different parts of that country.
Notably, Sardinians are excluded from Italians, Azores
from Portugal and Canary Island from Spain. Middle Eastern Arabs included Arabs mainly from Saudia Arabia,
Qatar and Yemen.
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Acknowledgements
This work was supported by Indian Council of Medical Research (ICMR)
New Delhi. Authors are thankful to Sanjay Gandhi Post Graduate Institute
of Medical Sciences Lucknow for providing various lab facilities and other
assistance. We thank Ms. Sudha Talwar, Ms. Manorama Tripathi and Mr.
Atul Pandey for providing technical support.
References
1.
2.
3.
4.
5.
6.
7.
8.
9.
10.
Statistical analysis
Allele frequencies were calculated by a simple gene count
method. A total analysis was executed based upon the
allelic frequency distribution of the five STR. Heterozygosity, HWE, PIC and power of exclusion was calculated
using Cervus v1 [23]. Further, Statistical analysis was executed based upon the allelic frequency distribution of the
five STR. A 1000 replicate bootstrap data was generated
from SEQBOOT option in PHYLIP version 3.5c [13]. Distance values were estimated using Nei's formula [14], and
a phylogeny was inferred by the neighbor joining (NJ)
option in PHYLIP version 3.5c [13]. Phylogenetic reconstruction was also done based on maximum likelihood
(ML) and the STR frequency distribution (CONTML in
PHYLIP version 3.5c)[13]. Finally, a principal component
(PC) analysis was generated by POPSTR and first and second PC was plotted as described elsewhere [24].
Authors' contributions
SA has conceptualized the paper provided important
intellectual inputs in intrepretation of data and preparation of the manuscript and FK carried out statistical analysis and drafted the manuscript. Both authors read and
approved the final manuscript
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