Essay: Primary Colonization Models for Peopling of the Americas

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Over the past few decades, genetics has become essential in calculating the arrival time of the first migrations into present day America as well as determining the genetic composition of these first inhabitants. While the archaeological record is demonstrably useful in the reconstruction of migration patterns, a bias exists which poses that the likelihood of finding the first of any specific fossil or artefact is almost entirely unlikely. Thus meaning, that while archaeology can provide us with direct evidence of the first peopling of the Americas, it is unwise to depend on this field of study independently. Genetics, therefore, has proven essential in filling the gaps left by archaeologists and contributing probable dates of population splits from East Asia and then Beringia. This founder’s effect which inevitably lead to the population of North and South America has been largely uncovered by sequencing the genome of modern indigenous Americans and comparing these haplogroups to the genome-wide database. By sequencing both Mitochondrial DNA (mtDNA) and Ancient DNA (aDNA), it has now been confirmed that the Amerinds’ genetic history is mostly the result of one basal ancestral lineage. Exceptions to this will be analyzed in further detail, however, it is clear through genetics that one initial migration through the Bering Strait is responsible for the majority of ancient genetic makeup seen in Native Americans. Further, simulations of genetic variability and gene frequency of loci have been utilized in the debate on whether the initial colonization coincides with the Rapid Expansion or the Coastal Migration Model. Genetic sequencing has therefore provided scientists with further understanding of the potential initial routes into the Americas, indicating that this migration provided reoccurring gene flow with East Asia, and that given major mtDNA haplogroup lineages are largely responsible for the present-day allele frequency of indigenous American populations.

Two Primary Colonization Models for Peopling of the Americas:

When analyzing the initial colonization of the Americas, there are two widely debated models which aim to explain the migration route and time of this first expansion. One of these potential explanations, The Rapid Expansion (“Blitzkrieg”) Model (REM), was most widely excepted prior to the debunking of the “Clovis First” hypothesis (Fix, 2002). The Rapid Expansion Model was initially proposed by Martin (1973) and claimed that the first occupants of the Americas were hunters crossing the Beringian land bridge through the Ice Free Corridor when sea levels were lower approximately 11,500 years ago (Fix, 2002). There are two main implications with this model, one of which is the debunking of Clovis First with the discovery of Western Stemmed Points at the Gault Site in Texas in lower stratigraphic order than Clovis technologies (Williams et al., 2018). The second discrepancy in the REM model lies with the implications of Martin’s purported rate of population growth. Martin’s assumed population growth rate of 3.4% yearly would result in a doubled population after the 20 years following the initial founder’s effect from Siberia (Fix, 2002). He claims that in 17 generations, 100 initial individuals were capable of populating all of what is now North and South America (Fix, 2002). This hypothesis is incredibly problematic because such a fast rate of colonization means an extreme depletion of genetic variability. Therefore, even if one overlooks that REM does not coincide with the late occupation on Monte Verde, Chile 14,500 years ago, the depletion of genetic variability from a founding population of 100 would likely yield an extremely high heterogeneity. (Fix, 2002). This concept was simulated by Cavalli-Sforza (1986) using the equation (FST = 1 – π (1 – 1/2 Ne ) to calculate the expected within population variation, FST, when reoccurring budding events occur (Cavalli-Sforza 1986). Results indicated that after 20 generations over a potential 1000-year period, FST yields a heterogeneity of 0.855 which is so high that it almost reaches the maximum bracket of 1 (Cavalli-Sforza 1986). It’s further remarked that the among-population variation analyzed in Amerinds range from 0.1 to 0.2, thus indicating that the REM model does not reflect the FST accounted for in indigenous Americas (Cavalli-Sforza 1986).

The second and currently the more excepted route for the initial migration into the Americas is the Coastal Model (CM). The Coastal Model was initially suggested by Fladmark (1979) and posits an initial colonization along the coast by using rafts and then later spreading inland by utilizing river channels (Fladmark, 1979). Dixon (1999) suggested that the CM could have been accessible 13,500 years ago or prior, which allows for additional migration time and not requiring as large as a population expansion as the previously discussed REM (Fix, 2019). The CM is a preferred migration route genetically speaking due to the availability to spread over larger areas more rapidly and the availability to copulate with nearby groups who are not as genetically similar allowing for continuous gene flow. One explanation attempting to explain the further migration patterns once the initial colonization through the CM occurred, is termed the Leapfrog Hypothesis or Linear Model suggested by Anderson and Gilliam (2000). This concept suggests that when areas become overly occupied, the population growth no longer increases, but migration between surrounding population continues (Anderson and Gilliam 2000). This concept was simulated by Fix (2002) using 10 neural alleles with a frequency of 0.5 in the given population meant to represent the first individuals occupying the northwest coastal region of North America (Fix, 2002). The population growth in this given group and surrounding areas was Nt-1 = Nt (1+A(1-Nt)/Nmax) in which A represents the growth rate of 0.007 years and Nmax represents the maximum population size of 250 in a given group (Fix, 2002). It was purported that once a population size exceeded 250, migration to the next southward territory would occur within a portion of the population (Fix, 2002). This process of having a stepping-stone migration would permit each generation to have random intergenerational genetic drift. Further, a series of migrations would transpire while also allowing for returning colonies to further allow for gene flow. Under this model, a purported migration of 4km a year would allow for populations to reach Tierra de Fuego in a couple of thousand years without subsequently producing high heterogeneity. This can be seen in the result of the simulation which indicates that as opposed to REM, the Coastal Model had no fixed loci at the end of 100 generations and furthermore FST values indicate that the initial genetic variation was preserved in all original populations (Fix, 2002). Given the simulation of population growth using the Leapfrog Model, it appears that the Coastal Model would be more probable due to a higher frequency of intergenerational genetic drift allowing for the preservation of genetic variation between populations seen in current indigenous Americas.

Scenarios of Settlement

There is a common agreement that the founders effect of individuals dispersing into the Americas was through the Bering Strait; however, some discrepancy exists on the exact migration from Asia. While the initial settlement of the Americas occurred in one primary event, there has been multiple disagreements about the number of migratory waves following this preliminary founder’s effect and the timing of these models (Ray et al., 2010). Greenburg and colleagues suggested that the initial migration into the Americas were by the Clovis people approximately 13,000 years ago which resulted in the Amerind linguistic family (Greenberg et al., 1986). Two further migrations following were proposed to of been associated with the formation of the Na Dene and Eskimo Aleutian linguistic families (Greenberg et al., 1986). Greenburg and colleagues’ proposed sequence of settlement has been largely under criticism due to the archaeological findings that the first American populations predated Clovis and genetic data has concluded that it’s pre-Clovis (Ray et al., 2010; Williams et al., 2018). Therefore, recent statistical calculations by Ray and colleagues have been utilized in the attempts to compare Single-Wave (SW), Two-Wave (2W), and Recurrent gene flow (RGF) evolutionary models (Ray et al., 2010). Approximate Bayesian computation (ABC) has proved useful in analyzing these models by simulating data and comparing results in regards of sample size and frequency of loci (Ray et al., 2010).

The first model under scrutiny is a SW model, which claims that all Native American genetic diversity is the result of a single migration from Asia Tw1 generations ago, and claims no gene flow was present between the two continents after this initial migration (Ray et al., 2010). The depiction of the SW model can be found on the far-left side of figure 1 and illustrates the single Tw1 event from the Asia- America population resulting in a bottleneck (Nb) into present day America. 2W model builds off of the initial migration mentioned previously, but posits for a second more recent migration of individuals isolated for 10 generations from Asia prior to their arrival into the Americas (Ray et al., 2010). The center diagram in figure 1 shows illustrates this by the second red arrow later in time that the initial Tw1 event. This period of isolation is the 2W model would mean that a separate bottleneck from Asia occurred after the initial wave of migration (Ray et al., 2010). The third model, RFG, allows for continuous gene flow between Asia and the Americas as indicated on the far right side of figure 1 (Ray et al., 2010). In this particular simulation, it’s assumed that each population would have a short time of isolation between the migration from Asia to the Americas (Ray et al., 2010). To test these three varying waves of migration, Ray and colleagues utilized the world wide data set where 29 Amerindian populations were yielded and were subsequently compared with 39 Central Southern Siberian and East Asian populations (Ray et al., 2010). Microsatellites were recoded into number of repeats and those which did not fit a precise stepwise mutation model were coded as absent (Ray et al., 2010). Loci with high mutation rates due to dinucleotide repeats were also removed, thus resulting in a final set of 401 loci (Ray et al., 2010). The results from this simulation using a conventional ABC framework rejected the SW model and favored the RGF model. The SW model proved to be the least compatible fit yielding posterior probabilities lower than 2W (Ray et al., 2010). RGF proved to be the best fit for the models due to a posterior probability <0.96 for all six possible combinations of Asian and American data (Ray et al., 2010). Further, the results indicated that the level of Native American diversity would require frequent gene flow between Asia and America to reach the observed level seen in aDNA (Ray et al., 2010). Therefore, it seems highly probable that the there was a reoccurring gene flow between the two continents after the initial migration into what is now North America.

Primary mtDNA Haplogroups

When it comes to understanding the initial colonization of the Americas, the molecular genetic study of Native Americas has become increasingly useful. In particular, research on mitochondrial DNA (mtDNA) which is passed down through matrilineal decent, has indicated there are five major haplogroups (A,B, C, D, and X) found in Native American populations (O’Rourke and Raff, 2010). The frequency of these particular five haplogroups, indicated as A2, B2, C1b, C1c, C1d, D1, and X2a have given rise to approximately 95% of Amerindian mitochondrial DNA from a female founding population (Tamm et al., 2007). The additional 5% possesses the sub-haplogroups D2a, X2a, D4h3a, and C4c (Tamm et al., 2007). Haplogroup A is defined as Hae III enzyme restriction located at nucleotide 663 (Merriwether et al., 1995). This lineage is most common in North America and doesn’t appear dependent on a linguistic group (Merriwether et al., 1995). Haplogroup B is present in the case of a 9-bp Region V deletion, while Lineage C is defined when there is a loss of a Hinc II restriction on nucleotide (nt) 13259 (Merriwether et al., 1995). MtDNA from haplogroup B indicates at least one coastal entry due to it not being found in northern groups of North America and its rarity in South America (O’Rourke and Raff, 2010). Lineage D occurs when there’s a loss of an Alu I restriction at nt 5176 (Merriwether et al., 1995). The X haplotype is more rare and is found only in northeastern North America (O’Rourke and Raff, 2010). Further, the X haplogroup is particularly interesting due to it not being strongly associated with East Asia like the previous four groups (Tamm et al., 2007). Rather, the X haplogroup likely diverged genetically approximately 20,000 to 30,000 years ago into the X1 and X2 subgroups and is most strongly genetically associated with Mediterranean Europe and the Near East (Tamm et al., 2007). It has been purported by Perego and colleagues that the distribution of both the rare sub-haplogroups X2a and D4h3 indicate an initial migration route and then a subsequent passage when the Ice Free Corridor was open due to these lineages appearing to possess such strong geographic situation (O’Rourke and Raff, 2010). These five haplotypes are present due to a 9-base deletion, restriction fragment length polymorphisms, and through sequencing the primary hypervariable portion of the non-coding D-loop (O’Rourke and Raff, 2010). The number of polymorphisms which are particular to American haplotypes indicate a population expansion somewhat recently in evolutionary terms (O’Rourke and Raff, 2010; Raff et al., 2011). While there are some discrepancies when comparing the dates of haplogroups due to different potential mutation rates and calibrations, a commonly accepted date for indigenous American mtDNA haplogroups is 20-15 ka (O’Rourke and Raff, 2010). A relatively recent study conducted by Llamas and colleagues (2016) sequenced 92 entire mitochondrial genomes from pre-Columbus South American skeletonized individuals from 8.6 to 0.5 ka and applied previously discussed Bayesian coalescent analysis to reconstruct calibrated dates of the first peopling of the Americas (Llamas et al., 2016). The data yielded a group of individuals who eventually entered into the Americas were in isolation in eastern Beringia for approximately 2.4 to 9.0 years after separating from Siberia (Llamas et al., 2016). Further, it appears that a small group of this isolated population then entered the Americas 16.0 ka through the coastal route discussed previously (Llamas et al., 2016). Therefore, if the dates yielded from this sequencing and ABC method are accepted, this means that mtDNA sequencing has provided the most advanced reconstruction of the timing after the separation from East Asia and subsequently provides concrete genetic evidence in favor of the CM route.

Concluding Remarks

The migration paths and dates for the initial colonization of the Americas have widely been debated; however, with the relatively recent rise of sequencing whole genomes and applying statistical analysis, there has been quite a bit more clarity to some of these pressing questions. Throughout the entirety of this review paper, it has been illustrated that genetics has provided transparency to some of the most widely debated migration topics. It appears that the current verdict on whether the primary population entering from eastern Beringian into the Americas was by the Coastal Migration route. This route allows for frequent gene flow due to a leapfrogging effect, and it appears that this route coincides most with pre-Columbus mtDNA sequences, as seen in the Llama and colleagues article. Further, once entering into the Americas most likely through the CM, there seems to of been reoccurring gene flow between East Asia and Northern Europe. Ancient DNA of Native Americans indicated that the gene frequency seen would only be the result of frequent gene flow between the two continents, further supporting the CM route. Lastly summarized in this review paper, the importance of mtDNA in both understanding the unique five haplogroups found in the Americas and also recreating a calibrated sequence of dates for population divergence. These three main topics attempt to display the hypothesized routes through history and subsequently how particular migration paths have been supported by genetics in the aims to accurately refit the past. There does appear to be two primary ethical obstacles in sequencing the genome of indigenous American populations. The first is that the exact allele frequencies found in present day Native American populations was more than likely impacted by the colonization periods following first settlement prior to 15.0 ka (i.e. Columbus, European pilgrims, etc.). Second, to sequence aDNA from deceased pre-Columbus Native Americans is increasingly difficult due to current laws in place rightfully protecting the land and the deceased individuals of these groups. Due to the recent history and detrimental impacts on Native American populations, extra care must be maintained when working with genome sequencing in these indigenous groups. Nonetheless, when explicit consent is given to a geneticist and hopefully the results are shown to these individuals, the outcome of these sequences can provide monumental in uncovering pieces of the past.

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