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ts. Already in 1690, the chronicler Francisco Antonio de Fuentes y Guzmán described the ‘Ladinos’ as ‘mestizos, mulatos and negros’. There is extensive historical docu- mentation indicating trend in Guatemala to marriages between different ethnic groups [1]. Although the demo- graphic impact of Europeans in Guatemala is difficult to quantify, it is estimated that in the beginning of the XVII century, the indigenous population surviving in Guatemala (and other Central American countries such as El Salvador) constituted only 10% of the total popula- tion living in the region before the arrival of Europeans [1]. The impact of the slave trade in Guatemala is also difficult to estimate. Some documentation indicate that in 1773, the population of Santiago de Los Caballeros de la Antigua Guatemala (‘the capital of Centro America’) had 30.000 people, and about 36% of them were ‘mulatos’ (admixed between Africans and Europeans or Natives), and in 1782, the ‘mulatos’ constituted 32% of a total of 13.000 inhabitants in the city of Nueva Guatemala de la Asunción [1] (the present Capital city of Guatemala). These figures could indirectly indicate the existence of an important amount of slaves in the regions. In contrast, the Trans-Atlantic Slave Trade Database (
http://www.slave voyages.org/) shows that only a few hundred slaves dis- embarked directly in Guatemala. However, the arrival of important amounts of slaves from other neighboring
countries that were more connected to the slave trade (such as Honduras and Belize) cannot be disregarded.
Among the present-day Maya from Guatemala, there are more than 20 different ethnic groups including the K’iche’ (9.1%), Kaqchikel (8.4%), Mam (7.9%), Q’eqchi’ (6.3%), and minority groups such as Achi, Akatek, Chuj, Ixil, Jakaltek, Poqomam, Poqomchi’, Q’anjob’al, Tz’utujil, Uspantek, etc. (altogether 8.6%; according to the 2001 census). Ethnicity names usually refer to the indigenous language spoken by the group members. Although Spanish is the official language in Guatemala today, there are 23 officially recognized Native American languages. It is not uncommon that people from one region of Guatemala do not understand the language of a neighboring region. For most Mayan inhabitants, Spanish is a second lan- guage, and many Maya do not speak Spanish at all in some areas of the country. Today, the largest proportion of the Guatemalan Maya population lives in the highlands (where the majority of the studied samples of the present study have been taken), but there are also inhabitants in other rural areas, such as El Quiché department. Other minority Native American groups in Guatemala are the Garifuna and Xinka (0.1%).
The Maya constituted vast kingships during a long period over the Mesoamerican landscape (a term de- scribing Mexico and Central America within which a number of pre-Columbian societies flourished before the
Spanish colonization in the XVI century [2]), a reign that lasted for about three thousand years (kya) and was one of the most advanced civilizations within the New World. The first concrete traces of the Mayan civilization (dating back to the Pre-Classic period around 1,800 BCE) were found in the Mirador Basin of the northern depart- ment of Petén (Guatemala), though some settlements are thought to be over 6 kya old [3]. The Mirador Basin is part of a larger region (known as the Guatemala’s Maya Biosphere Reserve) that overall is considered to be the cra- dle of ancient Maya civilization (>175 archaeological sites).
According to current knowledge, a single language existed among the earliest Maya. This Proto-Mayan is thought to have been spoken at least ~4 kya ago and may be the common ancestor of all modern Mayan lan- guages today, as well as the Classic Maya languages docu- mented in the hieroglyphic inscriptions [4]. Reconstructive and descriptive linguistic studies of ancient Proto-Mayan target the Guatemalan highlands as the birthplace of this ancestral language [5]. Because of the isolation of Maya posted by vast distances and the ecological diversity of their territories, regional conflicts, sporadic migrations, and ever-changing political systems, their language has had acquired many pronunciations, and over time, those dialects have spawned new languages [6].
During the Pre-Classic Period (2000 BCE–250 CE), a great linguistic diversity developed, comprising 16 lan- guage families. Unlike other scattered populations of Mesoamerica, the Maya were centered in one geograph- ical area covering the entire Yucatan Peninsula and modern-day Guatemala; Belize and parts of East Mexico; and the western region of El Salvador and Honduras.
It was during the Classic period (AD 250–900) that the Maya civilization reached the peak of its power and influence and it was one of the most dominant indigen- ous societies of Mesoamerica. During this period, the Mayan civilization had become a complex and dynamic entity of independent city-states undergoing a series of population expansions and contractions [5,7,8]. These fluctuations may reflect episodes of migration at various times during the Classic period. By the Late Classic period (AD 600–900), much of the Maya region was or- ganized into two competing “super-states,” headed by the hegemonic powers of Tikal and Calakmul [2,9]. By the terminal Classic period, massive declines in population size led to the abandonment of many Maya territories. The reason for this subsidence remains largely unknown, although theories invoke environmental over-exploitation with all of its consequences as well as constant warfare in a landscape divided among numerous competing city- states as the main reasons.
In the Post-Classic (AD 900–1,500) period, the frag- mentation process led to a fusion of Maya settlements from the southern Yucatán highlands into the regionally
dominating K’iche’ and later Kaqchikel states [5]. Con- stant strains within the Maya region and with non- Mayan groups (Aztecs and Toltec of Mexico) led to the final collapse of the civilization prior to the arrival of the Spanish [5].
Nowadays, Maya descendants occupy the territories of Mexico, Guatemala, Belize, El Salvador, and Honduras. Maya people mostly follow their traditional way of life, including costumes, indigenous languages, and religious ceremonies. One of their most remarkable cultural traits is the faithful count of days according to the Maya calendar.
Historic evidence based on patterns of material culture (ceramics), as well as geographic variability in agricul- tural practices and socio-political structures suggest a degree of regional isolation which leads to an explan- ation of the Classic Maya population structure as a model of isolation by distance (IBD). This model de- scribes the tendency of populations that are geographic- ally closer to be more similar than populations that are further apart [10]. Such a model would consider ancient Maya as relatively non-mobile population groups and inter-population gene flow restricted to neighboring sites. Over their millenary history and given the great distances between their communities, strengthened by separation through geographical barriers, warfare, and their political system of independent city-states, it may be expected that the Maya would have diverged into sev- eral distinct populations. Contradictory evidence (mostly inscription based) shows however long-distance trade, elite visits and marriage and intercity conflicts with captive-taking, as well as the mobility of general popula- tions. On the other hand, Mayan art, architecture and rituals suggest a high degree of cohesiveness throughout their domain. Overall, there is enough evidence indicat- ing that certain gene flow occurred across the entire Maya area during the Classic period.
While both a rich archaeological record and hiero- glyphic dataset led to a better understanding of the Clas- sic Maya population history compared to most other ancient Native American cultures [2], biological investi- gations of ancient Guatemala population history are mainly limited to osteology [11] and dental studies [12,13]. These studies arrived however to contradictory findings. Thus, dental morphology examinations found evidence for biological discontinuity at Seibal (Petén) be- tween the Late and Terminal Classic periods [14]. Using the same approach, it could be shown that skeletons of Jaina (Yucatán, Mexico) demonstrated a stronger affili- ation to the Petén site than they did to nearby Chichen Itza in Mexico [15]. In addition, distinct regional cluster- ing could not be found by odontometric comparison of individuals from five Maya sites in the Yucatán Peninsula [16]; these studies suggested that extensive gene flow