Widespread population decline in South America correlates with mid-Holocene climate change

Abstract

Quantifying the impacts of climate change on prehistoric demography is crucial for understanding the adaptive pathways taken by human populations. Archaeologists across South America have pointed to patterns of regional abandonment during the Middle Holocene (8200 to 4200 cal BP) as evidence of sensitivity to shifts in hydroclimate over this period. We develop a unified approach to investigate demography and climate in South America and aim to clarify the extent to which evidence of local anthropic responses can be generalised to large-scale trends. We achieve this by integrating archaeological radiocarbon data and palaeoclimatic time series to show that population decline occurred coeval with the transition to the initial mid-Holocene across South America. Through the analysis of radiocarbon dates with Monte Carlo methods, we find multiple, sustained phases of downturn associated to periods of high climatic variability. A likely driver of the duration and severity of demographic turnover is the frequency of exceptional climatic events, rather than the absolute magnitude of change. Unpredictable levels of tropical precipitation had sustained negative impacts on pre-Columbian populations lasting until at least 6000 cal BP, after which recovery is evident. Our results support the inference that a demographic regime shift in the second half of the Middle Holocene were coeval with cultural practices surrounding Neotropical plant management and early cultivation, possibly acting as buffers when the wild resource base was in flux.

Full text

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Widespread population decline in
South America correlates with mid-
Holocene climate change
Philip Riris & Manuel Arroyo-Kalin
Quantifying the impacts of climate change on prehistoric demography is crucial for understanding
the adaptive pathways taken by human populations. Archaeologists across South America have
pointed to patterns of regional abandonment during the Middle Holocene (8200 to 4200 cal BP) as
evidence of sensitivity to shifts in hydroclimate over this period. We develop a unied approach to
investigate demography and climate in South America and aim to clarify the extent to which evidence
of local anthropic responses can be generalised to large-scale trends. We achieve this by integrating
archaeological radiocarbon data and palaeoclimatic time series to show that population decline
occurred coeval with the transition to the initial mid-Holocene across South America. Through the
analysis of radiocarbon dates with Monte Carlo methods, we nd multiple, sustained phases of
downturn associated to periods of high climatic variability. A likely driver of the duration and severity
of demographic turnover is the frequency of exceptional climatic events, rather than the absolute
magnitude of change. Unpredictable levels of tropical precipitation had sustained negative impacts
on pre-Columbian populations lasting until at least 6000 cal BP, after which recovery is evident. Our
results support the inference that a demographic regime shift in the second half of the Middle Holocene
were coeval with cultural practices surrounding Neotropical plant management and early cultivation,
possibly acting as buers when the wild resource base was in ux.
e initial human colonisation of South America was a rapid process that led to the dispersal of hunter-gatherer
populations to every major biome on the continent within a few millennia, starting at the latest around 14 k
calendar years before present (cal BP). Colonising groups successfully adapted to a broad range of environments
during the Terminal Pleistocene and early Holocene, from the Amazonian rainforest and Patagonian grasslands
to the high Andes1–4. e genetic and demographic structure of early populations have been the focus of sub-
stantial recent research5,6. In parallel, a growing body of archaeological evidence from several regions has sug-
gested that climatic transitions acted as a driver of signicant regional depopulation during the mid-Holocene.
Discontinuities in archaeological records have specically been linked to increasingly unpredictable climatic
regimes around this transition. Abandonment or retreat to refugia is suggested to have occurred in central
Amazonia7, the south-central Cordillera8,9, eastern Brazil10, the Sabana de Bogotá11 and the Puna de Atacama12.
e inferred existence of mid-Holocene demographic regime shis in these widely distributed environments
indicates that exogenous factors inuenced human populations across the continent concurrently at this time.
Here we investigate pre-Columbian demographic dynamics to investigate the resilience of early South
American foraging adaptations to periods of abrupt climate change. We focus specically on the initial transition
to the Middle Holocene (8.2–4.2 k cal BP13), during which South America was characterised by overall more arid
conditions14. Large-scale analyses using of South American radiocarbon data as a population proxy have previ-
ously noted exceptionally low relative population around ~8.2 k cal BP5. We posit a connection between sudden,
high-amplitude alterations to hydroclimate and widespread archaeological evidence of upheaval among human
populations associated to the mid-Holocene transition. Globally, demographic overturn together with climate
change has been suggested as a major driver of prehistoric culture change over this interval, with radiocarbon
data proving especially instrumental in this regard15–18. In South America, the broad range of research intensities,
historical trends in scholarship, preservation conditions, and site formation processes, against the backdrop of
its cultural and ecological diversity3, requires any analysis to be undertaken in explicitly quantitative terms. We
attend to this by assessing relative change in prehistoric South American demography using summed probability
UCL Institute of Archaeology, 31-34 Gordon Square, London, WCH1 0PY, United Kingdom. Correspondence and
requests for materials should be addressed to P.R. (email: p.riris@ucl.ac.uk)
Received: 4 December 2018
Accepted: 16 April 2019
Published: xx xx xxxx
OPEN
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distributions of calibrated radiocarbon dates (Fig.1, hereaer SPDs) combined with Monte Carlo simulation
as an indirect proxy for demographic patterns over time19–21. To contextualise these ndings, we also identify
the frequency of hydroclimatic anomalies during the mid-Holocene across multiple palaeoclimatic time series
(Methods), with the assumption that ecological shis of direct consequence to human adaptations will track
hydroclimatic regimes.
We initially test the radiocarbon record of South America against the same null hypothesis of exponential
growth for the period 12–2 k 14C years before present, based on an assessment of curve shape and goodness-of-t.
Following the detection of statistically signicant negative departures from this model starting at ~8.2 k cal
BP, we expand our approach through a two-phase demographic model with the goal of pinpointing where a
demographic regime change is most likely to start (Fig.2). Next, following preceding research22, we dene our
mid-Holocene demographic expectations with reference to prevailing dynamics prior to the phase of decline in
order to condition our expectations of what constitutes a signicant departure against the prevailing trend iden-
tied in the prior regime.
We also disaggregate the data into three regions for further analyses, comprised of: (a) the northern and central
Andean Highlands, foothills, and foreland basin, (b) the tropical Lowlands of Amazonia and circum-Amazonia,
and (c) the Southern Cone, incorporating the southern Andes, Pampas, and Patagonia. ese subdivisions
target variation in the structure of the archaeological data within broad topographic, biogeographical, and cli-
matic realms. With reference to the systems driving rainfall variability across South America (Supplementary
Information), these regions respectively approximate areas principally inuenced by moisture transportation
from the Atlantic, areas inuenced by the Atlantic and potentially Pacic sources, and predominantly South
Pacic/South Atlantic-inuenced zones13,23–25. e Southern Cone, as dened here, also acts as a geographical
proxy for the southern limits of tropical domesticates prior to the beginning of the late Holocene6,26. We take
consistent patterns in the radiocarbon data to reect robust and independent trends in human population across
regions rather than specic archaeological cultures. ese patterns permit identication of demographic sensitiv-
ity to climatic variability on a scale below that of the continent as a whole (Methods). We discuss the behavioural
and social consequences of climatic variability during the mid-Holocene for the pre-Columbian population of
South America based on the available archaeological data, as well as the role of climate as a driver of cultural
change in general.
Results
Our results show that the demographic trend for South America falls signicantly below expectations for popu-
lation growth aer 8.6 k cal BP. Aer this point in time, periodic and statistically signicant population deation
in the archaeological 14C record is apparent on a continental level, lasting at least until 6 k cal BP (p < 0.001,
Fig.2, le). is indicates that exceptional deviations from early Holocene demographic regimes occurred. e
millennial-scale downturns associated to the initial Middle Holocene can be subdivided into three phases begin-
ning with the initial dip in the demographic proxy at ~8.6 k cal BP, followed by ~7.7 k cal BP and nally ~6.9 k cal
Figure 1. Archaeological sites and radiocarbon data: (a) Kernel-smoothed intensity of sites (white dots) for
12–2 k 14C years before present, measured in points/km2, (b) Histogram of median calibrated radiocarbon ages
placed in 200-year bins, (c) Summed probability distribution of calibrated radiocarbon dates for entire South
American dataset with a 100-year rolling mean (black solid line), shown with the highly correlated exploratory
model tted to data (exponential red dotted line), R2 = 0.971, Pearson.
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BP. ese are bracketed by brief periods of recovery lasting two centuries or less. Aer the initial mid-Holocene,
there is a return to model expectations, which are exceeded by ~5.3 k cal BP, likely marking the transition to a
new demographic regime aer ~6 k cal BP5. Our index of variability (Fig.2, right) is derived from a robust outlier
analysis of multiple palaeoclimatic records that together provide spatial coverage of precipitation patterns across
South America. Our summary index shows a rapid increase starting at 8.6 k cal BP, concurrent with the rst
phase of downturn, peaking more than two standard deviations above the dataset mean at ~8.4 and 8.2–8.1 k
cal BP. Following a short hiatus coincident with recovery, a second spike prefaces a second bout of demographic
reduction aer ~7.7 k cal BP. A third (~6.9–6 k cal BP) phase of sustained population decline spans the transition
to more arid conditions that are typically recognised in the mid-Holocene of South America23. is is visible as a
trough in our variability index punctuated by less intense yet above-average variability around 7.2 k and 6.5 k cal
BP. Placing the frequency of hydroclimatic anomalies before and during the mid-Holocene transition alongside
our demographic proxy illustrates the extent to which these patterns are coeval in time.
e next set of analyses aims to identify spatial variability in demographic dynamics associated to the middle
Holocene. Disaggregating the archaeological 14C record into three regions formally describes signicant variation
in the distribution and intensity of demographic downturns, underscoring that the impacts of climatic variability
are themselves variable in space (Fig.3). Negative and positive deviations in the permutation tests reect periods
where subsets of the data signicantly exceed the overall continental trend27, indirectly conrming the existence
of a continent-wide decline starting at ~8.6 k cal BP. It is important to note the reason for conformity between the
summed probability distributions around 8.2 k cal BP. We nd a lack of signicant downturn in relation to the
overall trend in the continental dataset consistent with the South America-wide downturn identied separately
(see Fig.2). As indicated by the null model test, the entire modelling domain is experiencing a demographic con-
traction at this time, which masks the statistical distinctiveness of coeval downturns in subsets of the data. e
absence of a signicant negative signal at this time in this test is therefore to be expected.
Together, the permutation tests reveal a staggered temporal structure in the summed probability distributions
over the mid-Holocene chron. e tropical Highlands and Lowlands trends both show signicant yet out of phase
negative deviations from the continental condence envelope. e Highlands appear responsive to heightened
aridity around ~6 k and ~5 k cal BP, while declines in the Lowlands appear around 7 k cal BP. Inverse demographic
trends exist between the Lowlands and Southern Cone at this time and between the Highlands and Southern
Cone around 6 k cal BP. We observe that the most sustained local deviations in the Highland and Southern Cone
data occur aer 6 k cal BP, albeit opposite trends (negative and positive, respectively), while the Lowlands experi-
ences only centennial-scale negative deviations. Pairwise regional comparisons with permutation tests (Fig.S2)
concordantly show that the tropical Lowland and Highland SPDs return non-signicant p-values, indicating
statistical similarity, while both are signicantly dierent from the Southern Cone. Together, our results indicate
that a common mechanism may have inuenced tropical South America, separately from the subtropical and
temperate biomes of the Southern Cone. To this eect, we note signicantly higher relative population in this
region already by 7.5 k cal BP and repeatedly thereaer, with none of the negative phases experienced elsewhere.
In summary, we performed a parameter sweep on a broad range of possible null models for the Early and
Middle Holocene. is indicated a critical breakpoint occurred at 8.6 k cal BP. To investigate the degree of depar-
ture from this stable (weakly linear) post-colonisation trend, we conditioned our null model on this data. When
Figure 2. Test of summed probability distribution of calibrated archaeological 14C dates against a null model
(grey shading) and climatic variability index. Le: Starting at 8.6 k cal BP South America experiences three
phases of signicant population deation (blue shading). By the end of the mid-Holocene, the continental
summed probability curve exceeds the null model (red shading). Right: (I) Exceptionally high climatic
variability characterises the beginning of the mid-Holocene, with three time steps within 200 years of 8.2 k cal
BP having an incidence of anomalies more than two standard deviations (light blue dashed line) above the mean
(dark blue dashed line). (II) A second phase of cyclical high variability persists in the early mid-Holocene until
6.5 k cal BP.
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tested against simulated radiocarbon data generated with Monte Carlo methods, our results show a repeated and
statistically signicant downturn of varying duration and intensity aer 8.6 k cal BP, concurrent with increas-
ing climatic variability from this point in time. ese phases last until at least 6 k cal BP, at which point a sec-
ond regime shi appears likely5. Further testing reveals centennial-scale depressions in the archaeological 14C
record are present across highly diverse environmental and cultural settings, revealing widespread population
decline during the mid-Holocene. Regional dierences are detected through comparison with the structure of
the continent-wide dataset (Fig.3), and identies separate phases of downturn in the tropical Highlands and
Lowlands data. In contrast, the Southern Cone remains largely above or within the continental condence enve-
lope. In statistical terms, the tropical Highlands and Lowlands reveal approximately equivalent demographic
Figure 3. Permutation test of regional summed probability distributions, highlighting mid-Holocene
asynchrony in the period 9 k – 3 k cal BP. Top: Tropical Highlands, the Northern Andes and Pacic Coast,
Middle: Tropical Lowlands, Amazonia and circum-Amazonia, Bottom: Southern Cone, Southern Andes,
Patagonia, and Pampas. Regional SPDs are compared against a 95% condence envelope generated by randomly
permuting the regional aliation of each radiometric date (1000 runs). Signicant deviations above (magenta)
and below (cyan) the continental trend (95% condence, grey) are asynchronous and frequently in antiphase
between tropical South America and the Southern Cone.
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trends with some local dierences, while the Southern Cone is signicantly dierent from both. Signicant posi-
tive divergences from the continental trend suggests that this region apparently did not suer the same degree of
downturn during periods of high climatic variability. Accounting for time-dependent site loss and spatial variabil-
ity in preservation and research intensity (Methods), the weight of the statistical evidence suggests that the depth
of the mid-Holocene downturn reects much more than an oscillation of local population levels around a stable
mean5. Rather, our results indicate that a phased demographic contraction over a period of several centuries
took place across South America. Strong synchrony is evident between all three regions following peak climatic
variability (Fig.2). Aer the initial mid-Holocene, however, regional demographic responses diverge. Below we
discuss possible impacts and consequences of this pattern in terms of the social and bioclimatic changes experi-
enced by indigenous South Americans during this period of interest.
Discussion
An initial period of high climatic variability spans the transition from the early to the middle Holocene. ree
steps (8.4k, 8.2k, and 8.1 k cal BP) have an exceptionally high frequency of anomalies and the ramping up of
frequent anomalous events shown in our index (Fig.2) correlates with the initial drop in relative population
observed across South America at and aer 8.6 k cal BP. Archaeologists have repeatedly pointed to mid-Holocene
aridity across South America as a mechanism driving occupational hiatuses in multiple localities, indicative of
abandonment or logistic range reductions tethered to more predictable resources7–12,27. As illustrated by our
archaeological summed probability distributions, signicant departures from the quasi-stable Early Holocene
regime occurred at least until 6 k cal BP, in the form of several protracted periods of population decline. A second,
attenuated phase of anomalous climatic events following the initial extreme phase reveals the continuing impact
of climatic variability on human populations. Our results indicate that precipitation variability, as well as absolute
reductions in moisture, may have acted as joint drivers of demographic change in leading up to and in the rst
half of the Middle Holocene28,29. Importantly, the point identied as a probable demographic regime shi here is
independent of the palaeoclimatic records included in our index.
A key inuence on summer monsoon precipitation is the seasonal procession of the Intertropical Convergence
Zone (ITCZ) and its interaction with the South Atlantic Convergence Zone (SACZ) over tropical South America.
As the magnitude of ITCZ movement southwards is ultimately driven by orbitally-forced changes in North
Atlantic surface temperature, negative anomalies result in a northerly (<10 °S) mean latitude of the ITCZ23. is
leads to a reduction in precipitation in eastern Brazil and southern Amazonia, generally in antiphase to wetter
conditions in the northern and western portions of the continent during such events, including the tropical
Andes24,30. Our selection of proxies (Fig.S3) provides a long-term average of variability in this mechanism in
latitudinal cross-section across tropical South America, as well as a separate index of precipitation in the southern
mid-latitudes of the continent, which are predominantly inuenced by the relative strength of Pacic wester-
lies31. Furthermore, simulated precipitation grids (Fig.4, top) suggest that the highest variance at the start of
the mid-Holocene occurred in a broad arc across the tropics, from the north of the continent to eastern Brazil,
inected via western Amazonia. e central Amazon and circumscribed areas of the Pacic coast experienced
the least variability in tropical precipitation patterns over this period. e latter agrees with the suppression of
the ENSO phenomenon in the Pacic during the mid-Holocene32, although overall the southern latitudes of
the continent present the least variable precipitation patterns. Although ora responded to overall more xeric
mid-Holocene conditions, biome-scale vegetational transitions appear not to have been severe when averaged
over approximately four millennia30,33,34. Foragers adapted to the diverse terminal- and post-glacial environments
of South America2,4 consequently also reacted in varying ways.
We propose that a combination of factors was responsible for sustained demographic downturn evident in the
summed probability distributions. Relatively sudden, high-amplitude variability in precipitation patterns acted
as “climatic shocks”35 that provoked the downturns observable in our demographic proxy (Figs2–4). Following
initial spikes in climatic variability, depressed tropical moisture availability in the mid-Holocene23,36 may have
caused small changes in precipitation to have disproportionate impacts on human-occupied niches. Populations
that were adapted to early Holocene conditions may have rst suered negative impacts to their resilience, trans-
lating to increased vulnerability to comparatively small-scale climatic events aer 8.2 k cal BP. Concordantly,
where climatic instability is less pervasive, for example in the Southern Cone as dened here (Fig.4, bottom), the
negative eects on demography are lessened in comparison to regions where some degree of climatic oscillations
endured, as in the tropical Highlands and Lowlands. Nonetheless, aer 6 k cal BP, our archaeological 14C proxy
in tropical regions is suciently recovered to be consistent with, or exceed, model expectations. e continental
condence envelope is surpassed in the Highlands by the onset of the early Holocene at 4.2 k cal BP, while the
Lowlands do so well before this point in time (Fig.3).
Amidst the geographically-variable eects of climate change, South American populations themselves enacted
modications to local ecosystems through the deployment of plant management and cultivation practices37–40.
e precocious use and dispersal of comestible and useful plants began in the Early Holocene in South America,
and the long-distance translocation of crops such as peanut (Arachis hypogaea), manioc (Manihot esculenta), and
maize (Zea mays) by the mid-Holocene40,41 highlights the deep antiquity of cultivation practices in the Neotropics.
ese and other species were integrated into diversied and likely regionally-specic multi-crop procurement
systems at various times aer 8.2 k cal BP37,39,42. e deliberate and incidental use of re to modify local ecolo-
gies also inuenced and shaped the environmental niches of which these crops were a part43–46. We suggest that
the development of these intertropical systems is a crucial development in the context of signicant population
reduction relative to earlier periods. Under the stresses induced by both demographic and environmental condi-
tions, anthropic ecologies that already incorporated cultivated or managed resources before the mid-Holocene
may have become proportionately more important to subsistence strategies in the face of an unstable climate28,47.
e increasing visibility of cultivated plants in the palaeobotanical record from the mid-Holocene could suggest
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that climate change may have promoted the incorporation of a greater proportion of managed plants into trop-
ical forager subsistence systems40. Population recovery during the second half of the mid-Holocene (aer 6 k
cal BP) is consistent with a orescence linked to a diversied and more stable resource base following climatic
stabilisation to a drier yet steady phase7,48–53. A possible outcome of these cultural and environmental trajecto-
ries was the emergence, in some regions, of population aggregation and social institutions for the coordination
and control of previously-unprecedented population densities among South American populations by the Late
Holocene26,47,50–55.
Understanding mid-Holocene demographic patterns is predicated on our consideration of climatic variability,
as well as against the backdrop of developments in cultivation practices. We follow recent research in noting that
the scale of anthropic environmental legacies is necessarily linked to relative population over time43,45,56. Our
examination of the archaeological and climatic record of South America provides a continental-scale framework
for understanding the interplay between population dynamics and food procurement diversication over the
mid-Holocene, as well as questioning at what point climate change or instability demands alternative pathways
be adopted by human populations. In this regard, the broadening of the trophic niche of humans through the
adoption of a greater proportion of plant resources may have functioned as a buer against environmental unpre-
dictability6,28,29,40. We can generalise that human populations in this period experienced signicant and sustained
periods of demographic downturn on a continental scale. ese demographic processes were not uniform in
either time or space and likely encompass substantial variation below the spatial scale we have adopted here. In
particular, previously-identied local responses to mid-Holocene climate change require further investigation in
the context of our ndings.
e demographic signals highlighted on a broad scale in this work are composites of local archaeological
records. Statistically signicant deviations, whether negative or positive, invite further investigation into the
trajectories adopted by human populations at a variety of spatial scales and settings. We anticipate that more
Figure 4. Correlating variance in Austral Summer (December-January-February) and Winter (June-July-
August) precipitation during period of highest Mid-Holocene instability (8.4–7.9 k cal BP) and tropical versus
extra-tropical demographic patterns. Top: Maps are based on 11 simulated grids of the TRaCE-21ka experiment
in 50-year time steps in 50-year intervals. Grid cell resolution of the circulation model is 2.5°, projected
to Albers Equal Area Conic for South America. e Southern Cone displays the overall lowest variance in
precipitation over the mid-Holocene in both summer and winter. Bottom: Inverse demographic trends in the
tropical highlands and lowlands during the Middle Holocene.
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research, ideally combining computational vegetation reconstructions and landscape modelling, will help to for-
mally characterise how the demography of South America was shaped by, and in turn shaped, environmental
conditions in the long term. Systematic assessments of cultural and biotic resilience to hydroclimatic variability
are necessary to understand the development of both domains in the millennia following the human colonisation
of South America.
Methods
Archaeological radiocarbon analysis. Our analysis employs a database of archaeological radiocarbon
determinations compiled from a continuous and ongoing survey of the published academic and grey literature,
with an especial focus on Amazonia. Our own collection is cross-referenced to large pre-existing databases5,57
and corrected with reference to the original published sources. Our data collection resulted in a set of 5450 radi-
ocarbon determinations for the interval 12 k – 2 k 14C years before present. In contrast to previous compilations
over this period5, we furnish a much larger sample of radiocarbon dates for Amazonia and circum-Amazonia,
providing better control over this area.
We make use of the R package ‘rcarbon 1.2’58 to perform statistical analyses on our data. Following estab-
lished frameworks for the aggregate analysis of archaeological 14C, we examine summed probability distributions
(SPDs) of calibrated radiocarbon dates as a proxy for relative change in population over time. is approach to
archaeological radiocarbon data rests on the assumption that higher past populations deposit more archaeo-
logical material to date, in turn resulting in the production of radiocarbon determinations commensurate with
ancient demography21,59–61, i.e. an assumption of monotony between dated archaeological charcoal and past pop-
ulation levels. Sampling bias, time-dependent and spatially variable taphonomic loss, laboratory errors, calibra-
tion curve uctuations, and sample contamination can potentially introduce systematic errors that obscure or
exacerbate genuine demographic signals in the 14C record. Our mitigation measures for these issues are described
in detail in the Supplementary Information. Deletion and loss of archaeological sites is unlikely to have operated
on spatiotemporal scale sucient to bias the record of an entire continent consistently7,8,10,50, and we take our 14C
data to be broadly representative despite expectations of some localised site loss.
We initially perform the analysis on the entire South America dataset. However, the global trend may mask
signicant regional variation in potential subsets of the data. With reference to spatial structure, sites tend to be
highly clustered in, for example, the desert coast of Peru, while being diuse in the central Amazon basin, ren-
dering a single clustering metric inappropriate for discovering viable subdivisions. Formal methods for group-
ing spatial point patterns such as k-means or density-based clustering are, respectively, unable to adapt to the
arbitrary shape of the point pattern and the high variation in the spatial density of sites. For the purposes of the
analysis, we choose to partition the South American radiocarbon data into three to investigate human population
patterns and capture variation in the structure of the data within broad biogeographical and climatic realms,
rather than any specic archaeological cultures or phenomena. e appearance of consistent patterns in the radi-
ocarbon data should therefore reect robust and independent cross-regional demographic trends. An objective
of our study is to consider coeval shis in demographic and climatic regimes at and around the transition to the
Middle Holocene (8.2 k cal BP).
We have opted to divide all sites located above the 300 m elevation contour into northern and southern subsets
along the Peru-Chile border, to form the core of the Highlands and Southern Cone datasets. Both sets include Pacic
coast sites located to the west of the elevation cut-o point. We assigned dates from Bolivia in La Paz, Oruro, and
Cochabamba departments to the Highlands, and those located in Chuquisaca, Tarija, and Potosí to the Southern
Cone. e remainder of the Southern Cone consists of dates from Uruguay, Argentina, Paraguay, and the Brazilian
states of Paraná, Rio Grande do Sul, and Santa Catarina. Sites located below 300 m above sea level and outside of
the abovementioned elevation boundaries form the Lowlands dataset. ese criteria produce three subsets of the
data that group lowland Amazonia with the Guianas, the Orinoco basin, and northeast Brazil (here the Tropical
Lowlands), the northern Pacic coast and Andes with the Amazonian foreland basin and foothills (here the Tropical
Highlands), and nally the southern Pacic coast and Andes with the Pampas, Patagonia and the southern Brazilian
highlands (the Southern Cone). With reference to the climatic systems that drive rainfall variability across South
America (Supplementary Information), our subdivisions correspond approximately (in order) to areas principally
inuenced by moisture transportation from the Atlantic, areas inuenced by the Atlantic and potentially Pacic
sources, and predominantly South Pacic/Atlantic-inuenced zones13,23–25. e Southern Cone also functions as a
geographical proxy for the southernmost range of tropical domesticates before the late Holocene6,26.
e statistical modelling presented here principally concerns the mid-Holocene, but we carry out our anal-
yses on dates in the interval 12–2 k cal BP. Dates pre-dating 12 k 14C years BP were excluded, as were those with
Gaussian errors of >200 years. Although the initial peopling of South America was underway by 14 k cal BP, and
possibly earlier4, the sparse evidence available for this period and its distance from the mid-Holocene makes it
less germane to this study. Our initial analyses on the 5450 radiocarbon determinations acquired for the entire
continent employ the following protocol:
i. Calibration. Radiocarbon dates are calibrated and aggregated by site into non-overlapping phases over the
period 12–2 k 14C BP, and we report on the results from a focused time range of 9 k – 3 k cal BP. Aggrega-
tion of dates from the same site into bins of 200 years is carried out to account for the overrepresentation
of well-dated sites. We principally make use of the SHCal13 curve62 for calibration (Fig.S4), except for
determinations on marine shells, for which the Marine13 curve63 is used. is calibration curve is oset
from the terrestrial curves by several centuries to account for the incorporation of ancient carbon from
ocean upwelling into mollusc exoskeletons. In addition, we calibrate marine dates using local averaged ΔR
osets and errors by interpolating to the geographically-closest sampling site, acquired through an online
repository64.
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ii. Summation. e probability distributions of the calibrated dates are summed for the entire South Amer-
ican continent. We do not normalise the post-calibration probability distributions, to reduce the eect of
peaks and plateaus in the calibration curves on the shape of the nal SPDs19 (Sensitivity Analysis).
iii. Model testing. We initially test the South America-wide SPD against a simple tted exponential population
growth trend. Our choice is guided by an information criterion indicating maximum goodness-of-t with
this model over linear and logistic growth models (Sensitivity Analysis). A sample of calendar dates equal to
the number of bins are drawn from the tted model, converted to 14C dates, re-calibrated, and their probabili-
ty distributions summed. We opt to draw from the uncalibrated date distribution. Errors for the re-calibration
were generated by sampling with replacement from the empirical 14C errors of both marine and terrestrial
dates58. rough a Monte Carlo procedure of 1000 runs, we derive condence intervals for the null model.
iv. Regional permutation tests. rough the random assignation of marks to each date in the complete dataset,
in this case the regional aliation, a distribution of simulated SPDs are generated from 1000 Monte Carlo
runs27, from which 95% condence intervals are derived. e empirical SPDs were directly compared
with the pan-regional trend produced from permuting the marks of the full dataset (n = 5450). We also
performed pairwise comparisons of each of the three regions (Fig.S2).
e above procedures controls for the global eects of taphonomy and rst-order spatial processes such as sea
level rise, as exponential model tting mimics the eects of time-dependent loss and the permutation tests makes
use of the 14C determinations directly, in eect integrating the eects of taphonomic loss into the analysis27,65. Our
initial results with this exploratory null model suggest statistically signicant relative population decline during
the Middle Holocene. Nonetheless, the initial formulation of the null hypothesis may be responsible for this nd-
ing (a Type I error) and thus we extend our model testing further to resolve this issue.
We follow Silva and Vanderlinden22 in specifying a null model based on prevailing patterns prior to a target
period of interest rather than the dataset as a whole. rough inspection of our exponential model (Fig.1), we
rst note that this null hypothesis performs particularly poorly in the Terminal Pleistocene and Early Holocene,
and second, the SPD suggests a slow decline in the South American 14C record may begin already around 9 k cal
BP. Further testing (Supplementary Information) indicates that the point of divergence from approximately sta-
ble, weakly linear Early Holocene demographic regimes5 is most likely to have occurred at 8.6 k cal BP (Fig.S1),
providing a point of departure for investigating the degree to which mid-Holocene demographic trends diverge
from prior patterns. at is, instead of a single null hypothesis for 12–2 k cal BP, we condition our new null model
on the period 12–8.6 k cal BP to satisfactorily identify the degree of deviation aer this point in time.
Our protocols allow us to examine salient features of the South American radiocarbon record, specically: (a)
the degree and signicance of deviation in demographic trends from the null hypothesis of steadily increasing
population throughout the Early Holocene in our domain, and (b) the similarity of population trajectories in
each regional setting. Both sets of tests permit local and global tests of signicance to be estimated, and regional
population histories to be compared through z-transformation of the empirical and simulated SPDs58. We plot
the null models against the empirical SPDs with a running average over a century applied to smooth out artefacts
of the calibration process in the probability distributions.
Climate variability index. To our knowledge there is no single prevailing criterion for dening a climatic
anomaly, with a variety of thresholds, methods, and selection procedures reported in the literature66. To derive
a robust index of climate variability we use the Median Absolute Deviation (MAD), a measure of statistical dis-
persion, on a set of precipitation records with near-complete latitudinal coverage of South America (Fig.S3).
MAD provides a symmetrical estimate of the central tendencies of a time series, and eectively accounts for the
value of any given data point in the context of a rolling window. It is not sensitive to isolated extreme outliers or
non-normal distributions, and therefore correctly identies sudden, large-amplitude changes and oscillations
while excluding general trends. Here, we impose ±3 times the rolling MAD as a conservative threshold for iden-
tifying an extreme outlier. We scale the window to the resolution of each individual palaeoclimatic record to
approximate a 100-year rolling average and have selected records with a resolution sucient to allow a minimum
of three points per interval. Where records have multiple sources of data, for example two speleothems reported
from Lapa Grande cave, Brazil, the outlier analysis has been performed separately on these sources and subse-
quently combined.
We sum the identied anomalies from each record into 100-year bins to present them on a common time scale
of calendar years before present (cal BP) and produce an intuitive summary index of climatic outliers for conti-
nental South America. In addition to the high initial MAD threshold for dening an abrupt event in each indi-
vidual record, we suggest that frequencies of binned anomalies that are two standard deviations over the dataset
mean are indicative of signicantly above-normal climatic variability. Finally, we underline that the results simply
reect the sum of anomalies in a given time step, not their magnitude, spatial distribution, or whether they are
negative or positive deviations from the rolling MAD of a given precipitation record. Deriving a composite meas-
ure of climatic variability aims to contextualise our demographic data (Figs2 and 3) rather than directly infer the
state of the climate or environment itself. We rely on the interpretations palaeoclimatologists and palaeoecologists
to understand the conditions and impacts of climate on humans in our modelling domain.
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Acknowledgements
Data collection was partially funded by a UCL CREDOC Small Grant awarded to M.A.K. P.R. was funded by a
Visiting Fellowship at the Sainsburys Research Unit, Sainsburys Centre for Visual Arts, University of East Anglia
and a British Academy Postdoctoral Fellowship (PF2\180065) at UCL. e authors acknowledge the help of Fabio
Silva in developing elements of the methods reported on here.
Author Contributions
P.R. and M.A.K. conceived of the study; M.A.K. was principally responsible for data collection with input from
P.R.; P.R. designed and conducted the analyses; P.R. produced the gures and supplementary material; M.A.K.
aided P.R. in interpretation and framing the results. P.R. led the writing of the manuscript with critical feedback
and input from M.A.K.
Additional Information
Supplementary information accompanies this paper at https://doi.org/10.1038/s41598-019-43086-w.
Competing Interests: e authors declare no competing interests.
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