mtDNA of Yumans and Athapaskans

Am J Phys Anthropol DOI: 10.1002/ajpa.22237
Exploring prehistory in the North American southwest with mitochondrial DNA diversity exhibited by Yumans and Athapaskans

Cara Monroe et al.
A recent study of mitochondrial DNA variation in Native American populations from the American Southwest detected signatures of a population expansion of subhaplogroup B2a, dated to 2,105 years before present (99.5% confidence interval, 1,273–3,773 YBP), following the introduction and intensification of maize agriculture in the region. Only one Yuman group and no Athapaskan speakers were analyzed in previous studies. Here we report mtDNA haplogroup and hypervariable region (HVR I, and II) sequence data from 263 extant Yuman speakers, representing the major branches of the Yuman language family, in addition to the Western Apache (Athapaskan) to further investigate the demographic context and geographic extent of this expansion. Data presented indicate that the expansion of B2a is only slightly older [2,410 YBP (99.5% CI: 1,458–4,320 YBP)] than previously estimated and not significantly. Despite large confidence intervals there are implications for the origin and expansion of the Yuman language family. Cultural transformations due to the inundation and draining of Lake Cahuilla may explain in part the frequencies of this lineage among the Kumeyaay and other Yuman and Takic groups in Southern California. This may have been the result of group fissions and fusions followed by migration and interaction that included expanded trade networks and intermarriage among Yuman speakers. In addition, a series of in-situ genetic bottlenecks is proposed to have occurred among the Western Apache leading to increasing homogeneity within haplogroup A, culminating in an admixture event with the Yavapai.
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Aztec conquest of Xaltocan led to population replacement

Aztec conquest of Xaltocan led to population replacement

This study represents a good example of how ancient DNA analysis can supplement traditional archaeology. Issues of population replacement/continuity are often encountered in archaeology, especially when there are traditions of conquest/resettlement, or such events might be hypothesized by changes in the material record.

But, such events are often difficult to interpret, because people living through periods of turmoil might have a tendency to exaggerate their importance, while culture is malleable and may shift without large-scale population replacement.

Am J Phys Anthropol DOI: 10.1002/ajpa.22152

The Genetic Impact of Aztec Imperialism: Ancient Mitochondrial DNA Evidence From Xaltocan, Mexico 

Jaime Mata-Mıguez et al.

In AD 1428, the city-states of Tenochtitlan, Texcoco, and Tlacopan formed the Triple Alliance, laying the foundations of the Aztec empire. Although it is well documented that the Aztecs annexed numerous polities in the Basin of Mexico over the following years, the demographic consequences of this expansion remain unclear. At the city-state capital of Xaltocan, 16th century documents suggest that the site's conquest and subsequent incorporation into the Aztec empire led to a replacement of the original Otomí population, whereas archaeological evidence suggests that some of the original population may have remained at the town under Aztec rule. To help address questions about Xaltocan's demographic history during this period, we analyzed ancient DNA from 25 individuals recovered from three houses rebuilt over time and occupied between AD 1240 and 1521. These individuals were divided into two temporal groups that predate and postdate the site's conquest. We determined the mitochondrial DNA haplogroup of each individual and identified haplotypes based on 372 base pair sequences of first hypervariable region. Our results indicate that the residents of these houses before and after the Aztec conquest have distinct haplotypes that are not closely related, and the mitochondrial compositions of the temporal groups are statistically different. Altogether, these results suggest that the matrilines present in the households were replaced following the Aztec conquest. This study therefore indicates that the Aztec expansion may have been associated with significant demographic and genetic changes within Xaltocan.

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Sweet potato genome provides link between South America and Polynesia

Sweet potato genome provides link between South America and Polynesia

The actual PNAS paper seems to be still under embargo, but here's a news story in Science about the new research:

By analyzing genetic markers specific to sweet potatoes in both modern samples of the plant and older herbarium specimens, the researchers discovered significant differences between varieties found in the western Pacific versus the eastern Pacific. This finding supports the so-called tripartite hypothesis, which argues that the sweet potato was introduced to the region three times: first through premodern contact between Polynesia and South America, then by Spanish traders sailing west from Mexico, and Portuguese traders coming east from the Caribbean. The Spanish and Portuguese varieties ended up in the western Pacific, while the older South American variety dominated in the east, which would explain the genetic differences the French team saw.

Apart from the famous Heyerdahl voyage (which has recently become the subject of a 2012 movie), there was some other research regarding the introduction of Polynesian chickens to Chile. I have not followed the genetics of that part of the world very closely, but it's my impression that such a link between Polynesia and South America has not been found in the human populations of the two regions.

Y-haplogroup Q and Native American origins (Regueiro et al. 2013)

Y-haplogroup Q and Native American origins (Regueiro et al. 2013)

From the paper:

Table 2 provides coalescence time estimations based on 15 Y-STR loci for haplogroup Q-M242 and subhaplogroups Q1a3-M346, Q1a3a-L54 and Q1a3a1-M3. Due to the limitations and assumptions associated with the current calibrations of Y-STR mutation rates (Zhivotovsky et al., 2004; Goedbloed et al., 2009; Ravid-Amir and Rosset, 2010; Burgarella and Navascue/s, 2011), the dates generated in this study should only be taken as relative estimates. However, these relative values may be useful for comparisons among populations. Using the pedigree mutation rate (average mutation rate of 0.0025 per locus per generation; Goedbloed et al., 2009), we obtained coalescence estimates that were approximately three times younger than those calculated with the evolutionary rate (average mutation rate of 0.00069 per locus per generation; Zhivotovsky et al., 2004). In general, the genealogical estimates are more compatible with archeological data than the evolutionary rates 

According to Table 2, the oldest TMRCA for M242 chromosomes is ~11ky using the pedigree rate and ~29ky using the evolutionary rate. In a previous post, I argued that in order to account for the fact that modern-day haplogroups have millions of modern representatives, a fairly high growth rate must be assumed for them, with one estimate of the effective rate being 0.84μ, where μ is the genealogical rate. Ergo, the ~11ky time estimate must be updated to something like ~13ky, which corresponds reasonably well -within the confidence limits- to the first colonization of the Americas.

The paper's conclusion:

Overall, our data are best explained by invoking a single major pre-Holocene migration that proceeded eastward in a trans-continental trek across Beringia and then southward to transverse the length of Americas-a scenario that fits nicely with the South Altaian origin of Native Americans as proposed by Dulik et al. (2012). The subsequent winnowing of the Native American gene pool via repeated founder effects and bottleneck events could have produced the Y chromosome distribution illustrated on the pie map (Fig. 2). The Q haplogroup frequency pattern of the Native Americans features: 1) a dramatic reduction of the ancestral L54 and MEH2 lineages of Central Asia and/or northeast Siberia and 2) a concomitant increase in the derived M3 state, which exerts total domination of the Q landscape in nearly all of South American reference populations examined. We also see evidence of a dramatic Mesoamerican postmigration population growth in the ubiquitous and diverse Y-STR profiles of the Mayan and other Mesoamerican populations in the PCA (Fig. 4), and the M242 and M3 networks (Fig. 5A,D). In the case of the Mayans, this demographic population growth was most likely fueled by the agricultural- and trade-based subsistence adopted during the pre-Classic age of their empire. Our results indicate that the oldest dates for Q-M242 are found in Northeast Siberia followed by populations from Mesoamerica, which is most likely a consequence of demographic expansion as discussed above. The diversity levels observed in the Altaian and Tuvinian regions of Central Asia, the lowest of all populations examined may be the consequence of bottleneck events fostered by the spatial isolation and low effective population size characteristic of a nomadic lifestyle. 

It seems likely that the migration of Q-M242 descendants corresponds mainly to the "First Americans" sensu Reich et al. (2012) which makes up the bulk of Amerindian Y-chromosomes. Interestingly:

The recently sequenced genome of a Paleo-Eskimo _ 4,000 years old, belonging to the Saqqaq culture, provides evidence for a more recent migration from Siberia into the New World some 5.5 kya, independent of the pre-Holocene penetration that gave rise to the modern Native Americans and Inuit (Rasmussen et al., 2010). In addition, the Paleo-Eskimo individual is a member of the haplogroup Q1a*-MEH2 suggesting that this lineage likely traces a population migration originating in Northeast Siberia across the Bering Strait (Rasmussen et al., 2010). 

and:

In the MDS plot, we observe a segregation between Eskimo populations from northeast Siberia and the Native American populations, differentiation likely due to the northeast Siberian presence of the MEH2 mutation which defines the Q1a* haplogroup.  

So, it would appear that the additional "Eskimo" wave may be discernible within Q itself; the third "Na-Dene" wave cannot be distinguished on the basis of Q alone, and probably reflects the later entry of haplogroup C.


Am J Phys Anthropol DOI: 10.1002/ajpa.22207

On the Origins, Rapid Expansion and Genetic Diversity of Native Americans From Hunting-Gatherers to Agriculturalists

Maria Regueiro et al.

Given the importance of Y-chromosome haplogroup Q to better understand the source populations of contemporary Native Americans, we studied 8 biallelic and 17 microsatellite polymorphisms on the background of 128 Q Y-chromosomes from geographically targeted populations. The populations examined in this study include three from the Tuva Republic in Central Asia (Bai-Tai, Kungurtug, and Toora-Hem, n = 146), two from the northeastern tip of Siberia (New Chaplino and Chukchi, n = 32), and two from Mesoamerica (Mayans from Yucatan, Mexico n = 72, and Mayans from the Guatemalan Highlands, n = 43). We also see evidence of a dramatic Mesoamerican post-migration population growth in the ubiquitous and diverse Y-STR profiles of the Mayan and other Mesoamerican populations. In the case of the Mayans, this demographic growth was most likely fueled by the agricultural- and trade-based subsistence adopted during the Pre-Classic, Classic and Post-Classic periods of their empire. The limited diversity levels observed in the Altaian and Tuvinian regions of Central Asia, the lowest of all populations examined, may be the consequence of bottleneck events fostered by the spatial isolation and low effective population size characteristic of a nomadic lifestyle. Furthermore, our data illustrate how a sociocultural characteristic such as mode of subsistence may be of impact on the genetic structure of populations. We analyzed our genetic data using Multidimensional Scaling Analysis of populations, Principal Component Analysis of individuals, Median-joining networks of M242, M346, L54, and M3 individuals, age estimations based on microsatellite variation utilizing genealogical and evolutionary mutation rates/generation times and estimation of Y- STR average gene diversity indices.

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