With the lower population estimates for the Taino population provided by one aDNA study, it is important to consider the estimates reached by historians. Although the case of Puerto Rico lacks reliable early censuses and maps of the various cacicazgos on the island at the time of Spanish contact and early colonial rule, Francisco Moscoso's Caciques, aldeas y población taína de Boriquén (Puerto Rico), 1492-1582 is a necessary read. Despite the limitations of our surviving sources and the incomplete state of archaeological research on contact-era sites in Puerto Rico, Moscoso's study is more careful than those of earlier historians who proposed unrealistically high figures (such as 600,000) or very low estimates, such as Brau's 16,000. Historians who were not methodological and consistent in their estimates of numbers of caciques and total population cannot be relied upon for those of us who are skeptical of the low population estimates from the aforementioned aDNA study.
In short, Moscoso concluded that the island probably had 44 caciques in the first two decades of the 16th century. This number is reached through corroborating the archival sources and chronicles, emphasizing the caciques who can be associated with a specific area or region. There may have been an additional 11 caciques whose existence Moscoso could not corroborate or cross-reference. Moreover, some of the identified 44 caciques may have been captains or nitainos serving under a cacique, but Spanish sources may have misidentified or reclassified Taino elites based on their own needs during and after the conquest. Some may disagree with Moscoso about the existence of female caciques, or cacicas, before the conquest. If Moscoso is correct, then the appearance of cacicas is actually a result of the Spanish manipulating and interfering with Taino indigenous political structures for their own benefit. We know that happened through the Spanish practice of using the Taino cacique and nitano as a privileged group for implementing the encomienda system. However, we still believe it is possible that women ruled as cacicas before contact, and that because women were already wielding such power, the Spanish found a way to intervene as husbands of cacicas in Hispaniola and Puerto Rico. Thus, the possibility of women cacicas and the likelihood that some of the 44 caciques identified in the Spanish may not have been original "caciques" suggests that the original number of caciques could have been lower or higher. The fragmentation of cacicazgo populations by splitting their populations between different encomiendas must have also changed or impacted demographics.
After establishing his estimate of around 44 caciques for the island, most of them in the key first two decades of the colonial era, Moscoso argued for a Taino population of around 110,000. This is proposed with reservations, but based on known data on Taino chiefdom's surplus-producing capacities and the figures derived from Las Casas. Intriguingly, we believe a similar reliance on Las Casas was used for Roberto Cassá's estimate of Hispaniola's indigenous population in 1492. If Las Casas was reliable, and our theories on the productivity of yuca agriculture and the structure of a typical aldea are correct, then perhaps such a high figure of 110,000 is plausible. But, Moscoso bases this on an average aldea possessing around 2500 people. This could have been the case for Puerto Rico, assuming each cacicazgo was producing a surplus of yuca based on mound agriculture and other crops. However, one would expect that each cacique ruled or controlled the tribute of cacicazgos with varying characteristics in productivity, types of crops, and political factors that shaped their relationship to other caciques. For that reason, we see an estimate of 2500 per cacique as too high.
Even if, one average, a typical Indian "head of household" included 10-15 relatives, that Las Casas may not have correctly identified the numbers associated with a family. Nor do we have sufficient knowledge of how many laborers enumerated in the larger encomiendas may have come from the same households. Of course, 600 Indians from Agueybana, likely only representing the laboring population, must have omitted perhaps 5 children per adult (as well as the aged and infirm). If so, then perhaps a high estimate of around 3000 can be reached for the case of some aldeas associated with powerful chiefs. But for those whose associated naborias only totalled around 100 or 150 in the 1510s, lower figures of around 500 or perhaps 1000 might be more reliable estimates. With that in consideration, perhaps the paramount caciques controlled populations of a few thousands while the rest may have headed aldeas or yucayeques of around 500-1000. We are inclined to therefore go for the lower range of estimates from Moscoso's model, perhaps somewhere between 44,000 to 88,000 Tainos inhabiting the entire island.
As for what happened to the 44,000-88,000 indigenous people of the island after the initial conquest, Moscoso rightly questions the low numbers provided in various sources after the de Lando census. The absence of "indios" in the late 1500s and 17th century sources does not constitute proof of a complete extinction narrative. Instead, it is very probable that colonial racial or color labels encompassed people who may have been classified as "indio" previously. Then, the reappearance of "Indios" in the later decades of the 18th century also suggests survival, although almost certainly not of any "pure" Indian communities. As the descendants of the indigenous population continued to exist, they also intermarried with people of African and European descent (like the cacica or widow of a cacique who married or became a lover to Pedro Mexia, a mulato). Over time, the indigenous culture continued to be the basis for much of the new mestizo culture of the rural population of the island. Their disappearance in the later sources may reflect a wish on the part of Spanish officials and encomenderos to minimize the populations under their control, hide illegal enslavement, and promote the African slave trade to repopulate the island with laborers. This, of course, does not minimize the horrors of the conquest as many indigenous people were slaughtered, enslaved, removed from their homes, subjected to raids, or sold into slavery. Many must have also fled Puerto Rico for other islands to escape the Spanish, causing a further decline in the native population.
