June 06, 2013

Population history of the Caribbean (Moreno-Estrada et al. 2013)

The placement of Caribbeans on a European "genetic map" is fairly interesting, as they appear to be "ultra-Iberian" (on the far left). The authors invoke drift as an explanation, which makes sense, given that a small portion of the Iberian gene pool entered into the composition of these populations.

On the other hand, it'd be nice to have Iberian data from a few centuries ago, to make sure, since Iberia, being a part of Europe may have had the opportunity to "right-shift" during the last few centuries due to gene flow, and even if it didn't there is a chance that gene flow within Iberia may have dulled population differentiation, while immigration to the Caribbean may not have originated from all parts of Iberia equally (and as I've shown, there is substantial population structure in Iberia down to this day).

arXiv:1306.0558 [q-bio.PE]

Reconstructing the Population Genetic History of the Caribbean

Andres Moreno-Estrada et al.

The Caribbean basin is home to some of the most complex interactions in recent history among previously diverged human populations. Here, by making use of genome-wide SNP array data, we characterize ancestral components of Caribbean populations on a sub-continental level and unveil fine-scale patterns of population structure distinguishing insular from mainland Caribbean populations as well as from other Hispanic/Latino groups. We provide genetic evidence for an inland South American origin of the Native American component in island populations and for extensive pre-Columbian gene flow across the Caribbean basin. The Caribbean-derived European component shows significant differentiation from parental Iberian populations, presumably as a result of founder effects during the colonization of the New World. Based on demographic models, we reconstruct the complex population history of the Caribbean since the onset of continental admixture. We find that insular populations are best modeled as mixtures absorbing two pulses of African migrants, coinciding with early and maximum activity stages of the transatlantic slave trade. These two pulses appear to have originated in different regions within West Africa, imprinting two distinguishable signatures in present day Afro-Caribbean genomes and shedding light on the genetic impact of the dynamics occurring during the slave trade in the Caribbean.

Link

25 comments:

truth said...

Caribbean populations have A LOT of Canarian ancestry, in fact most of the "spanish" ancestry there is of canarian origins-.

Bencomo Guanche said...

A few caveats:

The deviation observed between The Iberian and the Caribbean European component mostly due to the ASPC2, now the main reason for this deviation comes from Colombia, Honduras and Puerto Rico, as it can be seen in Figure-S10.

Per Figure-S7 it where both the Euro-Latino Insular and Euro-Latino mainland components form, I like to point out that the so called Euro-Latino Insular is very Puerto Rican centered, whereas the Euro-Latino mainland is very colombian centered. Neither one of the makes up the majority of the European component found in Cubans which is still the South-Euro(pink)+North-Euro(red) combo.

While Canary Islanders did contribute large quantities of their ancestry to the genetic make-up of Cubans, large waves of Galicians, Asturians, Catalans in the XIX and early XX century contributed equally.

Bencomo Guanche said...

The other caveat is that as per Table-1:

The log-likehood for the best fit for the Migration Model for Cuban population (EUR,NAT+AFR+AFR) is -326.12 which is still very poor compared to other fits. In fact, the "best migrational fit" is worse than any of the worst migrational fits for any of the other populations. This might be due to the fact that Cuba's demographic history is quite different from any of the three migrational models used in the study, hence why the log-likelihood errors are some big in the Cubans compared to other latin americans used in this study.

bau said...

Hi Dienekes.
I have some doubt in this result.
I think that we see the populations shifted because the Local Ancestry software identify as European the chunks from Europe exclusively. But what about the "North African chunks" that we know that are present in Iberia?. In my opinion the will be classified as african. As support e can see that the populations that shift more have more europe (Colombian and Dominican). Does it make sense? What do you think about it?

Kepler said...

Thanks for this. I don't have access to the article but will try to get it. This is interesting stuff.

I come from Valencia, Venezuela. That's Southern Caribbean. Basically according to the Geno 2.0 I'm 67% Iberian (the typical components of the Iberian within the 67%, with a bit more of 'South-west Asian'), 25% native American and 8% African. The 25% I mentioned is actually, according to Geno, 23% native American + 3% 'North-east Asian", but I suppose that 3% has to come from the native American part as it is not present in Iberians (unlike Finns or Russians).
My native American ancestors were probably from the Carib groupinhabiting the Valencia Lake region. A little bit to the East began the Arawak region. Arawak territory was also Hispaniola and most of those islands, while the Caribs were expanding from what is now Central and Eastern Venezuela+Guyana towards Trinidad and further to the North.


I know other Latinos from Mexico and Peru or Mexican Americans got South-east Asian or Oceania instead of North-east Asian.
It would be nice to see those Asian proportions distributed in America and try to see if they tell us something about the Arawak-Carib divide (well, there was much more than this but in the Carib that was the main picture when Europeans arrived).

There were many immigrants from the Canary Islands indeed but at the very start there were probably more from Extremadura and Andalusia. It seems part of my paternal ancestors (and may others from my region) came in the XVI century from Badajoz (Extremadura) . I have very specific data about the distribution of surnames across Venezuela and you can see very clearly the founder effect in the case of one of my surnames: from the coast in Borburata towards the place where my great-grandparents grew up (not far from the coast, actually), just as the records mention, and in Spain the clusters are in Badajoz and Almería.
The Canary Islands started to send a LOT of people to America specially after Portugal split from Spain in the XVII century and then later in the XVIII century (and after that). We then got a lot of people from the Basque country and Galicia in the XX Century, with less from the Castillas and even less, so it seems, from Catalonia.

Matt said...

It's interesting that a subgroup of Italians seems to be positioned parallel to the Latin European.

What's up with that?

I wonder if they could be the Sardinians...

I can see the argument that drift could shift, but would drift move this population aligned with the same vector which Sardinians and Basques are shifted on?

One possibility, seems to me that their process for isolating the European component in the Latin Americans (resurrecting a "zombie") may have inadvertently "scrubbed" (to use a Dienekes-ism) the European ancestry in an Iberian direction.

...

The largest dimension (PC1 is always the largest dimension in terms of explained variance) separating British Isles and ESE rather than NNE and ESE seems unusual as well.

truth said...

@ Matt

Yes, those are the Sardinians, you can see a very similar PCA here :

http://img801.imageshack.us/img801/3687/pca.png

Mark D said...

Kepler - IMO Geno2 is not the way to go if one is trying to distinguish Colonial from European admixture. 23and Me has a better product. Several of my Cuban friends (I live in Miami) have tested with Geno2, 23andMe and FTDNA. One has some native Canary Island ancestry which apparently shows up as North African, not Iberian. He also has Galician and Asturian ancestry which appears to show as a mixture of Northern Europe and Iberian (Celtic, Visigothic, Suevi?)

One question I have is how African was defined in this, as I too cannot access the article. Most admixture studies separate North African from Sub-Saharan African. The authors refer to slave-trade pulses, but clearly, some African component can predate emigration to the New World.

Grey said...

Apparently some of the Caribbean islands (but not all?) received many already mixed-race Creole slaves and laborers from the Atlantic islands. This population may have a Jewish component as Jews from Spain and Portugal fleeing the Inquisition had settled on those islands.

Baldric said...

When considering founder effects, take into account the disproportionate number of Basques engaging intercontinental travel until de 1700s.
Almost all basques were considered low-tier nobility, with provinces with as high as 97% of their population being hidalgos. Since nobles had much bigger chances of crossing to the indies (military, appointed civil sevants, etc), then they represent a big % of the ancestry.

They don't necessarily represent much of the male lineages because their daughters were more likely to marry into the next wave of migrants and stay in the higher end of society.

Grognard said...

Am I the only one tired of hearing about founder effects and drift? Especially in cases like this when we know, historically speaking, how much iberia has changed. Not just once but over and over. Portugal was practically speaking completely depopulated of portuguese people and castillans are probably not far behind.

Onur said...

The largest dimension (PC1 is always the largest dimension in terms of explained variance) separating British Isles and ESE rather than NNE and ESE seems unusual as well.

NNE is not a realistic grouping, as it includes populations as genetically distant as Hungarians and Finns. Note that Hungarians are genetically much closer to ESE (some of them are as close to ESE as some Romanians and some ex-Yugoslavians are) than Finns are.

terryt said...

"two pulses of African migrants, coinciding with early and maximum activity stages of the transatlantic slave trade. These two pulses appear to have originated in different regions within West Africa, imprinting two distinguishable signatures in present day Afro-Caribbean genomes and shedding light on the genetic impact of the dynamics occurring during the slave trade in the Caribbean"

That fits my understanding of the slave trade. The 'early' source was mainly the very far western tip af Africa (today Senegal and points immediately south) while the 'maximum' source tended further south from Sierra Leone, Nigeria and even as far south as Angola. I have no idea if the paper comes up with those regions however.

70b27f10-cfa3-11e2-8fa4-000bcdcb5194 said...

Grognard, there is no record of the Portuguese people being (practically speaking, lolz) completely replaced in the modern era or that displacement happened over and over. I think you're confusing what happened in the Neolithic with the modern era or perhaps you have a very interesting theory about space aliens beaming up the Portuguese.

Kepler said...

Crognar,

Spain hasn't changed that much. Surnames started to be used in Spain rather early compared to Northern Germany, what is now Benelux and probably Britain.
The initial settlers in Spanish America were by far from Andalusia and Extremadura. Cortés in Mexico, Pizarro in Peru were from Extremadura (actually, they were cousins). Narvaez was also from Extremadura. Some of my ancestors who arrived in Venezuela in the XVI century. Parts of Venezuela was going to be called Nueva Extremadura (by the leader of the expedition that took part of my relatives to the Caribbean). Chile in Southern South America was called for a longer time Nueva Extremadura. Colombia was called Nueva Granada until the Independence. The vast majority of settlers came from the South and that is not new. We have the records from the Archivos de Indias with lots of details about the origin of settlers from very early on, for centuries. So: XVI century was by far mostly Andalusia and Extremadura. There were also Basques in leading positions, but they did not go massively and were even less likely to take their women with them (even with the others, there were more men crossing over, as we know).
Some Portuguese went to America while Spain and Portugal were one kingdom, then this receded until the XX century.

The Canarios started to flow after Portugal became again independent from Spain and Portugal closed its markets to Canarias and poverty there increased (XVII century).

There were more Basques coming in to such places as Venezuela in the XVIII century with the Casa Guipuzcoana, but still, the inmigration was not massive. Canarios were still more, and Andaluces.

And in the XX century Spanish immigration changed: Canarios also came a lot (more to some countries than to others) but after Franco came to power in Spain, also more Basques, Gallegos and then, finally, Catalans, which were initially not so numerous (although there were some exceptions like the founder of Nueva Barcelona).

The statistics as well known.
I have data about surname distribution in Venezuela and you can clearly see founder effect. You see that incredibly in the case of some of the surnames found in my family, you can almost see the trace where they came from Extremadura, where their focus is, etc.

Castellanos migrated less.

As for Africans: this is also well known, as Terryt said.

The Portuguese were clearly having the control of slavery for several decades in the XVI century. Most of their slaves came from an area going from Senegal to the Gambia.

John Hawkins started to break through this monopoly by making several expeditions stealing slaves from the Portuguese and stealing them directly from the same region, around 1564-1569 (+-).
He took several hundred slaves then.


Afterwards Portugal established more colonies Southwards and eastwards and so did the English, the French...and they took more and more slaves from Congo and the South.

I think there were more Asturianos to Cuba than to Venezuela or other countries until the mid XX century, I think, but I have no details about that.

Here you can see a map of regions in Spain and emigration in the XX century:

http://es.wikipedia.org/wiki/Emigraci%C3%B3n_espa%C3%B1ola

It would be interesting if an expert in Spanish emigration could work together with the people investigating the DNA of the Caribbean.

Grognard said...

Portugal had a total population of a million and did a ton of colonizing. Even before colonizing the americas its manpower was taxed in spite of giving refuge to over 100,000 sephardic jews. There was a huge influx of people from castille just to keep the country populated, because so much of the population went to the ships and to India and other Asian ports.

That's not even counting effects of the effects of muslim expansion which had its greatest effect there. Just because someone was in castille at that point I am not sure you could truthfully call them "castillian". How long since any ruler was actually of the old kingdom of castille before the reconquista started, let alone all the common folk, once the colonization began?

If there's a big difference between the canarie islanders and basques that make them "hyper iberian" then it's obvious how that came about. They were a refugium for what iberia was like before.

Personally I don't put much stock in any of these population studies because you are in essence talking about averages of averages and comparing them to other averages of averages which makes it hard to put any real force into your conclusions, but a founder effect makes zero sense here.

This is more like irish americans versus the Irish in Ireland. Guess what, Ireland is not all that Irish any more compared to Irish Americans. There's more redheads and freckled faces in the USA PER CAPITA than in Ireland where it came from in the first place, let alone amongst Irish Americans without the other US citizens counted. Most of the immigrants were already the most irish in the first place, from connacht and ulster, ireland having been swarmed over many times and with steady influx from outside for a couple centuries has had a huge effect.

I suspect that's the case here. No, not suspect that's just fact.

Grognard said...

Sorry to double post but I think this should be adressed. Really this paper should not have been published, the conclusion is just absurd.

When you say something is caused by a founder effect it's like saying "it's all a big Co-Incidence!". It's basically the null hypothesis.

While I just said I don't really like the population comparisons, this is EXACTLY what they are good for, to DISPROVE stupid hypotheses like this.

If it were radom happenstance you could expect the change to be in any direction whatsoever given a random population. The fact it's EXACTLY in the direction of being more "Iberian" says a LOT. Without looking close at the maths I can't give exact details but it's simply implausible to make that conclusion. No other conclusion is reasonable except that they either came from a refugium or else the iberians now are a heck of a lock less iberian than the iberians of not that long ago.

El Lurker said...

Grognard, Kepler is right.

In the XVI and XVII centuries most of the colonizing was done by andalusians and extremadurans.
We have the date from the people who left Spain in Spain, and the latin american records of spaniard in Latin America. I think Boyd Bowman is the name of the historian who has a book with the geographical origin of 53 thousand spaniards who emmigrated to the americans in the XVI century.

The people from the Crown of Aragon were banned, so no catalans, valencians or aragonese. It was mostly done by people from southern spain.

Perhaps what should be taken into consideration is that southern spain was quite depopulated during the reconquista because spaniards that had converted to Islam feld, so the emmigrants to the Americas came from an area that had been quite depopulated and quite reconolinez by northerners.

It was not a massive phenomenon, perhaps 2000 or 3000 people per year (which in a century means hundreds of thousands of people)

Extremadura and the area of Sevilla were responsible for most of the ammigration.The population of extremadura went from half a million to half of that.
Both Cortés and Pizarro were from Extremadura, so, founder effect makes sense.

Matt said...

One possibility, seems to me that their process for isolating the European component in the Latin Americans (resurrecting a "zombie") may have inadvertently "scrubbed" (to use a Dienekes-ism) the European ancestry in an Iberian direction.

OK, so had a chance to look a bit more closely at this. My understanding of the method now is that they used ADMIXTURE K=3 based on a multi-continental panel to tag segments of the "Latino" genomes as European, African and Native American, then and then projected these onto a PCA generated from the continental European samples (and then African, etc.).

I think what would have been an interesting consistency check for them would have been to replicate this technique across all the populations they were including in their PCA and then see how this affects spatial relationships.

I wouldn't see that this would change the relationships *much* overall, but, for example, the Portuguese sample at K=3 (p27) registers with what looks like a few percent African and the Scandinavian samples reflect a few percent Native American (and the Italian and Greek samples have some of each to a lesser extent). If the Latino genomes are scrubbed to remove more non-European ancestry (as estimated by Admixture) than is actually the case in European genomes, it perhaps isn't a surprise that they look hyper-European.

And of course these Admixture components in Europe may not actually reflect any real population mixing in Europe subsequent to the departure of the European progenitors of the Latino populations (it may reflect admixture predating the Latino founders, or it may just not actually be admixture but an imperfect way to describe European patterns in genetic diversity).

Annie Mouse said...

All of the Caribbean nations studied in this paper were settled by the Spanish and are Spanish-speaking to this day. The exception is Haiti which was settled by the Spanish but became French. I cant find any of the 6 Haitians, identified with a cross, on this plot.

Basically all the populations studied/visible were settled by the Spanish and had ongoing population flow to this day. I would have been astonished if the European component had been non-Iberian, given the history.

Why not look at some of the many Caribbean nations that are not Spanish? Like Spanish-settled Trinidad which has been British since early in its history. That might show how much is old Spanish and how much is more recent. Or St Lucia which resisted European settlement. Or the French and Dutch settled islands.

This paper is a welcome contribution, but it is very Hispano-centric. Its like the rest of the Caribbean does not count. Its really a paper on the Spanish speaking Caribbean, not the Caribbean as a whole.

Grognard said...

But southern castille today isn't hyper iberian so the point still stands.

If it were a founder effect in the sense they are claiming then southern castille would show up as hyper iberian.

Since it's not it means iberianness has changed since then.

Annie Mouse said...

"Why not look at some of the many Caribbean nations that are not Spanish? Like Spanish-settled Trinidad which has been British since early in its history. That might show how much is old Spanish and how much is more recent."

On thinking about it. Jamaica would be a better test of old Spanish input. Settled by Spain and later the British. With very little Spanish contact afterwards. Trinidad has a small ongoing flow from Venezuela.

Grey said...

"The exception is Haiti which was settled by the Spanish but became French."

In the K diagrams in the PDF (pg 27) Haiti has a very different pattern to the other places.

Kepler said...

Annie Mouse,
There are many more Trinidarians in Venezuela than the other way around. When Britain invated Trinidag, most Spaniards (there were about 2000, if I remember well) fled to continental Venezuela.

fmgarzam said...

Sorry to join late.
Two things should be considered there.
Early settlers, founders, were mostly seafearing people, merchants.
Mortality. The rate was incredibly high.
Seafearing people and merchants with some sort of experience in tropical places would be the logical
origin.
That would place southern Andalucians and Portuguese ( lots of them went to populate Canarias) as main candidates. Italians there would probably be Genoese, Tuscan and the southerners (the alter ruled at that time by Castillians).
I sort of guess or extrapolate from my reading of Santo Domingo (lots of Portuguese-Sevillians there too) and pearl farming in early Venezuela (Lepe's Andalucians). Some Basque too.
In a few words, look at the make of Columbus' crews.
Boyd-Bowman is great work but does not reflect well early arrivals and special places. Say Caribbean, very north and very south of America.
Funny me, in North Mexico might be closer related to Caribbean people than Mexico City's.
I search for De La Garza and Lepe people trails in other places than Monterrey, Mexico.