Genetic Diversity in Southeastern Puerto Rico:

Implications for the Prehistoric and Historic

Peopling of the Greater Antilles

Miguel G. Vilar, Carlalynne Melendez, Akiva Sanders, Akshay Walia,

Jill B. Gaieski, Amanda C. Owings, Theodore G. Schurr,
Genographic Consortium
July 19, 2013
IACA Congress 2013
San Juan, Puerto Rico

The Caribbean Islands

Earliest Antillean People (7,000 500 BP)

Earliest sites in Cuba and Hispaniola date to 7,000 ybp (Haag 1963)

Casimiroid culture may have ties to Mesoamerica

Oldest sites in the Lesser Antilles date to 7,000 8,000 ybp in

Trinidad, less than 20 miles from Venezuela.

Earliest pre-ceramic sites in PR (6,000 ybp) Arcaico (Alegria 1971)

similar and contemporaneous with Ortoiroid culture in the Lesser
Antilles. Casimiroid assemblages have also been found in western PR.

Igneri culture (agricultural and fishing) with ties to northern South

America dating to 2,000 1,100 ybp (Rouse 1993)

Tainos, horticulutural and ceramic users, came to dominate the

Greater Antilles ~1,100 ybp until arrival of Europeans 520 ybp

Carib, newcomers from South America, encroaching on Tainos

Prehistoric Entry Ways into the Caribbean

Historic Times:
Earliest European colonies and first settlements in the Americas
Some colonies/territories remain today.
Small geographic area, historically controlled by four (or five) European powers

The Caribbean: 1500-Present

16th - 18th Centuries
-Hispanola becomes the colonial
headquarters for Spain in Caribbean
-Sugar cane is introduced, tens of
thousands of Africans are forced to work
19th Century
-1804 Haiti gains its independence
-Countries boarding the sea becoming
independent
-1898 USA defeats Spain, gains Cuba
and Puerto Rico.

Esemono 2008

20th Century
-Jamaica and most Lesser Antilles gain
their independence

(Pre)historic Questions Addressed with Genetic Data

~7000 bp

~6000 bp

~3000 bp

~7,000 bp

- Who were the first Caribbean people?

- How many waves of migration were associated with early Caribbean
settlement, and from where did they originate?
- How have historical events impacted the genetic make up of modern islanders?

Caribbean Participants (2010-12)

Bermuda
146 Individuals

Puerto Rico
326 people
(38 from Vieques)
Dominica
Fall of 2013
St. Vincent
66 participants
Campeche/Yucatan (Mexico)
210 Participants
Dominican Republic
Cuba
~180 Maya ancestry
Comparative data Fall of 2013

Trinidad
25 participants

Mitochondrial DNA (mtDNA) Genetics

-Highly-mutable
-Very small molecule
(16,569 bp)

-Inherited maternally
WITHOUT recombination

-Control region (~1,100 bp) exhibits many

mutations
-We study mtDNA diversity by looking at
haplogroups, or groups of related
haplotypes, in human populations

-Different haplogroups originate in

different regions of the world

mtDNA Control Region

-Two major regions (two simple PCRs)
HVS1: 16025 - 16400
HVS2: 70- 500
-Comparative data exists for hundreds
of thousands of individuals worldwide

-The region is non-coding, thus

mutations are not affected by selection,
they accumulate through time

Non-Recombining Region (NRY)

of the Y-chromosome
-Smallest human chromosome, only carried by men.
-All men inherited the Y-chromosome directly from their fathers, who got them from
their fathers, and so on.
-Studied through (a) individual mutations (single nucleotide polymorphism, or
SNPs), and (b) microsatellites (repeating regions of DNA, also known as STRs).
-Each NRY haplogroup has a specific list of known SNPs and specific STR patterns.

mtDNA Haplogroups
Haplogroup
A

Subgroup

A2
B
C
C1
D
D1

-A-D and X2a

-H-K , N and T-X2b
-L0, L1, L2, and L3
-A-G, M-S, Y-Zq

(HVS1) Mutations
16223, 16290, 16319
16111, 16223, 16290, 16319, 16362
16189, 16217
16223, 16298, 16327
16223, 16298, 16325, 16327
16223, 16362
16223, 16325, 16362

Native Americans
West Eurasians
Sub-Saharan Africans
Asians and Australians

NRY Haplogroups
-Q and C3
-E, G, I,J, R, T
-A, B, E
-C,D,H,J,L-Q,S

Native Americans
West Eurasians
Sub-Saharan Africans
Asians and Australians

mtDNA Results for Puerto Rico

326 samples collected in two expeditions (Nov 2010 & May 2011)

West
Eurasian

Sub-Saharan
African

Indigenous
American

Comparative mtDNA Data

Puert Cuba
Hg o Rico
A2
.30
.23

Bermuda

Dominica

Trinida
d

.01

.08

.04

African
American
s
.01

B2

.04

.02

C1

.22

.05

D1

.01

.03

.01

.03

.09

.09

.03

.04

.13

.01

.01

.01

.02

.02

.01

.01

.02

.02

.01

.08

.06

.03

.01

.01

.01

.04

.02

.16

.02
.06

.05

Eastern
Native
Amer

Native
Mexicans
Yucatan

.58

.78

.17

.07

.24

.09

.01

.03
.01

W. Africa
Senegal

W. Europe
Britain

.01

.53

.01
.22
.04

.01
.08
.12

.06
.04

.01

L0

.02

.02

.13

.12

.02

.06

L1

.10

.08

.14

.44

.23

.18

L2

.04

.13

.14

.12

.30

.24

L3

.10

.20

.24

.04

.30

.39

.01

.02

L4

.01

.02

.02

.20
.02

.24
.43

Haplogroup A2 in Puerto Rico

(16111, 16223, 16290, 16319, 16362)

Network of A2 in Puerto Rico

-Lines represent mutational events

16259
16218

16526

16129

-Blue circles represent individual types,

circle size represents frequency

16126
16189
16111*
16391

16083

16256
16189

16097

A2z

16234
16098

-Using published HVS1 mutation rate,

pattern suggests that this population is
26,000 years old.

16189

How is that possible?

16320

Puerto Rico A2 Haplotype

Where else is it found?
A2 + 16234
Mexico and El Salvador
A2 + 16218 (hvs2: 179, 385)
Cuba
A2 + 16083, 16126, 16256 (hvs2: 214)
Cuba
A2 + 16526
Cuba and Mexico
A2 + 16111*, 16391
part of A2k, Brazil and Venezuela
A2 + 16097, 16098, 16189, 16320
Brazil and Amazon
A2 + 16129
North, Central and South America

Haplogroup A2z in Puerto Rico

(16083, 16111, 16223, 16256, 16290, 16319, 16362)

16092

Cuba
Puerto Rico

16274

Mexico
16189

16126

South America
16083

16083

16390

-Highest diversity and most common in Cuba

-Not common in South America or Mexico

16256
16311
16256

16126
16311

16383

16256
Core
A2

Haplogroup C1 in Puerto Rico

(16223, 16298, 16325, 16327)
-The majority of the samples (95%) were C1b (hvs2: 493), further sub-typing and
complete genome typing indicates they are C1b2, C1b4 and C1b11.
-Using known HVS1 and HVS2 mutation rate indicated that the C1b2 types in Puerto
Rico are approximately 2,100 years old, while C1b4 types are ~4,100 years old.
- C1b2 and C1b4 are found in South America
- C1b2 is found in low frequency in Mexico
- C1c is common in Lesser Antilles
- C1 is rare among modern Cubans

C1c
C1b4

16093

C1b

16189

C1b2

Network Diagram of
Haplogroup C1 PR

What connects Cuba, Puerto Rico, and Mexico?

A2 is very common among indigenous Mexican populations (>60%), especially the Maya
(>80%) from the Yucatan Peninsula.
A specific haplogroup B haplotype (16092, 16189, 16217, 16249, 16312, 16344) is found in
all three regions.
In Hispaniola, Native American haplotypes are less frequent than in Puerto Rico, with many
being lost through European conquest, African slave, and disease, suggesting they existed
there in the past.
Ancient DNA from a Taino site in the Dominican Republic shows a high frequency of C1
and D1 haplotypes, but only one A2 type. Possibly a change in mtDNA haplogroup
frequencies with waves of Caribbean colonization.
Complete mtDNA genome data shows that two Mexican Americans and a Puerto Rican
type share a common A2 haplotype (coding region mutations: 5585, 9156, 11914, 12940,
14275, 15323). This represents the Puerto Rico A2 + 16234 HVS1 haplotype.

Summary from A2 and C1 Results

-Haplogroup A2 is the most common lineage in Mesoamerica, and also the
most common one in Cuba and Puerto Rico. It accounts for approximately
25% of individuals from northern regions of South America.
-Haplotype diversity and age suggests A2 arrived in the Greater Antilles from
both Mesoamerica and South America at different points in time.
-Haplogroup C1b appears at modest frequencies in Mesoamerica (<10%) and
is nearly absent in Cuba, but is the most common and diverse lineage in South
America. These facts suggest that C1b moved north from South America into
the Caribbean. A current study of 91 samples from Trinidad and St. Vincent
support this scenario.
-Limited work on ancient DNA from pre-Columbian Tainos (from Dominican
Republic) shows mostly haplogroups C1 and D1 and a very low frequency of
haplogroup A2. This finding further supports the hypothesis that new
populations replaced older ones, and that haplogroups A2 and C1 likely
arrived at different times, and from different locations, in the Caribbean.

?
A2d
A2d
A2u
B2b

A2e
B2b A2z

B2b

A2k

A2z
C1b
A2e
C1c
A2k

C1b

B2b

The Caribbean was settled in various waves originating from both Mesoamerica and
South America. Further sampling, complete mtDNA genome sequencing, and analysis of
other DNA markers will help clarify these patterns.

MDS plot of mtDNA Fst Estimates

1.0

Native American
Mexico - Yucatan
Puerto Rico

Dimension 2

0.5

N Brazil
SE Brazil

Dominica Cuba

NE Brazil
Afr Amer

0.0

West
Africa

S Brazil

Bermuda

Grenada
Trinidad

Madeira
Portugal

Azores
Great Britain

-0.5

Dimension 1
-0.5

0.0

0.5

1.0

1.5

Based on all haplogroups present

Puerto Rico is closest to populations from Cuba, Brazil, and the Yucatan in Mexico.
This pattern likely reflects a common origin for indigenous lineages and also
post-colonial contact and recent sharing/migrations among the different regions

mtDNA Fst Estimates Grouped by Colonial Power

1.0

Native American

UK
Mexico - Yucatan

Spain

Puerto Rico

0.5

N Brazil
SE Brazil

Dominica Cuba

Portugal

NE Brazil
Afr Amer

0.0

West
Africa

S Brazil

Bermuda

Grenada
Trinidad

Madeira
Portugal

Azores
Western Europe

-0.5

-0.5

0.0

0.5

1.0

1.5

-Is this pattern is indicative of the colonial practices of the time?

Spain did not introduce many maternal lineages, mostly men migrated
UK quickly replaced indigenous populations with predominantly African populations
Portugal showed a homogeneity of its colonies and the colonial power

Source of African Haplogroups L0 L3

L0 is common in south and southeast Africa

L1b, are common in West Africa (Senegal,

Mauritania and Gran Canaria). L1c is more
common in central Africa

L2a was the most common subgroup of L2,

found in East Africa, but is also common in the
Sahel and North Africa (Egypt, Algeria and
Morocco). L2c, have origins likely in Senegal
and the Cape Verde islands

L3e was the most common L3, found in westcentral Africa, but also among Afro-Brazilians.
L3b and L3d were also present, and are thought
to originate in West Africa. L3f was also
present, common to East Africa and the Sahel

North Africa played an important role in the

recent peopling of the Caribbean

L2a

L3

L1b
L3
L2c L1

L1c

L2
L3f

L3e
L0

L0

European Haplogroupsor are They?

Haplogroup U was common (7%), with three subgroups

being heavily represented:
U2e (common in Middle East)
U5b and U5b1 (common in central Europe)

4% were haplogroup H, including subgroups H1, H2 and

H3, which are common in Basques, Galicians, and some
Mediterranean populations.

4% were haplogroup J, dominated by J1b, which has

been found in South Asia and the Middle East

Distribution of West Eurasian haplogroups in Puerto Rico:

Likely reflects diversity of the Iberian Peninsula at
the time of colonization
Was influenced by the Spanish Inquisition since
1492
Some haplotypes could be representative of
Sephardic Jews fleeing Inquisition
mtDNA diversity is similar to modern day Moroccans

Y Chromosome Results

121 male participants

41 are Haplogroup E
20 E1b1a (Sub-Saharan African)
21 E1b1b
(Med/ N African)
7 are Haplogroup G (G2a)
(Med)
10 are Haplogroup I
5 are I2
(Med)
5 are I1
6 are Haplogroup J (J2a1)
(Med)
54 are Haplogroup R1
53 R1b
(Western Europe)
1 R1a
2 are Haplogroup T (Med/ N African)
1 is Haplogroup F

101 are European, Middle Eastern,

North African
84%
20 are Sub-African
16%
Indigenous lineages
0%

Network of NRY Haplogroup E1b1b

in Puerto Rico

-Some lineages originated in Mediterranean region (Spain, Sardinia and the

Balkans), but other form a monophyletic branch that originates in North Africa.

Interesting Facts & New Questions

Partial replacement of mtDNA haplogroups C1 and D1 in the Caribbean by A2 suggests

a paleodemographic shift. When and how did this replacement occur?

We see a genetic evidence of two or likely three distinct waves of migration from South
America, and one or two waves of migration from the Yucatan.

Several lineages suggest a Middle Eastern/North African origin as opposed to Western

Europe. Evidence of the Spanish Inquisition and the diverse ethnicity of early colonists.

Using mtDNA and Y haplogroups, we can infer from where Sub-Saharan African were
introduced from; is this modern genetic diversity an indication of original genotypes
introduction by colonial powers during the 16th century, or instead reflect more recent
movements into region?

Since the very recent discovery of indigenous male lineages in Trinidad and St. Vincent,
the absence in PR and Cuba is quite peculiar, given the size/topography of the islands

Through a recent NGS grant we have begun looking autosomal diversity (GenoChip),
and this study will help answer questions of genetic admixture.

GenoChip
Autosomal SNPs
GenoChip is a chip based assay for
SNP (mutation) detection designed
to identify known anthropologically
relevant mutations (130,000 SNPs)

Puerto Ricans (20 participants)

24% SubSaharan African
32% Mediterranean
18% Northern European
9% Southwest Asian
14% Native American
3% Other

Acknowledgements: Leaders of Puerto Rican communities and Puerto Rican

participants; National Geographic, IBM, Waitt Family Foundation and Penn for support.

Thank you!