<figure><img src="image_15.png" /></figure>

**Appendix 1—figure 3.** ABC Prior-checking for *MetHis* simulations for each island separately. 10,000 simulations are conducted under each four competing scenarios of historical admixture considered in Random-Forest ABC scenario-choice (see **Figure 6**). (A) Goodness-of-Fit tests: we use as goodness-of-fit statistic the median of the distance between one target vector of 42 summary-statistics and the vectors of 42 statistics obtained for the 1% simulations in the 40,000 simulations reference table that are closest to the target (as identified by simple rejection *Pritchard et al., 1999*). Results obtained with the observed data as target are indicated in the vertical red line. Null-distribution of the goodness-of-fit statistics as histograms are obtained by considering as target in-turn 1000 random simulations as pseudo-observed data, for each island and for the 225 Cabo Verde-born individuals grouped in a single random-mating population, separately. (B) First two axes of a principal component analysis performed on the 42 summary-statistics obtained for 40,000 simulations per island (10,000 simulations for each of four competing-scenarios). Each point corresponds to a single simulation colored per scenario: simulations under Scenario 1 are in blue; Scenario 2 in green; Scenario 3 in red; and Scenario 4 in yellow (*Figures 6–7*). The pink white-circled dot corresponds to the vector of summary-statistics from the observed dataset. (C) Axes 1 and 3 of the same PCA projection as in panel B.

The online version of this article includes the following figure supplement(s) for appendix 1—figure 3:

**Appendix 1—Figure 3 supplement 1.** Density distributions (black line) of each of 42 summary-statistics obtained from 40,000 simulations, 10,000 under each of four competing scenarios for Santiago, compared to the observed statistic obtained in this island (red vertical line).

**Appendix 1—Figure 3 supplement 2.** Density distributions (black line) of each of 42 summary-statistics obtained from 40,000 simulations, 10,000 under each of four competing scenarios for Fogo, compared to the observed statistic obtained in this island (red vertical line).

**Appendix 1—Figure 3 supplement 3.** Density distributions (black line) of each of 42 summary-statistics obtained from 40,000 simulations, 10,000 under each of four competing scenarios for Santo Antão, compared to the observed statistic obtained in this island (red vertical line). The four scenarios are synthetically described in **Figure 6** and the 42 summary-statistics in **Table 3**.

**Appendix 1—Figure 3 supplement 4.** Density distributions (black line) of each of 42 summary-statistics obtained from 40,000 simulations, 10,000 under each of four competing scenarios for São Nicolau, compared to the observed statistic obtained in this island (red vertical line).

**Appendix 1—Figure 3 supplement 5.** Density distributions (black line) of each of 42 summary-statistics obtained from 40,000 simulations, 10,000 under each of four competing scenarios for Brava, compared to the observed statistic obtained in this island (red vertical line).

**Appendix 1—Figure 3 supplement 6.** Density distributions (black line) of each of 42 summary-statistics obtained from 40,000 simulations, 10,000 under each of four competing scenarios for Maio, compared to the observed statistic obtained in this island (red vertical line).
**Appendix 1—Figure 3 supplement 7.** Density distributions (black line) of each of 42 summary-statistics obtained from 40,000 simulations, 10,000 under each of four competing scenarios for Boa Vista, compared to the observed statistic obtained in this island (red vertical line).

**Appendix 1—Figure 3 supplement 8.** Density distributions (black line) of each of 42 summary-statistics obtained from 40,000 simulations, 10,000 under each of four competing scenarios for São Vicente, compared to the observed statistic obtained in this island (red vertical line).

**Appendix 1—Figure 3 supplement 9.** Density distributions (black line) of each of 42 summary-statistics obtained from 40,000 simulations, 10,000 under each of four competing scenarios for Sal, compared to the observed statistic obtained in this island (red vertical line).

**Appendix 1—Figure 3 supplement 10.** Density distributions (black line) of each of 42 summary-statistics obtained from 40,000 simulations, 10,000 under each of four competing scenarios for the 225 Cabo Verde-born individuals grouped in a single random-mating population, compared to the observed statistic obtained in this dataset (red vertical line).

The four scenarios are synthetically described in **Figure 6** and the 42 summary-statistics in **Table 3**.

## 1d. Random-Forest (RF) ABC scenario-choice cross-validation

We used the Random-Forest ABC algorithm implemented in the *abcrf* package in R (*Pudlo et al., 2016; Raynal et al., 2019*) for scenario-choice, as in the *MetHis-ABC* pipeline previously described (Fortes-Lima et al., 2021). Random-Forest classification has been shown to allow for robust ABC scenario-choice with relatively small numbers of simulations and, most importantly, to be unaffected by correlations among summary statistics; thus outperforming local linear regression classically used in ABC scenario-choice (*Beaumont et al., 2002*). Here, we considered the same prior probability (25%) for the four competing scenarios.

First, for each island separately, we used the *abcrf* function in this R package to conduct ABC scenario-choice cross-validation. Each of 40,000 simulations served in-turn as pseudo-observed data and the remaining 39,999 simulations as training (**Appendix 1—figure 4A**), using 1000 decision trees in the Random-Forest. We visually checked that prior error rates (the rates of erroneously assigned scenario in the cross-validation) were minimized for this number of decision trees, using the *err.abcrf* function in the same R package. Each summary-statistic's importance to the cross-validation accurate decision was calculated and plotted using the *abcrf* function (**Appendix 1—figure 4B**).

Second, for each birth-island and for Cabo Verde as a whole, separately, we used the *predict.abcrf* function on the trained Random Forest with all simulations in the reference table, to determine which competing scenario produced simulations whose summary statistics most resembled those from the observed data. We then estimate the posterior probability of accurately finding such winning scenario in our framework (indicated as "Post. prob. Scen." in **Figure 7B**).
<figure><img src="image_16.png" /></figure>

**Appendix 1—figure 4.** Random-Forest ABC scenario-choice cross validation results and summary-statistics' importance. We considered four competing scenarios as described in Genetic admixture histories in Cabo Verde inferred with MetHis-ABC and in **Figure 6**, with associated prior parameter distributions in **Table 2** and 42 summary-statistics described in **Table 3**, for each Cabo Verdean birth-island and the 225 Cabo Verde-born individuals grouped in a single random mating population, separately. Cross-validation results are obtained by conducting RF scenario-choices using, in-turn, each 40,000 simulations (10,000 per competing scenario) as pseudo-observed data and the remaining 39,999 simulations as the reference table. We considered 1,000 trees in the random-forest for each analysis. Cross-validation results and associated summary-statistics' importance for the RF decisions are obtained from the function *abcrf* in the R package *abcrf*.

**1e. Neural Network ABC posterior parameter inference procedures**

While RF-ABC scenario-choice procedures are specifically designed to accurately work with a relatively small number of simulations compared to classical regression ABC (*Beaumont et al., 2002; Pudlo et al., 2016*), posterior joint-estimations of all scenario-parameters under the winning scenario remain difficult in Random-Forest (Fortes-Lima et al., 2021; *Raynal et al., 2019*). In this context, our previous benchmarking of various ABC posterior-parameter estimation under the *MetHis* framework showed that Neural Network ABC joint parameter estimations outperformed other approaches (Fortes-Lima et al., 2021). However, Neural Network ABC posterior parameter inferences have been shown in multiple previous investigations, including ours with *MetHis*, to require substantial amounts of information in the reference table to perform satisfactorily (Fortes-Lima et al., 2021; *Csilléry et al., 2012; Jay et al., 2019*). Therefore, we conducted anew 90,000 simulations with *MetHis*, for each birth-island and for Cabo Verde as a whole, separately, under the winning scenario determined with RF-ABC, thus obtaining a total 100,000 simulations under the winning scenario, for each birth-
island or for Cabo Verde as a whole, separately, for further Neural Network ABC posterior parameter estimation using the *abc* package in R (Csilléry et al., 2012).

## NN-ABC parameter inference settings

We followed the same empirical approach as in *MetHis-ABC* (Fortes-Lima et al., 2021) to determine the most suitable number of neurons in the hidden layer and associated number of simulations closest to the target data and retained for training the Neural Network (called "tolerance level") for further NN-ABC posterior parameter estimation for this target. Indeed, there is no rule-of-thumb to determine these parameters a priori in order to obtain the most informative posterior parameter inference while minimizing overfitting using a Neural-Network approach under a given scenario (Csilléry et al., 2012; Jay et al., 2019).

Therefore, we empirically tested three different tolerance-level values to be used in NN-ABC posterior parameter estimation: 1%, 5%, or 10% of the total 100,000 simulations generated under the winning scenario determined by our RF-ABC procedure for each Cabo Verdean island and for Cabo Verde as a whole, respectively. Furthermore, for each one of the three tolerance-level values, we tested associated numbers of neurons in the hidden layer between 5 and 11, or 12, the number of free parameters minus one in the winning scenario for each Cabo Verdean island and for Cabo Verde as a whole, respectively (Figures 6–7).

Then, for each pair of tolerance-level value and number of neurons for each targeted data separately, we performed 1,000 cross-validation NN-ABC posterior parameter inferences using the *cv4abc* function in the *abc* package (Csilléry et al., 2012). This procedure draws 1,000 simulations at random and considers them, in turn, as pseudo-observed data for posterior-parameter inference using the remaining 99,999 simulations as the reference table. For the 1,000 pseudo-observed cross-validations and each pair of tolerance level and number of hidden neurons, we calculated the error between the median posterior point-estimate of each parameter ($\hat{\theta}_i$) and its' known true-value used for simulation ($\theta_i$), as the mean-square error (MSE) scaled by the parameter's variance across the 1,000 cross-validations (Csilléry et al., 2012):

$$ \text{Scaled MSE} (\hat{\theta}_i) = \sum_{1}^{1000} (\hat{\theta}_i - \theta_i)^2 / (1000 \times \text{Variance}(\theta_i)). $$

Therefore, we conducted, in total, 219,000 NN-ABC cross-validation parameter inference procedures to identify the NN-ABC settings most suitable for further posterior parameter estimations using the observed data for each Cabo Verdean birth-island and for Cabo Verde as a whole. For each Cabo Verdean island and for Cabo Verde as a whole, separately under the corresponding winning scenario, we chose the pair of tolerance-level values and number of hidden neurons that minimized the average error across all estimated parameters, as the Neural-Network setting used in further ABC posterior parameter inferences based on the observed data (Appendix 1—table 1).

## NN-ABC posterior parameter estimation

For each Cabo Verdean island and for all Cabo Verde-born individuals grouped in a single population, separately, under the winning scenario identified with RF-ABC, we jointly estimated the posterior distributions of all parameters using NN-ABC "neuralnet" method option in the function *abc* of the R package *abc* (Csilléry et al., 2012), with logit-transformed parameters ("logit" transformation option) using the tolerance level and number of neurons in the hidden layer identified previously in Appendix 1—table 1. For each birth-island and for Cabo Verde as a whole, separately, a synthetic schematic figure of the complex admixture processes identified using median point estimates of the posterior scenario-parameter distribution is provided in Figure 7, and full posterior parameter distributions with 95% Credibility-Intervals (CI) are provided in Figure 7—figure supplements 1–3 and Appendix 5—Tables 1–10.

## NN-ABC posterior parameter errors

We evaluated posterior parameter error rates and 95% CI accuracies in the vicinity of the observed data, for each island and for Cabo Verde as a whole, separately, and for each corresponding NN-ABC posterior parameter joint estimation.
<caption>**Appendix 1—table 1.** Average parameter posterior random cross-validation error across all model parameters as a function of the number of neurons in the hidden layer and the rejection tolerance level (number of simulations retained for training the Neural-Network) under the winning scenario for each island respectively.</caption>

For each island separately, and for the 225 Cabo Verde-born individuals grouped as a single "Cabo Verde" population, we considered, 1,000 random simulations in-turn as pseudo-observed data to estimate posterior parameter distributions and 100,000 total simulations in the reference table. For each cross-validation procedure, we considered between 5 and 11 neurons in the hidden layer ("NN-HL") for the winning scenarios with 12 original parameters, and between 5 and 12 NN-HL for the winning scenarios with 13 original parameters. We considered three different tolerance levels of 0.01, 0.03, and 0.1 ("Tol.") corresponding,

respectively, to 1,000, 3,000, and 10,000 simulations, in turn closest to each one of the 1,000 cross-validation pseudo-observed simulation retained for training the NN. The median values of posterior parameter distributions were used as point estimates for the calculation of the error of each parameter (Cilléry et al., 2012).

For each birth-island and Cabo Verde as a whole, and corresponding winning scenario, separately, we considered, for further posterior parameter estimation using the observed "real" data, only the pair of tolerance level and number of hidden neurons that minimized the average error on posterior parameter estimations across all parameters (indicated in bold in the table).

<table><thead><tr><th>Individual birth-island</th><th>SANTIAGO</th><th>FOGO</th><th>SANTO ANTAO</th><th>SAO NICOLAU</th><th>BRAVA</th><th>MAIO</th><th>BOA VISTA</th><th>SAO VICENTE</th><th>SAL</th><th>CABO VERDE</th></tr></thead><tbody><tr><td>Winning scenario</td><td>Scenario 1:<br>Afr2pulses-Eur2pulses</td><td>Scenario 1:<br>Afr2pulses-Eur2pulses</td><td>Scenario 1:<br>Afr2pulses-Eur2pulses</td><td>Scenario 1:<br>Afr2pulses-Eur2pulses</td><td>Scenario 1:<br>Afr2pulses-Eur2pulses</td><td>Scenario 1:<br>Afr2pulses-Eur2pulses</td><td>Scenario 2:<br>Afr2pulses-EurRecurring</td><td>Scenario 3:<br>AfrRecurring-Eur2pulses</td><td>Scenario 2:<br>Afr2pulses-EurRecurring</td><td>Scenario 1:<br>Afr2pulses-Eur2pulses</td></tr><tr><td>Number of scenario parameters</td><td>12</td><td>12</td><td>12</td><td>12</td><td>12</td><td>12</td><td>13</td><td>13</td><td>13</td><td>12</td></tr><tr><td>NN-HL=5</td><td>Tol.=0.01</td><td>0.79264</td><td>0.79943</td><td>0.80170</td><td>0.79380</td><td>0.81251</td><td>0.83232</td><td>0.79972</td><td>0.77795</td><td>0.82888</td><td>0.79532</td></tr><tr><td>NN-HL=5</td><td>Tol.=0.03</td><td>0.80866</td><td>0.81252</td><td>0.81257</td><td>0.80711</td><td>0.81703</td><td>0.83470</td><td>0.79708</td><td>0.80208</td><td>0.81783</td><td>0.83438</td></tr><tr><td>NN-HL=5</td><td>Tol.=0.1</td><td>0.84002</td><td>0.84001</td><td>0.84662</td><td>0.84970</td><td>0.84526</td><td>0.85366</td><td>0.83374</td><td>0.82312</td><td>0.83264</td><td>0.85271</td></tr><tr><td>NN-HL=6</td><td>Tol.=0.01</td><td><strong>0.77139</strong></td><td>0.80186</td><td>0.79800</td><td>0.80765</td><td>0.81085</td><td>0.82516</td><td>0.78239</td><td>0.77743</td><td>0.81601</td><td>0.82118</td></tr><tr><td>NN-HL=6</td><td>Tol.=0.03</td><td>0.79501</td><td>0.81397</td><td>0.80533</td><td>0.80483</td><td>0.83318</td><td>0.83673</td><td>0.80492</td><td>0.80127</td><td>0.81325</td><td>0.82982</td></tr><tr><td>NN-HL=6</td><td>Tol.=0.1</td><td>0.84684</td><td>0.84072</td><td>0.84028</td><td>0.84484</td><td>0.85753</td><td>0.85428</td><td>0.82136</td><td>0.81617</td><td>0.83773</td><td>0.84745</td></tr><tr><td>NN-HL=7</td><td>Tol.=0.01</td><td>0.78525</td><td>0.79836</td><td>0.79075</td><td>0.81595</td><td>0.82657</td><td>0.82662</td><td>0.79304</td><td>0.77898</td><td>0.80415</td><td>0.80413</td></tr><tr><td>NN-HL=7</td><td>Tol.=0.03</td><td>0.80899</td><td>0.81151</td><td>0.81000</td><td>0.81035</td><td>0.83069</td><td>0.83474</td><td>0.80060</td><td>0.79491</td><td>0.81855</td><td>0.83622</td></tr><tr><td>NN-HL=7</td><td>Tol.=0.1</td><td>0.85600</td><td>0.84844</td><td>0.83704</td><td>0.84737</td><td>0.85071</td><td>0.85582</td><td>0.81083</td><td>0.81619</td><td>0.83779</td><td>0.85601</td></tr><tr><td>NN-HL=8</td><td>Tol.=0.01</td><td>0.78512</td><td>0.79805</td><td>0.79127</td><td>0.80886</td><td>0.82241</td><td>0.83397</td><td><strong>0.77998</strong></td><td>0.78077</td><td>0.80992</td><td>0.80783</td></tr><tr><td>NN-HL=8</td><td>Tol.=0.03</td><td>0.80595</td><td>0.81077</td><td>0.81353</td><td>0.82455</td><td>0.82334</td><td>0.83718</td><td>0.79490</td><td>0.78639</td><td>0.80666</td><td>0.83396</td></tr><tr><td>NN-HL=8</td><td>Tol.=0.1</td><td>0.83938</td><td>0.84904</td><td>0.83681</td><td>0.85231</td><td>0.84982</td><td>0.84614</td><td>0.83499</td><td>0.81671</td><td>0.82696</td><td>0.84774</td></tr><tr><td>NN-HL=9</td><td>Tol.=0.01</td><td>0.77910</td><td>0.79899</td><td>0.81027</td><td>0.80103</td><td>0.81898</td><td>0.82483</td><td>0.79744</td><td>0.78619</td><td>0.81770</td><td>0.80542</td></tr><tr><td>NN-HL=9</td><td>Tol.=0.03</td><td>0.81192</td><td>0.81046</td><td>0.81474</td><td>0.81642</td><td>0.82593</td><td>0.82631</td><td>0.80830</td><td>0.78640</td><td>0.82212</td><td>0.84165</td></tr><tr><td>NN-HL=9</td><td>Tol.=0.1</td><td>0.84379</td><td>0.84721</td><td>0.83676</td><td>0.84813</td><td>0.85218</td><td>0.85223</td><td>0.83254</td><td>0.81696</td><td>0.81723</td><td>0.85381</td></tr><tr><td>NN-HL=10</td><td>Tol.=0.01</td><td>0.78593</td><td><strong>0.79615</strong></td><td>0.80225</td><td>0.79444</td><td><strong>0.80692</strong></td><td><strong>0.82095</strong></td><td>0.80121</td><td>0.77644</td><td>0.81801</td><td>0.80485</td></tr><tr><td>NN-HL=10</td><td>Tol.=0.03</td><td>0.80159</td><td>0.80818</td><td>0.81143</td><td>0.80949</td><td>0.82496</td><td>0.82787</td><td>0.79994</td><td>0.78673</td><td>0.81565</td><td>0.82157</td></tr><tr><td>NN-HL=10</td><td>Tol.=0.1</td><td>0.85245</td><td>0.84242</td><td>0.84222</td><td>0.83444</td><td>0.85410</td><td>0.85424</td><td>0.83049</td><td>0.81742</td><td>0.84950</td><td>0.84183</td></tr><tr><td>NN-HL=11</td><td>Tol.=0.01</td><td>0.79994</td><td>0.81073</td><td><strong>0.78479</strong></td><td><strong>0.78709</strong></td><td>0.82527</td><td>0.84091</td><td>0.79414</td><td><strong>0.77365</strong></td><td><strong>0.79984</strong></td><td>0.80239</td></tr><tr><td>NN-HL=11</td><td>Tol.=0.03</td><td>0.82611</td><td>0.80802</td><td>0.80825</td><td>0.81653</td><td>0.82511</td><td>0.82334</td><td>0.80234</td><td>0.80333</td><td>0.81750</td><td>0.82959</td></tr><tr><td>NN-HL=11</td><td>Tol.=0.1</td><td>0.84914</td><td>0.83930</td><td>0.84011</td><td>0.84941</td><td>0.85471</td><td>0.85756</td><td>0.82120</td><td>0.81919</td><td>0.83044</td><td>0.85282</td></tr><tr><td>NN-HL=12</td><td>Tol.=0.01</td><td>na</td><td>na</td><td>na</td><td>na</td><td>na</td><td>na</td><td>0.79915</td><td>0.78138</td><td>0.81418</td><td>na</td></tr></tbody></table>

Appendix 1—table 1 continued on next page
<table><caption>Appendix 1—table 1 continued</caption><thead><tr><th>Individual birth-island</th><th>SANTIAGO</th><th>FOGO</th><th>SANTO ANTAO</th><th>SAO NICOLAU</th><th>BRAVA</th><th>MAIO</th><th>BOA VISTA</th><th>SAO VICENTE</th><th>SAL</th><th>CABO VERDE</th></tr></thead><tbody><tr><td>Winning scenario</td><td>Scenario 1:<br>Afr2pulses-<br>Eur2pulses</td><td>Scenario 1:<br>Afr2pulses-<br>Eur2pulses</td><td>Scenario 1:<br>Afr2pulses-<br>Eur2pulses</td><td>Scenario 1:<br>Afr2pulses-<br>Eur2pulses</td><td>Scenario 1:<br>Afr2pulses-<br>Eur2pulses</td><td>Scenario 1:<br>Afr2pulses-<br>Eur2pulses</td><td>Scenario 2:<br>Afr2pulses-<br>EurRecurring</td><td>Scenario 3:<br>AfrRecurring-<br>Eur2pulses</td><td>Scenario 2:<br>Afr2pulses-<br>EurRecurring</td><td>Scenario 1:<br>Afr2pulses-<br>Eur2pulses</td></tr><tr><td>Number of scenario parameters</td><td>12</td><td>12</td><td>12</td><td>12</td><td>12</td><td>12</td><td>13</td><td>13</td><td>13</td><td>12</td></tr><tr><td>NN-HL=12</td><td>Tol.=0.03</td><td>na</td><td>na</td><td>na</td><td>na</td><td>na</td><td>0.79959</td><td>0.79306</td><td>0.81551</td><td>na</td></tr><tr><td>NN-HL=12</td><td>Tol.=0.1</td><td>na</td><td>na</td><td>na</td><td>na</td><td>na</td><td>0.81731</td><td>0.82090</td><td>0.82284</td><td>na</td></tr></tbody></table>
First, we identified the 1,000 simulations closest to the observed "real" data for each target data separately using a 1% tolerance level in the "neuralnet" option from the abc function. We then used each one of these 1,000 specific simulations, in turn, as pseudo-observed target data for cross-validation NN-ABC posterior parameter estimation using the same NN settings as previously, logit-transformed parameters, and the 99,999 remaining simulations in the reference table. We then compared the median posterior estimate of each scenario parameter ($\hat{\theta}_i$), with the original parameter value used for the simulation ($\theta_i$), respectively for each 1,000 cross-validation posterior parameter estimation; and calculated the cross-validation mean absolute error (MAE), for each scenario parameter (Appendix 5—Tables 1–10):

$$MAE(\hat{\theta}_i) = \sum_{1}^{1000} |\hat{\theta}_i - \theta_i| / 1000.$$

Second, for each island and for Cabo Verde as a whole, and for each scenario-parameter separately, we calculated how many times the true parameter values ($\theta_i$), used for simulating the 1,000 simulations closest to the observed data, fell within the 95% CI [2.5% quantile ($\hat{\theta}_i$); 97.5% quantile ($\hat{\theta}_i$)] estimated using the observed data. Thus, if the 1,000 cross-validation true parameter values fell more than 95% of the time within the estimated 95% CI, the length of the estimated 95% CI was considered over-estimated and thus excessively conservative; and, alternatively, if it was the case less than 95% of the time, the length of the 95% CI was considered under-estimated thus indicating a less conservative behavior of our CI estimation procedure (Appendix 5—Tables 1–10).
# Appendix 2

## Genetic diversity patterns with ASD-MDS at different geographical scales

At the worldwide scale (Appendix 2—figure 1), the first MDS axis is mainly driven by genetic differentiation between African individuals and non-African individuals, the second MDS axis by differentiation between European and East Asian individuals, and the third axis by differentiation between South Asian and American individuals.

We explored successive subsamples of this worldwide dataset in order to decompose apparent preferred relationships between each admixed population related to the TAST with respect to African and European populations only. We find (Appendix 2—figure 2) that the first MDS axis differentiates African and European individuals; the second axis differentiates mainly Senegambian West Western African individuals from Congo Basin hunter-gatherer individuals (namely the Baka, Ba.Bongo, Ba.Koya, Ba.Mbuti, Ba.Twa and Bezan); and the third axis differentiates further these latter populations from Eastern African individuals. In this context, we find Cabo Verdean individuals clustering along an axis going from the European cluster to a cluster formed mainly by West Western African individuals, with the sole exception of two individuals with fathers born on Angola as per our familial anthropology questionnaires and consistently clustering closer to our Angolan samples. Instead, ASW, ACB and PUR individuals are found on a slightly different trajectory going from European individuals towards East Western Africa mainly (Appendix 2—figure 2).

Further resampling our ASD matrix (Appendix 2—figure 3), we find no signs of particular genetic affinity, along the first three MDS axes, between enslaved-African descendants and Eastern and Southern African individuals.

Notably, we find Cabo Verdean individuals clustering similarly to Senegambian Fulani individuals in between European and other Senegambian populations, the Fulani being known to have historically received gene-flow from Northern African populations (Busby et al., 2016; Gurdasani et al., 2015; Pereira et al., 2010; Henn et al., 2012). In the absence of Northern African populations in our dataset, the South-Western European Iberian-IBS population represented the best such proxy-populations with known historical relationship with Northern Africa, hence resulting, at this geographical scale, in the similar clustering of Cabo Verdean and Fulani individuals. Note that Fulani and Cabo Verdean individuals substantially departed from each other along higher MDS axes, the Cabo Verdeans remaining on a European-African axis while the Fulani departed from this trajectory on the European side (Appendix 2—figure 3).

Finally, considering only populations related to the TAST with respect to European and East, Central, and West Western African populations (excluding the Fulani), we find (Appendix 2—figure 4) that Cabo Verdeans cluster separately from other TAST populations not only with respect to African populations, but also with respect to their relationships to European populations (Figure 2).
<figure><img src="image_17.png" /></figure>

<figure><img src="image_18.png" /></figure>

<figure><img src="image_19.png" /><figcaption>**Appendix 2—figure 1.** Multidimensional scaling three-dimensional projection of allele sharing pairwise dissimilarities, for all worldwide populations in our dataset. Each individual in the plot is represented by a single point. See *Figure 1—source data 1* for the population list used and *Figure 1* for sample locations and symbols. (A) Axis 1 and 2; (B) Axis 1 and 3. 3D animated plot is provided in.gif format. We evaluate the Spearman correlation between 3D MDS projections and the original ASD pairwise matrix to evaluate the precision of the dimensionality reduction along the first three axes of the MDS. We find significant Spearman *ρ* of 0.9796 (*p*<2.2 × 10⁻¹⁶).</figcaption></figure>

The online version of this article includes the following video for appendix 2—figure 1:

**Appendix 2—figure 1—animation 1.** 3D animated MDS of pairwise allele sharing dissimilarities for all worldwide populations in our dataset.
<figure><img src="image_20.png" /></figure>

**Appendix 2—figure 2.** Multidimensional scaling three-dimensional projection of allele sharing pairwise dissimilarities, for all of the African, European and other admixed populations related to the TAST. Each individual is represented by a single point. We removed all Asian and South American samples compared to the sample set employed in **Appendix 2—figure 1**, and recomputed the MDS based on this reduced sample set. See **Figure 1—source data 1** for the population list used in these analyses. The sample map used in these analyses is extracted from **Figure 1** and provided in panel D. (A) Axis 1 and 2; (B) Axis 2 and 3; (C) Axis 1 and 3. 3D animated plot is provided in .gif format. We evaluate the Spearman correlation between 3D MDS projections and the original ASD pairwise matrix to evaluate the precision of the dimensionality reduction along the first three axes of the MDS. We find Spearman ρ of 0.9392 (p<2.2 × 10⁻¹⁶).

The online version of this article includes the following video for appendix 2—figure 2:

**Appendix 2—figure 2—animation 1.** 3D animated MDS of pairwise allele sharing dissimilarities for all of the African, European and other admixed populations related to the TAST.
<figure><img src="image_21.png" /></figure>

**Appendix 2—figure 3.** Multidimensional scaling three-dimensional projection of allele sharing pairwise dissimilarities, for a subset of African, European and other admixed populations related to the TAST. Each individual is represented by a single point. We removed all East African and Central African hunter-gatherer samples (Baka, Bezan, Ba.Bongo, Ba.Koya, Ba.Twa, Bi.Aka, Mbuti) compared to the sample set employed in **Appendix 2—figure 2**, and recomputed the MDS based on this reduced sample set. See **Figure 1—source data 1** for the population list used in these analyses. Sample map used in these analyses is extracted from **Figure 1** and provided in panel D. (A) Axis 1 and 2; (B) Axis 2 and 3; (C) Axis 1 and 3. 3D animated plot is provided in .gif format. We evaluate the Spearman correlation between 3D MDS projections and the original ASD pairwise matrix to evaluate the precision of the dimensionality reduction along the first three axes of the MDS. We find Spearman $\rho$ of 0.9450 ($p<2.2 \times 10^{-16}$).

The online version of this article includes the following video for appendix 2—figure 3:

**Appendix 2—figure 3—animation 1.** 3D animated MDS of pairwise allele sharing dissimilarities for a subset of African, European and other admixed populations related to the TAST.
<figure><img src="image_22.png" /></figure>

**Appendix 2—figure 4.** Multidimensional scaling three-dimensional projection of allele sharing pairwise dissimilarities, for the closest subsets of West African, European and other admixed populations related to the TAST. Each individual is represented by a single point. We removed all West and South-West Central African samples, as well as South African samples, compared to the sample set employed in **Appendix 2—figure 3**, and recomputed the MDS based on this reduced sample set. See **Figure 1—source data 1** for the population list used in these analyses. Sample map used in these analyses is extracted from **Figure 1** and provided in panel **D**. (A) Axis 1 and 2; (B) Axis 2 and 3; (C) Axis 1 and 3. 3D animated plot is provided in .gif format. We evaluate the Spearman correlation between 3D MDS projections and the original ASD pairwise matrix to evaluate the precision of the dimensionality reduction along the first three axes of the MDS. We find Spearman ρ of 0.9636 (p<2.2 × 10⁻¹⁶).

The online version of this article includes the following video for appendix 2—figure 4:

**Appendix 2—figure 4—animation 1.** 3D animated MDS of pairwise allele sharing dissimilarities for the closest subsets of West African, European and other admixed populations related to the TAST.
# Appendix 3

## Alternative ADMIXTURE modes, complementary to Results **Figure 3A**

In **Figure 3A**, ADMIXTURE results at K=3 show that the new pink cluster is maximized in East Asian Chinese-CHB individuals, with a few African-American ASW and Barbadian-ACB individuals exhibiting relatively high membership to this cluster as visually identified in the ASD-MDS analysis (Appendix 2—figure 1), and previously reported (Mathias et al., 2016). While Finnish-FIN individuals all exhibit low membership to this cluster, such signal probably emerges from unresolved clustering for this population geographically between Western Europe and East Asia. This is further evidenced by the almost complete disappearing of this resemblance of FIN individuals with the pink cluster at higher values of K. No other individuals or populations in our analysis show signals of strong resemblance with the East Asian Chinese-CHB for higher values of K.

The fourth gray cluster at K=4 in **Figure 3A** is maximized in Southern African individuals from the Soto and Zulu populations. At this value of K, the original orange cluster is maximized in the West Western African Jola from Senegambia and all other African populations exhibit intermediate membership between the gray and the orange cluster. Interestingly, the average membership to the gray "Southern African" cluster decreases with increasing geographic distance from Southern Africa, along the Atlantic Ocean coast of the continent. This echoes the relatively continuous clustering observed in the ASD-MDS analysis for the Atlantic African populations in our dataset (Appendix 2—figures 2-4). Notably, the Cabo Verdean individuals born on Brava, Fogo, Santiago, and Maio, exhibit membership to both the orange and the gray clusters, albeit with a majority of membership to the orange cluster rather than the gray cluster. All other Cabo Verdean individuals show virtually no membership to the gray cluster. While indicating the stronger resemblance between all Cabo Verdean individuals with genetic patterns observed mostly in West Western Africa and Senegambian populations, this provides a first indication of differentiated genetic structure across islands within Cabo Verde. Conversely, the orange cluster previously identified in the ASW and ACB is, at K=4 in **Figure 3A**, divided into gray and orange with a slight excess of gray. A similar pattern is found among Central and East Western African populations, such as the Yoruba-YRI, the Nigerian-ESN, the Igbo, and the Ga-Adangbe populations, hence providing a first indication of a closer resemblance of the individuals of these two enslaved-African descendant populations with East Western Africa rather than with West Western Africa.

At K=5 in **Figure 3A**, note that West Central and South-West African populations exhibit a distinctive unique pattern with high membership to both the red and gray clusters. However, note that ADMIXTURE clustering is largely unresolved at this value of K as no individuals exhibit close (<1%) to 100% membership to the red cluster, and as only 27 out of the 30 ADMIXTURE iterations provide similar results. Indeed, an alternative minor mode is identified at this value of K (Appendix 3—figure 1).

At K=7 in **Figure 3A**, the novel light-blue cluster is maximized only in Finnish-FIN individuals, while the blue cluster is now maximized only in Tuscan-TSI individuals. British-GBR and USA-CEU individuals exhibit intermediate membership between the two clusters while Iberian-IBS individuals strongly resemble TSI individuals. This clustering patterns further echoes the observed ASD-MDS clustering of European populations identified in **Figure 2**. Importantly, the 'European' membership of all Cabo Verdean islands resembles, relatively, the patterns exhibited in TSI and IBS individuals (with high proportions of blue and minimal proportion of light-blue), while African-American ASW and Barbadian-ACB individuals show relatively much higher proportions of light-blue, hereby resembling, for this genotype membership, GBR and CEU individuals rather than other Europeans. Nevertheless, variable results across runs at this value of K indicate unresolved clustering and these interpretations should be considered cautiously at this point (see alternative ADMIXTURE modes at K=7, Appendix 3—figure 1).

At K=8 in **Figure 3A**, the novel dark-red cluster is maximized in West Central African Tsogho individuals and at very high proportions in all other individuals from West-Central and South-West Africa, hence resolving the unresolved clustering identified for these populations at K=5. Interestingly, substantial traces of this cluster are found in YRI, Igbo and ESN East Western African populations as well as ASW and ACB individuals, but virtually absent from Cabo Verdeans or any other African population. This further indicates the closer resemblances of ASW and ACB African genetic component to East Western and West Central Africa than to other African populations in our dataset, as echoed in our ASD-MDS analyses (Figure 2, Figure 2—figure supplement 1).
At K=9 in **Figure 3A**, the novel light-yellow cluster is maximized in Sierra Leone-MSL population from Central West Africa, albeit imperfectly. This further illustrates the intermediate clustering of Central Western African populations in between Senegambian and East Western African populations, largely overlapping on both sides, and observed in ASD-MDS analyses (**Appendix 2—figures 1–4**). Nevertheless, patterns should be interpreted with caution at this value of K, as clustering is largely unresolved, also indicated by the alternative ADMIXTURE solutions (**Appendix 3—figure 1**).

At K=11 in **Appendix 3—figure 1**, we find five alternative ADMIXTURE solutions to **Figure 3**. In one alternative solution, the novel dark blue cluster is maximized either in the Fang from West Central Africa hereby distinguished from the Tsogho from the same geographic region. Other modal results show this novel dark-blue cluster maximized instead in the Wolof from West Western Africa, hence distinguished from the Jola from the same geographic region; or instead in the British GBR, thus distinguishing three different ADMIXTURE patterns among Western European populations and hence resolving minoritarian modes observed previously at K=10; or, finally, among individuals from Fogo island, and Brava to a lesser extent, thus indicating further sub-structure among Cabo Verdean islands. Interestingly, note that for all ADMIXTURE solutions at this value of K, the light-yellow cluster is majoritarian in Sierra Leone MSL individuals, hence more clearly differentiated from either West Western and East Western African individuals compared to results obtained at previous values of K.

At K=12 in **Appendix 3—figure 1**, we find three alternative modes to the results presented in **Figure 3**. These results resolve alternative modes obtained at the previous values of K, thus further differentiating populations within Africans and Europeans sub-regions, respectively.

At K=13 in **Appendix 3—figure 1**, we find five alternative mode results compared to the one presented in **Figure 3**. These further resolve the various modal results obtained at previous values of K=10, 11, and 12. Furthermore, note that three minoritarian such modes maximize the novel light-brown cluster in Boa Vista individuals, while memberships to this specific cluster are virtually absent from all other individuals in our data set, except for a substantial proportion in individuals born on Maio.

At K=14 in **Appendix 3—figure 1**, we find three alternative solutions compared to **Figure 3**. Note that some such solutions resolve separate modal solutions obtained at previous values of K. Furthermore, interestingly, in one modal solution, the novel bright yellow cluster is maximized in Ga-Adangabe individuals, hence differentiating this population from others in the East Western African sub-region.

Finally, at K=15 in **Appendix 3—figure 1**, we obtain four alternative solutions compared to **Figure 3** results. Interestingly, in two such solutions, the novel dark-green cluster is maximized in Nzebi West Central Africans thus further differentiating the three populations from Gabon (the Fang, the Tsogho, and the Nzebi) in three different cluster. Note that in this cases, geographically close South-West Central African individuals from Angola exhibit membership proportion patterns resembling more the Nzebi than the two other Gabonese populations. An alternative mode interestingly differentiates some individuals within the CHB East Asian population, and is virtually absent from all other individuals in our data set. Finally, the last alternative mode encompasses the smallest number of runs and resolves some of the alternative solutions previously obtained at K=14 (Figure 3A, Appendix 3—figure 1).
<figure><img src="image_23.png" /></figure>

**Appendix 3—figure 1.** Alternative ADMIXTURE mode results for the individual genetic structure among Cabo Verdean, Barbadian-ACB and African-American ASW populations related to the TAST. ADMIXTURE (Alexander *et al., 2009*) analyses using resampled individual sets for the population sets originally containing more than 50 individuals (Figure 1—source data 1). 225 unrelated Cabo Verdean-born individuals are grouped by island of birth (Figure 1—source data 1). All analyses considered 102,543 independent autosomal SNPs, for values of K between 2 and 15. 30 independent ADMIXTURE runs were performed for each value of K, and groups of runs (>2) providing similar results (all pairwise SSC >99.9%) were averaged in a single ‘mode’ result using CLUMPP (Jakobsson and Rosenberg, 2007), and plotted with DISTRUCT (Rosenberg, 2003). Number of runs in the presented modes are indicated below the value of K. All other modes are presented in Figure 3.
# Appendix 4

## Runs of homozygosity patterns in Cabo Verde and other admixed populations related to the TAST, complementary to Figure 4

Examining patterns of ROH less than 1 cM long, we find generally low levels of short and medium ROH in continental Africa (Appendix 4—figure 1), with the lowest levels in Southern Africa. Conversely, we found high levels of such short and medium-size ROH among European and East Asian populations, likely reflecting ancient migration bottlenecks during the Out-of-Africa expansion (Szpiech et al., 2019). We note that the Cabo Verdean individuals have slightly elevated levels of short and medium ROH compared to continental Africa, similarly to the ACB and ASW populations. This may stem from the known admixture with European populations that occurred recently during the TAST. Admixture can be intuitively expected to decrease ROH levels compared to the source populations in general. However, recent admixture between African and European populations, the latter who exhibit much higher levels of short and medium ROH than the former (Appendix 4—figure 1), may inflate levels of such ROHs in the admixed population compared to continental African sources. Consistently with our findings for the African American ASW and Barbadian ACB (Appendix 4—figure 1), such phenomenon had been previously reported (Mooney et al., 2018). Finally, overall total ROH levels reflected the generally higher levels of ROH in Cabo Verde compared to continental African and other admixed populations from the Americas (Appendix 4—figure 1C), patterns likely related to the relative isolation of populations within the archipelago (Figure 5, Table 1).

Exploring how local ancestry intersects with ROH less than 1 cM long, since short and medium ROH are comprised of old haplotypes that likely predate over 50 generations ago (Thompson, 2013), the colonization of the Cabo Verde islands and the subsequent admixture histories of their populations, we expected that the local ancestry content of these ROH classes should be correlated with total non-ROH local ancestry levels. Appendix 4—figure 2 illustrates the relationship between total ancestry in a given ROH size class versus the total ancestry not in that ROH size class for all Cabo Verdean individuals. We find strong correlations among the short ROH and local ancestry (Appendix 4—figure 2A; African local ancestry: Pearson ρ=0.9372, p<2.2 × 10⁻¹⁶; European local ancestry: Pearson ρ=0.9496, p<2.2 × 10⁻¹⁶; Asian local ancestry: Pearson ρ=0.7516, p<2.2 × 10⁻¹⁶), and medium ROH and local ancestry (Appendix 4—figure 2B; African local ancestry: Pearson ρ=0.9071, p<2.2 × 10⁻¹⁶; European local ancestry: Pearson ρ=0.9379, p<2.2 × 10⁻¹⁶; Asian local ancestry: Pearson ρ=0.3905, p<1.298 × 10⁻⁹).
<figure><img src="image_24.png" /></figure>

<figure><img src="image_25.png" /></figure>

<figure><img src="image_26.png" /></figure>

**Appendix 4—figure 1.** The distribution of (A) short, (B) medium, and (C) all ROH per individual, for each Cabo Verdean birth-island and other worldwide populations.
A

<figure><img src="image_27.png" /></figure>

B

<figure><img src="image_28.png" /></figure>

C

<figure><img src="image_29.png" /></figure>
**Appendix 4—figure 2.** Individual total ancestry contained in (A) short, (B) medium, and (C) long ROH versus total ancestry not in that class ROH, for each Cabo Verdean birth-island and other worldwide populations.
# Appendix 5

## Genetic admixture histories of each Cabo Verdean island of birth inferred with *MetHis-ABC*, complementary to *Figure 7* and Discussion sections

Results for the detailed admixture history of each island separately are henceforth presented in the chronological order of the first time in an island's history when more than 100 individuals are reported in historical census information, and after which further census reports always exceeded this number until today; hereafter called 'first perennial peopling' of an island (Figure 7D, Figure 7—source data 1). As in the main text of the article, note that this historical date can vastly differ from the date for the first official settlement of an island inferred via political, administrative and tax records, and witnessed by parishes foundations, illustrating the complex and versatile peopling history of each Cabo Verdean island after the initial establishment of the Portuguese dominion over the archipelago.

## Admixture history of Santiago (First official settlement 1460; Perennial peopling: 1470)

### *MetHis-ABC* inferences detailed results for Santiago

For individuals born on Santiago island, we find that the most recent pulses of admixture from Africa and Europe, respectively, occurred after the official abolition of the TAST in the Portuguese Empire in the 1830s, and after the effective abolition of slavery in the Portuguese empire in the 1860s (Figure 7). Both admixture pulses are characterized by posterior distributions with narrow 95%Cl s clearly departing from their respective priors, both for the timing of each pulse and their respective intensities, in particular for the European admixture pulse (Figure 7—figure supplements 1–3, Appendix 5—table 1). For these recent events, observed genetic patterns are consistent with a relatively intense African admixture event (median = 0.5913, mode = 0.6837, 95%CI=[0.0642–0.9038]), occurring between generation sixteen and seventeen after the founding of Cabo Verde at generation 0 (generation median = 16.6, mode = 17.2, 95%CI=[10.0–18.9]). Furthermore, we find strong evidence for the most recent European admixture pulse being weak (median = 0.0684, mode = 0.0258, 95%CI=[0.0028–0.6021]), and having occurred between one and two generations before the sampled generation (generation median = 18.7, mode = 19.1, 95%CI=[11.7–19.6]).

NN-ABC posterior parameter estimations perform less accurately to infer the dates of the earlier admixture pulses and their associated intensities, both from Africa and Europe respectively, as shown by posterior distribution departing less clearly from their respective priors and overall large 95% CI. Nevertheless, results indicate that both the African and European pulses may have occurred in a more remote past; the African pulse was inferred at generation 9.2 (median) after founding at generation 0 (mode = 13.9, 95%CI=[1.7–16.8]); the European pulse at generation 7.5 (median, mode = 3.4, 95%CI=[2.3–15.9]), towards the beginning of the plantation economy era in the Americas and during the intensification of the TAST in the second half of the 17th century (Eltis and Richardson, 2015; Fortes-Lima and Verdu, 2021; Figure 7D). Conversely, the initial founding admixture pulse, set to occur at generation 0 at the beginning of Cabo Verde settlement history in the 1460s, is more accurately estimated a posteriori, as indicated by substantial departure from the prior distribution and relatively narrow CI. Results here indicate a stronger contribution from Africa than Europe (median = 0.6365, mode = 0.8816, 95%CI=[0.0538–0.9858]), at the root of the genetic make-up of Santiago-born individuals in our sample set.

Finally, effective population sizes in Santiago indicate a strong, relatively linear ($u_{Ne}$ median = 0.365, mode = 0.440, 95%CI=[0.150–0.494]), increase since the 1460s up to 80,077 effective individuals (median, mode = 92,109, 95%CI=[30,408–98,975]), in the sampled generation born on average between the 1960s and the 1980s.

## Discussion for the admixture history of Santiago

Altogether, our results indicate that admixture in Santiago occurred mainly between Senegambian and South Western European populations (Figures 2–3), at the very beginning of the Portuguese colonization of the archipelago in the 15th century. This early admixture history is likely due to an initial peopling of Cabo Verde strongly biased towards solitary males (familial permanent migrations from Portugal being a minority), who reproduced with African enslaved women, and whose admixed
**Appendix 5—table 1.** SantiagoNN-ABC posterior parameter estimations for Santiago island, cross-validation posterior parameter errors, and cross-validation 95% Credibility Interval accuracies. Cross-validation errors and 95% CI accuracies are based on 1000 NN-ABC posterior parameter inferences using, in turn, each one of the 1000 simulations closest to the observed data used as pseudo-observed data, and the remaining 99,999 simulations as the reference table. Error calculations are based on the mode and, separately, the median point estimate for each 1000 pseudo-observed simulations posterior parameter estimation, compared to the known parameter used for simulation. We considered six neurons in the hidden layer and a tolerance level of 0.01 (1000 simulations) for all posterior parameter estimation in this analysis as identified in **Appendix 1—table 1**. Plotted distributions for posterior parameter estimations can be found in **Figure 7—figure supplements 1–3**.

<table><thead><tr><th rowspan="2">SANTIAGO<br>Afr2P-Eur2P<br>scenario<br>parameters</th><th colspan="4">Parameter posterior estimation</th><th colspan="3">1,000 cross-validation errors</th></tr><tr><th>Mode</th><th>Median</th><th>50% Credibility<br>Interval</th><th>95% Credibility<br>Interval</th><th>Mode<br>mean<br>absolute<br>error</th><th>Median<br>mean<br>absolute<br>error</th><th>95% CI<br>length<br>accuracy</th></tr></thead><tbody><tr><td>Ne.0</td><td>142</td><td>431</td><td>[194 - 692]</td><td>[28 - 974]</td><td>305</td><td>255</td><td>0.059</td></tr><tr><td>Ne.20</td><td>92109</td><td>80077</td><td>[63220 - 91349]</td><td>[30408 - 98975]</td><td>25426</td><td>21558</td><td>0.045</td></tr><tr><td>u.Ne</td><td>0.440</td><td>0.365</td><td>[0.284 - 0.438]</td><td>[0.150 - 0.494]</td><td>0.113</td><td>0.096</td><td>0.042</td></tr><tr><td>sAfr,0</td><td>0.8816</td><td>0.6365</td><td>[0.3884 - 0.8415]</td><td>[0.0538 - 0.9858]</td><td>0.3147</td><td>0.2507</td><td>0.056</td></tr><tr><td>tAfr,p1</td><td>13.9</td><td>9.2</td><td>[4.9 - 13.4]</td><td>[1.7 - 16.8]</td><td>5.3</td><td>4.2</td><td>0.101</td></tr><tr><td>sAfr,tAfr,p1</td><td>0.7844</td><td>0.5986</td><td>[0.3421 - 0.7861]</td><td>[0.0420 - 0.9479]</td><td>0.2618</td><td>0.2204</td><td>0.054</td></tr><tr><td>tAfr,p2</td><td>17.2</td><td>16.6</td><td>[15.2 - 17.5]</td><td>[10.0 - 18.9]</td><td>1.8</td><td>1.6</td><td>0.199</td></tr><tr><td>sAfr,tAfr,p2</td><td>0.6837</td><td>0.5913</td><td>[0.3894 - 0.7241]</td><td>[0.0642 - 0.9038]</td><td>0.1597</td><td>0.1458</td><td>0.052</td></tr><tr><td>tEur,p1</td><td>3.4</td><td>7.5</td><td>[4.3 - 11.1]</td><td>[2.3 - 15.9]</td><td>4.0</td><td>3.1</td><td>0.161</td></tr><tr><td>sEur,tEur,p1</td><td>0.1617</td><td>0.3969</td><td>[0.1957 - 0.6606]</td><td>[0.0185 - 0.9564]</td><td>0.3042</td><td>0.2439</td><td>0.056</td></tr><tr><td>tEur,p2</td><td>19.1</td><td>18.7</td><td>[17.7 - 19.2]</td><td>[11.7 - 19.6]</td><td>3.0</td><td>2.9</td><td>0.115</td></tr><tr><td>sEur,tEur,p2</td><td>0.0258</td><td>0.0684</td><td>[0.0250 - 0.1501]</td><td>[0.0028 - 0.6021]</td><td>0.2749</td><td>0.2254</td><td>0.057</td></tr></tbody></table>

offspring constituted the first Cabo Verdean generations, as shown by some recorded instances of legitimizations of the admixed offspring to allow them to legally inherit dating back to the early 16th century (Carreira, 2000).

Our results further indicate that two substantial admixture events from Africa and Europe, respectively, occur concomitantly to the early expansion of the TAST during the 17th-century, although we are unable to precisely date both events. Nevertheless, our results support a more tenuous genetic admixture history from Africa experienced by Cabo Verdeans from Santiago during the most intense period of the TAST (18th-century) and the height of plantation economy in European colonial empires (Eltis and Richardson, 2015; Fortes-Lima and Verdu, 2021). This apparent reduced influence of the most intense period of the TAST on admixture pattern in Santiago is also echoed in our ASD-MDS, ADMIXTURE, and SOURCEFIND results, where Santiago Cabo Verdeans today share ancestry with Senegambian Mandinka almost exclusively (Figures 2–3). However, historical records unquestionably demonstrated that numerous other populations from West Central and South Western Africa were enslaved and forcibly deported to Cabo Verde during this era (Carreira, 2000). Thus, our results highlight that the strong and recurrent demographic migrations of enslaved Africans brought to Santiago during the second half of the TAST do not seem to have left a similar genetic admixture signature. This is consistent with several, mutually non-exclusive, historical scenarios, where enslaved African populations brought to Santiago may have been mostly re-deported to the Americas and Europe after the 17th century, without substantially contributing to the genetic landscape of this island, whether due to rapid re-deportation, and/or to slave-owners and colonial society strongly preventing marriages and reproduction between newly arrived enslaved individuals and pre-existing enslaved or non-enslaved communities in Santiago (see Discussion in main text).
Conversely, our results indicate an intense introgression event from Africa in Santiago, occurring shortly after the TAST and the abolition of slavery in the Portuguese empire in the 1860s. This may have been caused by a relaxation of the socio-economic constraints that predominated during most of the TAST against marriages between enslaved and non-enslaved communities as well as the control of marriages among enslaved individuals imposed by slave-owners; concomitant with the strong intensification of the illegal slave-trade which deported numerous enslaved Africans in a short amount of time shortly after the end of the TAST (Carreira, 2000; Albuquerque and Santos, 1991; Albuquerque and Santos, 1995; Albuquerque and Santos, 2007).

Our results also clearly identify a European introgression event in Santiago having occurred at the beginning of the 20th century, which may be explained by the European migrations towards African colonies triggered by European empires' policies during the first half of this century. Interestingly, we find that this recent admixture event was of very limited intensity, thus indicating that European emigration to Santiago during the 20th century only had a quantitatively limited, albeit precisely detectable, influence on genetic admixture patterns.

Finally, Santiago-born individuals also show the lowest ROH levels and generally some of the shortest ROH in Cabo Verde (Figure 4 and Appendix 4—figures 1–2). When examining ancestry patterns within ROH in Santiago-born individuals, although proportions within ROH are on average consistent with an individuals’ overall genetic ancestry, there are some outlier individuals with much higher European ancestry within ROH compared to the remainder of the genome. This could possibly reflect historical marriage prohibitions and other social constraints against intercommunity reproductions (see Discussion in main text). These ROH results combined with the evidence for the relatively constantly increasing reproductive population in Santiago over the course of the peopling of Cabo Verde (Figure 7C), was consistent with this island being the administrative historical capital, and principal entry to the archipelago throughout its’ history (Albuquerque and Santos, 1991; Albuquerque and Santos, 1995).

# Admixture history of Fogo (First official settlement 1460; Perennial settlement: 1570)

## *MetHis-ABC inferences detailed results for Fogo*

For individuals born on Fogo island, we find that both European admixture pulses were precisely inferred with NN-ABC, for the time of their occurrence and for their respective intensities, as posterior parameter distributions and 95% CI substantially depart from their respective priors (Figure 7, Figure 7—figure supplements 1–3, Appendix 5—table 2). The most recent European admixture pulse in Fogo occurred concomitantly to the abolition of the TAST and of slavery in the Portuguese empire in the 1860’s (generation median = 15.5 after the founding of Cabo Verde at generation 0, mode = 16.7, 95%CI=[6.7–18.2]), and was of substantial intensity (median = 0.2428, mode = 0.2101, 95%CI=[0.0157–0.8485]). The older European pulse occurred much more remotely in the past (generation median = 5.3, mode = 2.5, 95%CI=[1.9–13.9]), shortly after the first perennial census above 100 individuals in 1570 for this island, and long before the increase in TAST intensity due to the expansion of Plantation Economy in the Americas in the second half of the 17th century. Furthermore, note that our results indicate that this European pulse is of relatively similar intensity compared to the most recent one (median = 0.2234, mode = 0.1149, 95%CI=[0.0223–0.8383]).

Interestingly, we find that the African admixture history of individuals from Fogo occurred at very different periods of time than the European ones, the timing for both African admixture pulses being also well estimated with substantial departure from the prior and relatively narrow 95% CI. Indeed, we find strong indications of a very recent pulse of African admixture of overall limited intensity (median = 0.2034, mode = 0.1174, 95%CI=[0.0120–0.8225]), having occurred around the first part of the 20th century (generation median = 19.3 after the founding of Cabo Verde at generation 0, mode = 19.5, 95%CI=[15.6–19.8]). Furthermore, we find that the previous African admixture pulse likely occurred between six and eight generations before the sampled one (generation median = 12.0 after Cabo Verde founding, mode = 13.3, 95%CI=[4.7–16.9]), in the midst of the most intense period of the TAST and plantation economy in the Americas, around the 1760s. However, we cannot recover a precise estimation for the intensity of this older pulse, as its’ posterior parameter distribution seldom depart from its’ prior. We also find that the founding admixture event set to occur at the beginning of the colonization history of the archipelago in the 1460’s is substantially departing from its’ prior distribution and very similar to the founding admixture event found for individuals born on Santiago (median = 0.6831, mode = 0.7407, 95%CI=[0.1679–0.9600]).
Finally, our posterior estimation of the demographic history of Fogo-born individuals substantially differs from that of Santiago. Indeed, while we find similar effective sizes towards the present between the two islands (median = 72,023, mode = 90,370, 95%CI=[18,011–98,846]), we find that the demographic increase was much more recent and rapid in Fogo (u<sub>Ne</sub> median = 0.150, mode = 0.115, 95%CI=[0.055–0.447]) than in Santiago.

**Appendix 5—table 2.** Fogo NN-ABC posterior parameter estimations for Fogo island, cross-validation posterior parameter errors, and cross-validation 95% Credibility Interval accuracies. Cross-validation errors and 95% CI accuracies are based on 1000 NN-ABC posterior parameter inferences using, in turn, each one of the 1000 simulations closest to the observed data used as pseudo-observed data, and the remaining 99,999 simulations as the reference table. Error calculations are based on the mode and, separately, the median point estimate for each 1000 pseudo-observed simulations posterior parameter estimation, compared to the known parameter used for simulation. We considered 10 neurons in the hidden layer and a tolerance level of 0.01 (1000 simulations) for all posterior parameter estimation in this analysis as identified in **Appendix 1—table 1**. Plotted distributions for posterior parameter estimations can be found in **Figure 7—figure supplements 1–3**.

<table><thead><tr><th rowspan="2">FOGO<br>Afr2P-Eur2P<br>scenario<br>parameters</th><th colspan="4">Parameter posterior estimation</th><th colspan="3">1000 cross-validation errors</th></tr><tr><th>Mode</th><th>Median</th><th>50% Credibility<br>Interval</th><th>95% Credibility<br>Interval</th><th>Mode<br>mean<br>absolute<br>error</th><th>Median<br>mean<br>absolute<br>error</th><th>95% CI<br>length<br>accuracy</th></tr></thead><tbody><tr><td>Ne.0</td><td>349</td><td>511</td><td>[274–737]</td><td>[44–969]</td><td>295</td><td>253</td><td>0.063</td></tr><tr><td>Ne.20</td><td>90370</td><td>72023</td><td>[50948–87248]</td><td>[18011–98846]</td><td>27142</td><td>22749</td><td>0.057</td></tr><tr><td>u.Ne</td><td>0.115</td><td>0.150</td><td>[0.104–0.230]</td><td>[0.055–0.447]</td><td>0.085</td><td>0.081</td><td>0.074</td></tr><tr><td>sAfr,0</td><td>0.7407</td><td>0.6831</td><td>[0.5218–0.8152]</td><td>[0.1679–0.9600]</td><td>0.2936</td><td>0.2432</td><td>0.069</td></tr><tr><td>tAfr,p1</td><td>13.3</td><td>12.0</td><td>[8.1–14.4]</td><td>[4.7–16.9]</td><td>4.2</td><td>3.3</td><td>0.157</td></tr><tr><td>sAfr,tAfr,p1</td><td>0.4667</td><td>0.4549</td><td>[0.2286–0.6721]</td><td>[0.0251–0.9555]</td><td>0.2498</td><td>0.2315</td><td>0.056</td></tr><tr><td>tAfr,p2</td><td>19.5</td><td>19.3</td><td>[18.9–19.5]</td><td>[15.6–19.8]</td><td>2.6</td><td>2.5</td><td>0.100</td></tr><tr><td>sAfr,tAfr,p2</td><td>0.1174</td><td>0.2034</td><td>[0.1051–0.3560]</td><td>[0.0120–0.8225]</td><td>0.2032</td><td>0.1891</td><td>0.060</td></tr><tr><td>tEur,p1</td><td>2.5</td><td>5.3</td><td>[2.7–8.8]</td><td>[1.9–13.9]</td><td>3.6</td><td>3.0</td><td>0.216</td></tr><tr><td>sEur,tEur,p1</td><td>0.1149</td><td>0.2234</td><td>[0.1146–0.3943]</td><td>[0.0223–0.8383]</td><td>0.2804</td><td>0.2371</td><td>0.062</td></tr><tr><td>tEur,p2</td><td>16.7</td><td>15.5</td><td>[13.1–16.8]</td><td>[6.7–18.2]</td><td>3.2</td><td>3.0</td><td>0.070</td></tr><tr><td>sEur,tEur,p2</td><td>0.2101</td><td>0.2428</td><td>[0.1393–0.3966]</td><td>[0.0157–0.8485]</td><td>0.1751</td><td>0.1686</td><td>0.060</td></tr></tbody></table>

## Discussion for the admixture history of Fogo

Our results indicate a very similar founding admixture event for Fogo island compared to that of Santiago, strongly suggesting that the admixture event at the root of Fogo peopling occurred early in Cabo Verde history, likely in Santiago island. This scenario is consistent with historical data suggesting an initial peopling of Fogo from Santiago at the end of the 15th century and the beginning of the 16th century, rather than independent founding events between islands (*Albuquerque and Santos, 1991; Albuquerque and Santos, 1995*).

Interestingly, we find a European pulse of admixture concomitant with the perennial peopling of the island at the end of the 16th century and the establishment of Fogo as an important center of agricultural and free-range cattle herding in the economic triangle between Europe, Cabo Verde, and continental Africa. Later on, we identify traces of an African admixture pulse having occurred during the most intense period of the TAST in the mid-18th century, thus consistent with increased African enslaved individuals' forced deportations to Fogo as showed by historical records, but we could not infer its intensity, suggesting the difficult identifiability of such admixture event in the genetic landscape of Fogo island today with the methods here deployed.

This history of admixture is likely related to the intense control on the island's economic expansion and regulated immigration imposed after 1532 by the central political, administrative, and commercial
power of Santiago, with the notable exception of direct commercial relationships allowed between Fogo and Europe under the rule of the Portuguese crown (Albuquerque and Santos, 1991; Albuquerque and Santos, 1995; Albuquerque and Santos, 2007). This could thus explain the limited African admixture during Fogo history and more intense European admixture on this island, identified with our ASD-MDS/ADMIXTURE, and SOURCEFIND results (Figures 2–3). Furthermore, these socio-political factors likely also explain the maintaining of a relatively low reproductive population size on Fogo until very recently, as opposed to the more continuous population increase on Santiago (Figure 7C). In addition, this demographic history may be further explained by the recurrent eruptions of the Fogo volcano, which unquestionably chronically disrupted the island's development, although historical records showed limited direct mortality due to these events and that communities fleeing the island often migrated back after each cataclysm (Albuquerque and Santos, 1991).

We identify a much more recent pulse of European admixture, having occurred in the first half of the 19th century, shortly after the abolition of the TAST in the Portuguese empire, possibly due to the profound socio-cultural changes in marital relationships between enslaved and non-enslaved communities during the abolition of slavery in colonial empires (see **Discussion** in main text). Finally, we identify precisely a weak African admixture pulse having occurred in Fogo during the 20th century possibly consistent with more recent work-related migrations from Africa to Cabo Verde (Albuquerque and Santos, 2007).

Finally, ROH patterns in Fogo are similar to Santiago, in that ROH levels are relatively low and individual ROH are relatively short (Figure 4, Appendix 4—figures 1–2). This is consistent with Fogo's history of economic control and influx of European individuals. Interestingly, when exploring ancestry proportions within ROH relative to the remainder of the genome, we see on average more European ancestry within ROH. This could possibly reflect the historical influx of Europeans onto the island and/or a legacy of preferential marriages between individuals of shared family origin.

# Admixture history of Santo Antão (First official settlement 1570; Perennial settlement: 1580)

## *MetHis-ABC* inferences detailed results for Santo Antão

For individuals born on Santo Antão island, we find that both European admixture pulses after the founding admixture event are substantially departing from their respective priors and have relatively narrow 95% CI, both for the timing of their occurrence and their respective intensities (Figure 7, Figure 7—figure supplements 1–3, Appendix 5—table 3). We find that Santo Antão-born individuals have experienced a recent European admixture pulse of weak intensity (median = 0.0847, mode = 0.0467, 95%CI=[0.0056–0.6382]), that occurred roughly three generations before the sampled generation, at the turn of the 20th century (generation median = 17.2 after Cabo Verde founding at generation 0, mode = 18.1, 95%CI=[7.6–19.1]). Furthermore, we find a much more ancient European admixture pulse of strong intensity (median = 0.3592, mode = 0.1542, 95%CI=[0.0216–0.9522]), occurring concomitantly (generation median = 5.8, mode = 3.2, 95%CI=[2.6–15.6]) with the first perennial census in this island dated in 1580, and before the massive increase of TAST during the 17th century.

Interestingly, we find that the first African admixture pulse after founding at generation 0 occurred at generation 4.9 (median, mode = 2.4, 95%CI=[1.9–11.9]), almost synchronically to the oldest European admixture pulse and the first perennial settlement of the island recorded in 1580. Furthermore, this African admixture pulse was intense (median = 0.6255, mode = 0.7574; 95%CI=[0.0451–0.9749]), which summed close to 100% with the European admixture pulse having occurred at very similar times. This obliterated any older admixture events, consistently with the wide 95% CI obtained for the intensity of the founding admixture event for this island (median sAfr,0=0.5681, mode = 0.8047, 95%CI=[0.0260–0.9839]). Importantly, our NN-ABC posterior parameter estimation fail to infer the second African admixture pulse identified by our RF-ABC scenario-choice. Indeed, the posterior distributions of both the timing of this most recent pulse and its' intensity depart little from their respective priors.

Finally, despite the relatively poor performances of our inferences of demographic changes in Santo Antão, our results are indicative of a very reduced population in this island over the course of Cabo Verdean peopling history until a very recent increase up to 41,256 individuals (median, mode = 12,056, 95%CI=[3570–96,855]).
**Appendix 5—table 3.** Santo AntãoNN-ABC posterior parameter estimations for Santo Antão island, cross-validation posterior parameter errors, and cross-validation 95% Credibility Interval accuracies. Cross-validation errors and 95% CI accuracies are based on 1000 NN-ABC posterior parameter inferences using, in turn, each one of the 1000 simulations closest to the observed data used as pseudo-observed data, and the remaining 99,999 simulations as the reference table. Error calculations are based on the mode and, separately, the median point estimate for each 1000 pseudo-observed simulations posterior parameter estimation, compared to the known parameter used for simulation. We considered 11 neurons in the hidden layer and a tolerance level of 0.01 (1000 simulations) for all posterior parameter estimation in this analysis as identified in **Appendix 1—table 1**. Plotted distributions for posterior parameter estimations can be found in **Figure 7—figure supplements 1–3**.

<table><thead><tr><th rowspan="2">SANTO<br>ANTAO<br>Afr2P-Eur2P<br>scenario<br>parameters</th><th colspan="4">Parameter posterior estimation</th><th colspan="3">1,000 cross-validation errors</th></tr><tr><th>Mode</th><th>Median</th><th>50% Credibility<br>Interval</th><th>95% Credibility<br>Interval</th><th>Mode mean<br>absolute<br>error</th><th>Median<br>mean<br>absolute<br>error</th><th>95% CI<br>length<br>accuracy</th></tr></thead><tbody><tr><td>Ne.0</td><td>411</td><td>469</td><td>[254 - 706]</td><td>[26 - 964]</td><td>254</td><td>228</td><td>0.071</td></tr><tr><td>Ne.20</td><td>12056</td><td>41256</td><td>[17145-69559]</td><td>[3570-96855]</td><td>32106</td><td>25308</td><td>0.051</td></tr><tr><td>u.Ne</td><td>0.035</td><td>0.053</td><td>[0.033-0.093]</td><td>[0.015-0.334]</td><td>0.072</td><td>0.067</td><td>0.056</td></tr><tr><td>sAfr,0</td><td>0.8047</td><td>0.5681</td><td>[0.2995-0.7964]</td><td>[0.0260-0.9839]</td><td>0.3029</td><td>0.2586</td><td>0.068</td></tr><tr><td>tAfr,p1</td><td>2.4</td><td>4.9</td><td>[2.9-7.4]</td><td>[1.9-11.9]</td><td>3.3</td><td>2.6</td><td>0.164</td></tr><tr><td>sAfr,tAfr,p1</td><td>0.7574</td><td>0.6255</td><td>[0.3644-0.7916]</td><td>[0.0451-0.9749]</td><td>0.2512</td><td>0.2283</td><td>0.055</td></tr><tr><td>tAfr,p2</td><td>13.6</td><td>11.6</td><td>[7.7-14.9]</td><td>[3.0-18.5]</td><td>2.8</td><td>2.7</td><td>0.072</td></tr><tr><td>sAfr,tAfr,p2</td><td>0.6294</td><td>0.4716</td><td>[0.2596-0.6733]</td><td>[0.0338-0.9233]</td><td>0.2435</td><td>0.2150</td><td>0.049</td></tr><tr><td>tEur,p1</td><td>3.2</td><td>5.8</td><td>[3.2-10.2]</td><td>[2.6-15.6]</td><td>2.6</td><td>2.4</td><td>0.265</td></tr><tr><td>sEur,tEur,p1</td><td>0.1542</td><td>0.3592</td><td>[0.1709-0.6051]</td><td>[0.0216-0.9522]</td><td>0.2767</td><td>0.2347</td><td>0.059</td></tr><tr><td>tEur,p2</td><td>18.1</td><td>17.2</td><td>[14.8-18.2]</td><td>[7.6-19.1]</td><td>3.2</td><td>3.0</td><td>0.074</td></tr><tr><td>sEur,tEur,p2</td><td>0.0467</td><td>0.0847</td><td>[0.0416-0.1656]</td><td>[0.0056-0.6382]</td><td>0.1868</td><td>0.1763</td><td>0.059</td></tr></tbody></table>

## Discussion for the admixture history of Santo Antão

Our results for the admixture history of Santo Antão indicate that individuals born today on this island experienced an African-European admixture event concomitant with the first perennial settlement of the island in the 1580s, at the root of the genetic makeup of this island.

Most interestingly, we find no identifiable genetic admixture events, from Europe or Africa, throughout the height of the TAST on Santo Antão, albeit this island experienced a strong agricultural expansion during the plantation economy era which triggered recurrent African enslaved individuals' deportations to this island, as shown by historical records (Albuquerque and Santos, 1991; Albuquerque and Santos, 1995; Albuquerque and Santos, 2007). Thus, even more strikingly than observed in Santiago, our results indicate that the enslaved-African forced deportations to Santo Antão during most of the TAST did not leave a statistically significant genetic contribution to the genetic landscape of the island, for likely the same complex socio-cultural reasons suggested for the rest of Cabo Verde (see Discussion in main text).

In this context, our ADMIXTURE and SOURCEFIND results identify two different Senegambian populations, the Mandinka and the Wolof, sharing significant African haplotypic ancestry with Santo Antão-born individuals, as well as a much more limited shared ancestry with the West Central Africa Igbo population (Figure 3B). Our ABC results would thus be consistent with a scenario where different enslaved-African populations from Senegambia and West Central Africa where brought together to settle Santo Antão in the early stages of the TAST in the late 16th century, a pattern distinct to our findings for Santiago and Fogo. Alternatively, it is possible that the Igbo shared ancestry identified in our analyses stem from another admixture event that we failed to identify. This is likely due to an overall limited shared ancestry between this population
and Santo Antão identified only with haplotypic local ancestry inferences, as our *MetHis-ABC* procedure considered a single Senegambian population at the root of the admixture history of the island and a much more limited number of independent SNPs compared to the haplotypic local ancestry analysis.

Finally, we find that a weak but significant European admixture pulse occurred at the turn between the 19th and the 20th centuries, substantially later than the end of the TAST and the abolition of slavery and before the 20th European colonial migrations, whose putative historical causes remain to be elucidated. Furthermore, we find that the reproductive population of Santo Antão remained overall small during its' entire history until a very recent expansion, although much more limited than the expansions observed in Santiago and Fogo. This is somewhat surprising with the census records showing that Santo Antão was the second most peopled island after Santiago during most of Cabo Verde history (*Figure 7—source data 1*). Nevertheless, our results could be explained by the demographic collapse experienced by Santo Antão since the beginning of the 20th century, due to several intense famine episodes and rural-urban emigration from the island; a demographic history scenario thus much more complex than the relatively simple scenario here explored. Reflecting the historically small population size on the island, Santo Antão show high total ROH and generally quite long individual ROH among the islands (*Figure 4* and *Appendix 4—figures 1-2*).

# Admixture history of São Nicolau (First official settlement 1580; Perennial settlement: 1580)

## MetHis-ABC inferences detailed results for São Nicolau

For individuals born on São Nicolau island, we find that the two most recent admixture pulses from Europe and Africa, respectively, are precisely estimated with posterior distributions substantially departing from their priors and reduced 95% CI, for the pulses' timing and intensities (*Figure 7*, *Figure 7—figure supplements 1-3*, *Appendix 5—table 4*). We find that the most recent pulse of European admixture is weak in intensity (median = 0.0731, mode = 0.0297, 95%CI=[0.0038-0.6642]), and occurred very recently at the generation before that of the sampled individuals (generation median = 19.0 after the founding at generation 0, mode = 19.2, 95%CI=[10.3-19.8]). Furthermore, we find that the most recent African admixture pulse is very intense (median = 0.6398, mode = 0.7132, 95%CI=[0.0877-0.9380]), and occurred at generation 14.5 after founding (median, mode = 14.6, 95%CI=[8.3-16.4]), during the abolition of the TAST in the first half of the 19th century.

Interestingly, for both the more ancient admixture pulses from either Africa or Europe, our NN-ABC posterior parameter estimation provide reasonably informative posterior distributions pointing towards relatively weak African and European admixture intensities (median = 0.3133, mode = 0.1695, 95%CI=[0.0171-0.9262]; and median = 0.3240, mode = 0.1193, 95%CI=[0.0145-0.9460], respectively). However, our results only provide indications that both pulses were ancient and occurred synchronically (generation median = 5.2 after founding, mode = 2.4, 95%CI=[1.3-15.5]; generation median = 6.7, mode = 2.7, 95%CI=[2.0-16.1], for the African and European older pulses, respectively), as posterior distributions for the timing of these events are largely confounded with their respective priors.

Finally, we obtain a posterior distribution of the founding admixture intensity largely confounded with its prior, similarly as for the demographic parameters, thus showing a limit of our ABC inferences procedures.

# Discussion for the admixture history of São Nicolau

Our results for the admixture history of São Nicolau indicate that two moderate admixture pulses from Africa and Europe occurred synchronically between the date for the first perennial settlement of this island in the 1580s and the onset of the intensification of the TAST at the beginning of the 17th century. Much later in the course of Cabo Verde peopling history at the beginning of the 19th century, we find an intense introgression event from Africa, probably occurring for the same reasons as in Santiago (see above) and other Cabo Verde islands (see below and **Discussion** in main text).

Interestingly, our haplotypic local ancestry inferences identify three African populations with shared ancestries with São Nicolau-born individuals (*Figure 3*); Senegambian Wolof and Mandinka shared-ancestry representing the majority similarly to the rest of Cabo Verde and as expected historically (see **Discussion** in the main text, *Carreira, 2000; Albuquerque and Santos, 1991; Albuquerque*
**Appendix 5—table 4.** São NicolauNN-ABC posterior parameter estimations for São Nicolau island, cross-validation posterior parameter errors, and cross-validation 95% Credibility Interval accuracies. Cross-validation errors and 95% CI accuracies are based on 1000 NN-ABC posterior parameter inferences using, in turn, each one of the 1000 simulations closest to the observed data used as pseudo-observed data, and the remaining 99,999 simulations as the reference table. Error calculations are based on the mode and, separately, the median point estimate for each 1000 pseudo-observed simulations posterior parameter estimation, compared to the known parameter used for simulation. We considered 11 neurons in the hidden layer and a tolerance level of 0.01 (1000 simulations) for all posterior parameter estimation in this analysis as identified in **Appendix 1—table 1**. Plotted distributions for posterior parameter estimations can be found in **Figure 7—figure supplements 1–3**.

<table><caption>SAO<br>NICOLAU</caption><thead><tr><th rowspan="2">Afr2P-Eur2P<br>scenario<br>parameters</th><th colspan="4">Parameter posterior estimation</th><th colspan="3">1000 cross-validation errors</th></tr><tr><th>Mode</th><th>Median</th><th>50% Credibility<br>Interval</th><th>95% Credibility<br>Interval</th><th>Mode<br>mean<br>absolute<br>error</th><th>Median<br>mean<br>absolute<br>error</th><th>95% CI<br>length<br>accuracy</th></tr></thead><tbody><tr><td>Ne.0</td><td>360</td><td>457</td><td>[238 - 734]</td><td>[34 - 979]</td><td>309</td><td>255</td><td>0.059</td></tr><tr><td>Ne.20</td><td>28767</td><td>48793</td><td>[25155-70475]</td><td>[3686-96753]</td><td>27,502</td><td>23,452</td><td>0.055</td></tr><tr><td>u.Ne</td><td>0.135</td><td>0.238</td><td>[0.133-0.358]</td><td>[0.025-0.483]</td><td>0.132</td><td>0.113</td><td>0.057</td></tr><tr><td>sAfr,0</td><td>0.3249</td><td>0.4730</td><td>[0.2491-0.7393]</td><td>[0.0327-0.9752]</td><td>0.3017</td><td>0.2461</td><td>0.051</td></tr><tr><td>tAfr,p1</td><td>2.4</td><td>5.2</td><td>[2.7-9.5]</td><td>[1.3-15.5]</td><td>5.9</td><td>4.5</td><td>0.145</td></tr><tr><td>sAfr,tAfr,p1</td><td>0.1695</td><td>0.3133</td><td>[0.1584-0.5404]</td><td>[0.0171-0.9262]</td><td>0.2897</td><td>0.2363</td><td>0.069</td></tr><tr><td>tAfr,p2</td><td>14.6</td><td>14.5</td><td>[13.2-14.9]</td><td>[8.3-16.4]</td><td>1.5</td><td>1.4</td><td>0.522</td></tr><tr><td>sAfr,tAfr,p2</td><td>0.7132</td><td>0.6398</td><td>[0.4900-0.7736]</td><td>[0.0877-0.9380]</td><td>0.1044</td><td>0.0981</td><td>0.055</td></tr><tr><td>tEur,p1</td><td>2.7</td><td>6.7</td><td>[3.5-10.8]</td><td>[2.0-16.1]</td><td>4.6</td><td>3.5</td><td>0.139</td></tr><tr><td>sEur,tEur,p1</td><td>0.1193</td><td>0.3240</td><td>[0.1547-0.5711]</td><td>[0.0145-0.9460]</td><td>0.2806</td><td>0.2394</td><td>0.048</td></tr><tr><td>tEur,p2</td><td>19.2</td><td>19.0</td><td>[17.7-19.4]</td><td>[10.3-19.8]</td><td>3.3</td><td>2.9</td><td>0.199</td></tr><tr><td>sEur,tEur,p2</td><td>0.0297</td><td>0.0731</td><td>[0.0295-0.1465]</td><td>[0.0038-0.6642]</td><td>0.2419</td><td>0.2067</td><td>0.065</td></tr></tbody></table>

and Santos, 1995; Albuquerque and Santos, 2007), and South West Central African Angolan Ovimbundu a small minority. Analogous to the Santo Antão inferences' limitations, our analyses cannot disentangle whether either or both African pulses in São Nicolau involved the limited South West Central African populations shared ancestry here identified.

Finally, we identify, much later during the 20th century, a weak event of European introgression for the genetic admixture history of São Nicolau (Figure 7D), similarly likely due to labor-induced migrations in the former Lusophone empire as for other islands, and in particular possibly due to the expansion of fishing and cannery industry in São Nicolau at this time (Albuquerque and Santos, 2007).

Altogether, our genetic data contain little identifiable information for the demographic history of this island (Figure 7C, Figure 7—figure supplement 1). This may be due to the recurrent demographic collapses of the permanent settlement in this island due to intense starvation events, epidemic outbreaks, and destructive pirate raids that affected the peopling of this island throughout history (Figure 7—source data 1). Nevertheless, one genetic pattern that was consistent with these recurrent demographic collapses is the high total levels of ROH observed in the data (Figure 4 and Appendix 4—figures 1–2).

## Admixture history of Brava (First official settlement 1580; Perennial settlement: 1580)

### *MetHis-ABC* inferences detailed results for Brava

For individuals born on Brava island, we find that the most recent pulse of European admixture is relatively weak (median = 0.1697, mode = 0.1281, 95%CI=[0.0188–0.6504]), and occurred towards
the abolition of slavery in the Portuguese empire in the second half of the 19th century (generation median = 16.3 after the founding of Cabo Verde at generation 0, mode = 17.9, 95%CI=[4.2–19.3]), as indicated by posterior distributions of parameters for this event largely differing from their priors (Figure 7, Figure 7—figure supplements 1–3, Appendix 5—table 5). We identify a similarly intense pulse of admixture from Africa (median = 0.2473, mode = 0.1261, 95%CI=[0.0191–0.8266]), for which our inferences only bore indications that it occurred during the second half of the 18th century during the TAST, as the 95% CI for the timing of this event is wide (generation median = 13.6 after founding at generation 0, mode = 15.7, 95%CI=[2.4–19.2]).

More remotely in the past, we identify strong indications that a very weak European admixture pulse (median = 0.0352, mode = 0.0157, 95%CI=[0.0007–0.7239]) may have occurred at the beginning of the 17th century (generation median = 7.3 after founding, mode = 3.6, 95%CI=[2.8–16.1]). Furthermore, we identify a strong signal for an intense African admixture pulse (median = 0.6688, mode = 0.7403, 95%CI=[0.1358–0.9685]), occurring at the beginning of Cabo Verdean peopling history, during the early 16th century, at generation 2.8 after the founding of the archipelago at generation 0 (median, mode = 1.6, 95%CI=[1.1–12.2]), and thus largely before the first perennial settlement of this island.

Finally, our results strongly support a very limited effective size linear increase ($u_{Ne}$ median = 0.420, mode = 0.435, 95%CI=[0.243–0.494]) throughout the entire history of the island reaching 7337 effective individuals (median, mode = 3278, 95%CI=[647–73,114]) in the present.

**Appendix 5—table 5.** Brava NN-ABC posterior parameter estimations for Brava island, cross-validation posterior parameter errors, and cross-validation 95% Credibility Interval accuracies. Cross-validation errors and 95% CI accuracies are based on 1000 NN-ABC posterior parameter inferences using, in turn, each one of the 1000 simulations closest to the observed data used as pseudo-observed data, and the remaining 99,999 simulations as the reference table. Error calculations are based on the mode and, separately, the median point estimate for each 1000 pseudo-observed simulations posterior parameter estimation, compared to the known parameter used for simulation. We considered 10 neurons in the hidden layer and a tolerance level of 0.01 (1000 simulations) for all posterior parameter estimation in this analysis as identified in **Appendix 1—table 1**. Plotted distributions for posterior parameter estimations can be found in **Figure 7—figure supplements 1–3**.

<table><thead><tr><th rowspan="2">BRAVA<br>Afr2P-Eur2P<br>scenario<br>parameters</th><th colspan="4">Parameter posterior estimation</th><th colspan="3">1000 cross-validation errors</th></tr><tr><th>Mode</th><th>Median</th><th>50% Credibility<br>Interval</th><th>95% Credibility<br>Interval</th><th>Mode<br>mean<br>absolute<br>error</th><th>Median<br>mean<br>absolute<br>error</th><th>95% CI<br>length<br>accuracy</th></tr></thead><tbody><tr><td>Ne.0</td><td>495</td><td>501</td><td>[309–696]</td><td>[63–919]</td><td>308</td><td>254</td><td>0.068</td></tr><tr><td>Ne.20</td><td>3278</td><td>7337</td><td>[2908–17935]</td><td>[647–73114]</td><td>31523</td><td>24989</td><td>0.056</td></tr><tr><td>u.Ne</td><td>0.435</td><td>0.420</td><td>[0.374–0.455]</td><td>[0.243–0.494]</td><td>0.077</td><td>0.073</td><td>0.050</td></tr><tr><td>sAfr,0</td><td>0.7337</td><td>0.5666</td><td>[0.3452–0.7698]</td><td>[0.0497–0.9737]</td><td>0.2836</td><td>0.2405</td><td>0.059</td></tr><tr><td>tAfr,p1</td><td>1.6</td><td>2.8</td><td>[1.5–5.3]</td><td>[1.1–12.2]</td><td>3.9</td><td>3.1</td><td>0.159</td></tr><tr><td>sAfr,tAfr,p1</td><td>0.7403</td><td>0.6688</td><td>[0.4987–0.7995]</td><td>[0.1353–0.9685]</td><td>0.2418</td><td>0.2232</td><td>0.060</td></tr><tr><td>tAfr,p2</td><td>15.7</td><td>13.6</td><td>[8.4–16.3]</td><td>[2.4–19.2]</td><td>2.8</td><td>2.7</td><td>0.069</td></tr><tr><td>sAfr,tAfr,p2</td><td>0.1261</td><td>0.2473</td><td>[0.1272–0.3647]</td><td>[0.0191–0.8266]</td><td>0.2118</td><td>0.1905</td><td>0.058</td></tr><tr><td>tEur,p1</td><td>3.6</td><td>7.3</td><td>[4.1–11.1]</td><td>[2.8–16.1]</td><td>3.4</td><td>2.9</td><td>0.204</td></tr><tr><td>sEur,tEur,p1</td><td>0.0157</td><td>0.0352</td><td>[0.0116–0.1161]</td><td>[0.0007–0.7239]</td><td>0.2658</td><td>0.2338</td><td>0.064</td></tr><tr><td>tEur,p2</td><td>17.9</td><td>16.3</td><td>[12.5–18.0]</td><td>[4.2–19.3]</td><td>3.3</td><td>3.1</td><td>0.054</td></tr><tr><td>sEur,tEur,p2</td><td>0.1281</td><td>0.1697</td><td>[0.1054–0.2554]</td><td>[0.0188–0.6504]</td><td>0.1844</td><td>0.1716</td><td>0.057</td></tr></tbody></table>

## Discussion for the admixture history of Brava

We find an intense first African admixture pulse roughly three generations prior the first official and perennial peopling of the island in the 1580s (Figure 7—source data 1, Figure 7), thus
strongly suggesting that Brava was initially peopled by individuals already admixed and originating
from another Cabo Verdean island, similarly to what was suggested for Fogo (see above). We
hypothesize that Fogo admixed individuals were originally at the root of this peopling, as the
patterns of shared haplotypic ancestry in Brava-born individuals strongly resemble that of Fogo,
rather than Santiago, with shared ancestry exclusively with Senegambian Mandinka and in similar
proportion, as well as a significant (albeit very reduced) signal for a shared ancestry with Tuscan
TSI otherwise only found in Fogo (Figure 3). We find a limited introgression event from Europe
during the late 17th century, possibly consistent with a known immigration event from Madeira
and the Açores, and from Fogo after a volcano eruption, around this time (Albuquerque and
Santos, 1995). We also find a relatively weak African admixture pulse at some point during the
height of the TAST for which the timing remains poorly inferred, and which will require further
investigations.

Finally, we identify a more intense pulse of European admixture shortly after the abolition of
slavery in the Portuguese empire in the second half of the 19th century. This later event may be due
to the expansion of the whaling industry at this time, particularly in Brava due to favorable maritime
currents and routes for this industry, which brought European and European-North American sailors
to the island and increased locally contacts with Europe, and North America. Most interestingly,
this historical scenario is also consistent with the signal, virtually unique across Cabo Verde, of a
significant albeit reduced shared haplotypic ancestry between Brava-born individuals and the British
GBR.

Notably, our results indicate that the effective population of Brava remained low during the entire peopling history of Cabo Verde and until today (Figure 7C), consistent with this island being the smallest inhabited and the most south-west ward in the archipelago (Figure 7—source data 1). Surprisingly, in spite of the historically low effective population size, Brava shows low total ROH levels and relatively short ROH lengths (Figure 4 and Appendix 4—figures 1–2), which remains to be elucidated in the future by considering larger sample sizes from the island.

Admixture history of Maio (First official settlement 1529; Perennial settlement: 1650)

MetHis-ABC inferences detailed results for Maio

For individuals born on Maio island, we find evidence that the most recent pulse of European admixture was of relatively modest intensity (median = 0.1472, mode = 0.1134, 95%CI=[0.0233-0.5957]), and likely occurred during the 18th century, in the midst of the TAST (generation median = 12.7 after founding at generation 0, mode = 14.1, 95%CI=[3.7-17.9]), as both posterior distributions substantially departe from their respective priors (Figure 7, Figure 7—figure supplements 1-3, Appendix 5—table 6). Although our RF-ABC scenario-choice favors several pulses of admixture from both sources, our NN-ABC posterior parameter estimation fails to capture sufficient information to infer satisfactorily the most recent pulse of admixture from Africa, as both the posterior distribution of the timing of this event and its intensity seldom depart from their respective priors and have wide 95% CI.

However, we capture substantial information strongly suggesting two, much older, admixture
pulses from Europe and Africa, respectively, occurring virtually synchronically in the middle 16th
century (generation median = 4.1 after founding for the European pulse, mode = 2.3, 95%CI=[1.7-
14.2]; generation median = 4.2 after founding for the African pulse, mode = 2.4, 95%CI=[1.5-12.8]),
thus much earlier than the first perennial settlement of this island dated in 1650 by historians (Figure
7—source data 1). Furthermore, we find that the respective intensities of the two pulses (median =
0.3260 for the European pulse, mode = 0.1075, 95%CI=[0.0117-0.9497]; median = 0.5589 for the
African pulse, mode = 0.7703, 95%CI=[0.0346-0.9769]), sum close to 100%. This suggests a large
replacement of the Maio population at that time, with indications that these synchronic admixture
events occur on the basis of a founding admixed population largely of African origin (median
sAfr,0=0.6757, mode = 0.9135, 95%CI=[0.017-0.421]).

Finally, the demographic inference of reproductive size changes in Maio indicates, similarly as for
Brava, that the reproductive size of the island remained relatively small during its entire history, and
only very recently increased up to a median 21,454 effective individuals (mode = 7159), albeit with
a large 95% CI ([914-93,656]).
**Appendix 5—table 6.** MaioNN-ABC posterior parameter estimations for Maio island, cross-validation posterior parameter errors, and cross-validation 95% Credibility Interval accuracies. Cross-validation errors and 95% CI accuracies are based on 1000 NN-ABC posterior parameter inferences using, in turn, each one of the 1000 simulations closest to the observed data used as pseudo-observed data, and the remaining 99,999 simulations as the reference table. Error calculations are based on the mode and, separately, the median point estimate for each 1000 pseudo-observed simulations posterior parameter estimation, compared to the known parameter used for simulation. We considered 10 neurons in the hidden layer and a tolerance level of 0.01 (1000 simulations) for all posterior parameter estimation in this analysis as identified in **Appendix 1—table 1**. Plotted distributions for posterior parameter estimations can be found in **Figure 7—figure supplements 1–3**.

<table><thead><tr><th rowspan="2">MAIO<br>Afr2P-Eur2P<br>scenario<br>parameters</th><th colspan="4">Parameter posterior estimation</th><th colspan="3">1000 cross-validation errors</th></tr><tr><th>Mode</th><th>Median</th><th>50% Credibility<br>Interval</th><th>95% Credibility<br>Interval</th><th>Mode<br>mean<br>absolute<br>error</th><th>Median<br>mean<br>absolute<br>error</th><th>95% CI<br>length<br>accuracy</th></tr></thead><tbody><tr><td>Ne.0</td><td>122</td><td>500</td><td>[241 - 746]</td><td>[29 - 980]</td><td>276</td><td>240</td><td>0.059</td></tr><tr><td>Ne.20</td><td>7159</td><td>21454</td><td>[7388-49176]</td><td>[914-93656]</td><td>30301</td><td>25378</td><td>0.072</td></tr><tr><td>u.Ne</td><td>0.080</td><td>0.121</td><td>[0.071-0.210]</td><td>[0.017-0.421]</td><td>0.082</td><td>0.078</td><td>0.064</td></tr><tr><td>sAfr,0</td><td>0.9135</td><td>0.6757</td><td>[0.3486-0.8841]</td><td>[0.0177-0.9941]</td><td>0.3150</td><td>0.2509</td><td>0.061</td></tr><tr><td>tAfr,p1</td><td>2.4</td><td>4.2</td><td>[2.5-6.8]</td><td>[1.5-12.8]</td><td>4.1</td><td>3.2</td><td>0.126</td></tr><tr><td>sAfr,tAfr,p1</td><td>0.7703</td><td>0.5589</td><td>[0.2768-0.7758]</td><td>[0.0346-0.9769]</td><td>0.2630</td><td>0.2350</td><td>0.051</td></tr><tr><td>tAfr,p2</td><td>14.4</td><td>11.1</td><td>[6.6-15.1]</td><td>[2.4-18.8]</td><td>2.5</td><td>2.4</td><td>0.112</td></tr><tr><td>sAfr,tAfr,p2</td><td>0.6543</td><td>0.5276</td><td>[0.2918-0.7126]</td><td>[0.0452-0.9393]</td><td>0.2168</td><td>0.1937</td><td>0.052</td></tr><tr><td>tEur,p1</td><td>2.3</td><td>4.1</td><td>[2.2-7.4]</td><td>[1.7-14.2]</td><td>3.2</td><td>2.8</td><td>0.219</td></tr><tr><td>sEur,tEur,p1</td><td>0.1075</td><td>0.3260</td><td>[0.1376-0.5818]</td><td>[0.0117-0.9497]</td><td>0.3014</td><td>0.2415</td><td>0.068</td></tr><tr><td>tEur,p2</td><td>14.1</td><td>12.7</td><td>[8.7-14.9]</td><td>[3.7-17.9]</td><td>3.3</td><td>3.1</td><td>0.048</td></tr><tr><td>sEur,tEur,p2</td><td>0.1134</td><td>0.1472</td><td>[0.0957-0.2301]</td><td>[0.0233-0.5957]</td><td>0.2145</td><td>0.1899</td><td>0.057</td></tr></tbody></table>

## Discussion for the admixture history of Maio

Our results for the admixture history of Maio indicate a relatively simple scenario with a single pulse of European and African synchronic admixture having occurred in the mid-16th century in another Cabo Verdean island, long before the first perennial settlement of the island in 1650, similarly to Fogo or Brava. We hypothesize that this event occurred on Santiago, as shared local haplotypic ancestry patterns are highly resembling between islands (Figure 3), and also consistently with Maio being located very close to Santiago and historical records showing unequivocally the strong relationships between islands throughout history (Carreira, 2000; Albuquerque and Santos, 1991; Albuquerque and Santos, 1995; Albuquerque and Santos, 2007).

After the descendants of this initial admixture event settled Maio, they experienced only a single identifiable admixture pulse of weak intensity from Europe, which likely occurred at the turn between the 18th and the 19th century during the TAST, and no clearly identifiable further signal of African admixture in the island. As for some other Cabo Verde islands, we cannot conclude about the timing of the African admixture event that brought the reduced signal of West Central and South West Central Africa shared haplotypic ancestry with Maio, observed in our ADMIXTURE and SOURCEFIND analyses (Figure 3).

Finally, the reduced population size throughout the history of Maio is consistent with the island being located close to Santiago and with much less water resources, having made it difficult to maintain and expand the settlement on this island, despite its first peopling having occurred early in the history of Cabo Verde almost exclusively dedicated to free-range cattle herding (Carreira, 2000; Albuquerque and Santos, 1991; Albuquerque and Santos, 1995).

ROH patterns are also consistent with this history, with high total ROH indicating long term isolation and population bottlenecks. Similar to Santiago there were some outlier individuals with
much higher European ancestry within ROH compared to the remainder of the genome (Figure 4 and Appendix 4—figures 1–2). This could possibly reflect historical marriage prohibitions and other social constraints against intercommunity reproductions (see Discussion in main text).

## Admixture history of Boa Vista (First official settlement 1566; Perennial settlement: 1650)

### *MetHis-ABC* inferences detailed results for Boa Vista

For the admixture history of individuals born on Boa Vista, we find an intense admixture pulse from Africa (median = 0.6553, mode = 0.7516, 95%CI=[0.1262–0.8949]), that occurred in the mid-19th century (generation median = 15.0 after Cabo Verde founding at generation 0, mode = 14.8, 95%CI=[11.0–17.4]), during the abolition of the TAST, with posterior distributions for both these parameters substantially departing from their respective priors and relatively reduced 95% CI (Figure 7, Figure 7—figure supplements 1–3, Appendix 5—table 7). Prior to that event, we fail to estimate the timing and intensity of the older African admixture pulse into Boa Vista, as posterior parameter distributions seldom depart from their respective priors for this event.

However, our results strongly support a scenario with an intense period of recurring monotonically decreasing admixture from Europe (median admixture intensity at the period's start = 0.8057, mode = 0.9219, 95%CI=[0.2736–0.9907]; median admixture intensity at the period's end = 0.340, mode = 0.120, 95%CI=[0.021–0.880]), between the first official settlement of the island in 1566 (generation median at the start of the European period of admixture = 3.9 after founding, mode = 2.2, 95%CI=[1.7–11.8]), until shortly after its first perennial peopling dated in 1650 (generation median at the end of the European period of admixture = 8.2, mode = 8.6, 95%CI=[3.1–14.9]). Interestingly, the initial founding admixture event at the root of the genetic patterns of Boa Vista-born individuals supports a substantially lower amount of African admixture (median = 0.3917, mode = 0.1706, 95%CI=[0.1814–0.6678]), compared to the rest of Cabo Verde where this parameter could be reliably identified.

Finally, our results show that the demography of Boa Vista remained relatively constant throughout the history of Cabo Verde, and indicate a possible very recent increase in effective size, albeit posterior parameter estimation of the most recent effective size was ambiguous due to large 95% CI (median $Ne_{20}$=47,744, mode = 13,128, 95%CI=[2657–98,587]).

**Appendix 5—table 7.** Boa Vista NN-ABC posterior parameter estimations for Boa Vista island, cross-validation posterior parameter errors, and cross-validation 95% Credibility Interval accuracies. Cross-validation errors and 95% CI accuracies are based on 1000 NN-ABC posterior parameter inferences using, in turn, each one of the 1000 simulations closest to the observed data used as pseudo-observed data, and the remaining 99,999 simulations as the reference table. Error calculations are based on the mode and, separately, the median point estimate for each 1000 pseudo-observed simulations posterior parameter estimation, compared to the known parameter used for simulation. We considered 8 neurons in the hidden layer and a tolerance level of 0.01 (1000 simulations) for all posterior parameter estimation in this analysis as identified in **Appendix 1—table 1**. Plotted distributions for posterior parameter estimations can be found in **Figure 7—figure supplements 1–3**.

<table><thead><tr><th rowspan="2">BOA VISTA<br>Afr2P-Eur<br>Rec. scenario<br>parameters</th><th colspan="4">Parameter posterior estimation</th><th colspan="3">1,000 cross-validation errors</th></tr><tr><th>Mode</th><th>Median</th><th>50% Credibility<br>Interval</th><th>95% Credibility<br>Interval</th><th>Mode mean<br>absolute<br>error</th><th>Median<br>mean<br>absolute<br>error</th><th>95% CI<br>length<br>accuracy</th></tr></thead><tbody><tr><td>Ne.0</td><td>731</td><td>627</td><td>[357 - 793]</td><td>[57 - 977]</td><td>263</td><td>230</td><td>0.049</td></tr><tr><td>Ne.20</td><td>13128</td><td>47744</td><td>[20486 - 76777]</td><td>[2657 - 98587]</td><td>30386</td><td>25219</td><td>0.074</td></tr><tr><td>u.Ne</td><td>0.056</td><td>0.079</td><td>[0.051 - 0.125]</td><td>[0.014 - 0.346]</td><td>0.067</td><td>0.066</td><td>0.059</td></tr><tr><td>sAfr,0</td><td>0.1706</td><td>0.3917</td><td>[0.1814 - 0.6678]</td><td>[0.0188 - 0.9677]</td><td>0.3186</td><td>0.2517</td><td>0.061</td></tr><tr><td>tAfr,p1</td><td>14.6</td><td>10.4</td><td>[5.8 - 14.2]</td><td>[2.4 - 16.8]</td><td>4.6</td><td>3.7</td><td>0.137</td></tr><tr><td>sAfr,tAfr,p1</td><td>0.2027</td><td>0.3760</td><td>[0.1998 - 0.5640]</td><td>[0.0261 - 0.8771]</td><td>0.2494</td><td>0.2213</td><td>0.056</td></tr></tbody></table>

Appendix 5—table 7 Continued on next page
<table><caption>Appendix 5—table 7 Continued</caption><thead><tr><th rowspan="2">BOA VISTA<br>Afr2P-Eur<br>Rec. scenario<br>parameters</th><th colspan="4">Parameter posterior estimation</th><th colspan="3">1,000 cross-validation errors</th></tr><tr><th>Mode</th><th>Median</th><th>50% Credibility<br>Interval</th><th>95% Credibility<br>Interval</th><th>Mode mean<br>absolute<br>error</th><th>Median<br>mean<br>absolute<br>error</th><th>95% CI<br>length<br>accuracy</th></tr></thead><tbody><tr><td>tAfr,p2</td><td>14.8</td><td>15.0</td><td>[14.2–16.0]</td><td>[11.0–17.4]</td><td>1.7</td><td>1.7</td><td>0.113</td></tr><tr><td>sAfr,tAfr,p2</td><td>0.7516</td><td>0.6553</td><td>[0.4758–0.7671]</td><td>[0.1262–0.8949]</td><td>0.1962</td><td>0.1801</td><td>0.048</td></tr><tr><td>tEur,p1</td><td>2.2</td><td>3.9</td><td>[2.3–6.6]</td><td>[1.7–11.8]</td><td>3.7</td><td>3.1</td><td>0.192</td></tr><tr><td>tEur,p2</td><td>8.6</td><td>8.2</td><td>[6.0–10.2]</td><td>[3.1–14.9]</td><td>3.3</td><td>3.2</td><td>0.090</td></tr><tr><td>sEur,tEur,p1</td><td>0.9219</td><td>0.8057</td><td>[0.6300–0.9141]</td><td>[0.2736–0.9907]</td><td>0.2723</td><td>0.2319</td><td>0.076</td></tr><tr><td>sEur,tEur,p2</td><td>0.120</td><td>0.340</td><td>[0.1643–0.5832]</td><td>[0.021–0.880]</td><td>0.1721</td><td>0.1579</td><td>0.071</td></tr><tr><td>u.sEur</td><td>0.4444</td><td>0.2783</td><td>[0.151–0.398]</td><td>[0.0160–0.4907]</td><td>0.151</td><td>0.128</td><td>0.065</td></tr></tbody></table>

## Discussion for the admixture history of Boa Vista

Altogether, our results for the admixture history of Boa Vista born-individuals indicate a largely differing admixture history compared to all other islands of the archipelago. First, we find that the admixture event at the root of the genetic peopling of the island, although occurring long before the first perennial peopling of the island similarly to other islands such as Fogo, Brava, and Maio, is largely biased towards European admixture, as opposed to all other islands in the archipelago (Figure 7D). Second, we find the beginning of a period of recurring admixture from Europe before the mid-16th century, concomitantly with the first official settlement of the island, and until its first perennial settlement in the 1650s (Hakluyt, 2014)pp.⁵²⁹. Interestingly, this corresponds to a period when Boa Vista has been used by Cabo Verde as a penitentiary island for non-enslaved individuals which may explain the recurring admixture process here identified (Carreira, 2000; Albuquerque and Santos, 1991; Albuquerque and Santos, 1995).

Later-on towards the end of the TAST in the 19th century, Boa Vista experienced an intense pulse of African admixture, similarly to Santiago and Saõ Nicolau and probably for similar complex socio-cultural reasons (see Discussion in the main text). However, overall limited historical records specific to this island render speculative the interpretation of our results based on genetics only (Figure 7—source data 1).

Finally, the effective size of Boa Vista remained constant and low throughout the history of this island (Figure 7C), which echoes its’ small historical census sizes, mainly due to limited water resources on the island, up until today (Figure 7—source data 1). ROH patterns are also consistent with this history, with the highest total ROH among the Cabo Verdean islands indicating long term isolation and population bottlenecks (Figures F4 and Appendix 4—figures 1–2).

## Admixture history of São Vicente (First official settlement 1570; Perennial settlement: 1780)

### *MetHis-ABC* inferences detailed results for São Vicente

For the admixture history of individuals born on São Vicente, we find a recent European admixture pulse of substantial intensity (median = 0.2840, mode = 0.2596, 95%CI=[0.0397–0.8044]), having likely occurred towards the end of the 19th century (generation median = 17.4 after founding of Cabo Verde at generation 0, mode = 17.7, 95%CI=[10.6–18.9]); both posterior distributions have relatively narrow 95% CI and clearly depart from their respective priors (Figure 7, Figure 7—figure supplements 1–3, Appendix 5—table 8).

This most recent admixture event is preceded by a period of recurrent decreasing African admixture likely spanning the second half of the most intense period of the TAST starting in the early 18th century (generation median at the start of the African period of admixture = 9.7, mode = 12.6, 95%CI=[2.5–16.9]), and ending during the end of the TAST and the abolition of slavery in the Portuguese Empire in the mid-19th century (generation median at the end of the African period of admixture = 15.8, mode = 17.5, 95%CI=[7.4–19.1]), albeit our results are ambiguous for the estimate of the start of this admixture period as indicated by the large 95% CI. Furthermore, our results are also ambiguous to estimate the intensity of the African introgression during the period of recurring
admixture, as the posterior distributions for the onset and offset intensities, as well as the shape of the monotonic recurring admixture do not clearly depart from their respective priors and had large 95%Cl s.

We find traces of an older European admixture pulse of substantial intensity (median = 0.3403, mode = 0.1772, 95%CI=[0.0149–0.9133]), which likely occurred at the beginning of the 17th century (generation median = 6.4 after founding, mode = 2.8, 95%CI=[1.9–15.1]). Our results indicate that this first admixture event occurred on a root-population that exhibited a large African admixture proportion (median s<sub>Afr,0</sub>=0.5983, mode = 0.8596, 95%CI=[0.0529–0.9835]), albeit this result should be considered with cautious as CI is overall wide.

Finally, our results clearly indicate a strong effective population expansion since the perennial peopling of the island in the late 18th century, up to 66,715 effective individuals today (median, mode = 85,838, 95%CI=[12,159–98,375]).

**Appendix 5—table 8.** São Vicente NN-ABC posterior parameter estimations for São Vicente island, cross-validation posterior parameter errors, and cross-validation 95% Credibility Interval accuracies. Cross-validation errors and 95% CI accuracies are based on 1000 NN-ABC posterior parameter inferences using, in turn, each one of the 1000 simulations closest to the observed data used as pseudo-observed data, and the remaining 99,999 simulations as the reference table. Error calculations are based on the mode and, separately, the median point estimate for each 1000 pseudo-observed simulations posterior parameter estimation, compared to the known parameter used for simulation. We considered 11 neurons in the hidden layer and a tolerance level of 0.01 (1000 simulations) for all posterior parameter estimation in this analysis as identified in **Appendix 1—table 1**. Plotted distributions for posterior parameter estimations can be found in **Figure 7—figure supplements 1–3**.

<table><thead><tr><th rowspan="2">SAO VICENTE<br>Afr Rec.-<br>Eur2P<br>scenario<br>parameters</th><th colspan="4">Parameter posterior estimation</th><th colspan="3">1,000 cross-validation errors</th></tr><tr><th>Mode</th><th>Median</th><th>50% Credibility<br>Interval</th><th>95% Credibility<br>Interval</th><th>Mode<br>mean<br>absolute<br>error</th><th>Median<br>mean<br>absolute<br>error</th><th>95% CI<br>length<br>accuracy</th></tr></thead><tbody><tr><td>Ne.0</td><td>109</td><td>262</td><td>[115 - 486]</td><td>[19 - 918]</td><td>288</td><td>243</td><td>0.061</td></tr><tr><td>Ne.20</td><td>85838</td><td>66715</td><td>[42741-84818]</td><td>[12159-98375]</td><td>29947</td><td>23721</td><td>0.048</td></tr><tr><td>u.Ne</td><td>0.215</td><td>0.244</td><td>[0.174-0.338]</td><td>[0.072-0.469]</td><td>0.094</td><td>0.084</td><td>0.049</td></tr><tr><td>sAfr,0</td><td>0.8596</td><td>0.5983</td><td>[0.3334-0.8142]</td><td>[0.0529-0.9835]</td><td>0.3231</td><td>0.2499</td><td>0.063</td></tr><tr><td>tAfr,p1</td><td>12.6</td><td>9.7</td><td>[5.7-13.1]</td><td>[2.5-16.9]</td><td>3.9</td><td>3.4</td><td>0.153</td></tr><tr><td>tAfr,p2</td><td>17.5</td><td>15.8</td><td>[13.8-17.6]</td><td>[7.4-19.1]</td><td>2.8</td><td>2.7</td><td>0.235</td></tr><tr><td>sAfr,tAfr,p1</td><td>0.6796</td><td>0.7168</td><td>[0.5698-0.8525]</td><td>[0.2806-0.9795]</td><td>0.2031</td><td>0.1774</td><td>0.079</td></tr><tr><td>sAfr,tAfr,p2</td><td>0.2149</td><td>0.2786</td><td>[0.1561-0.4266]</td><td>[0.0256-0.7820]</td><td>0.1538</td><td>0.1457</td><td>0.063</td></tr><tr><td>u.sAfr</td><td>0.072</td><td>0.228</td><td>[0.111-0.360]</td><td>[0.015-0.484]</td><td>0.161</td><td>0.126</td><td>0.056</td></tr><tr><td>tEur,p1</td><td>2.8</td><td>6.4</td><td>[3.1-10.0]</td><td>[1.9-15.1]</td><td>4.1</td><td>3.3</td><td>0.214</td></tr><tr><td>sEur,tEur,p1</td><td>0.1772</td><td>0.3403</td><td>[0.1733-0.5442]</td><td>[0.0149-0.9133]</td><td>0.2448</td><td>0.2126</td><td>0.055</td></tr><tr><td>tEur,p2</td><td>17.7</td><td>17.4</td><td>[16.3-18.0]</td><td>[10.6-18.9]</td><td>2.0</td><td>2.1</td><td>0.143</td></tr><tr><td>sEur,tEur,p2</td><td>0.2596</td><td>0.2840</td><td>[0.1732-0.4177]</td><td>[0.0397-0.8044]</td><td>0.1585</td><td>0.1498</td><td>0.059</td></tr></tbody></table>

Discussion for the admixture history of São Vicente

Our results for the admixture history of individuals born on São Vicente indicate a strong European admixture event concomitant with the first official peopling of the island occurring at the same time as the nearby island of Santo Antão, consistently with historical records (Figure 7—source data 1). However, the perennial peopling of this island was difficult due to the very limited water resources, in particular compared to the much more hospitable, larger, and nearby Santo Antão. Thus, São Vicente essentially served as a coal and salt harbor depot during most of its history with a minimal
settlement (*Albuquerque and Santos, 2007*), which may explain the initial European admixture
pulse we identify (*Figure 7*), and our local haplotypic shared ancestry results (*Figure 3*).

Later-on and unique in Cabo Verde, our results support a long period of recurring African admixture occurring during the entire second half of the TAST and ending with the abolition of slavery in the Portuguese empire. However, only the final admixture event of this period could be precisely inferred to have occurred during the mid-19th<sup>th</sup> century during the abolition of the TAST and of slavery in the Portuguese empire (Figure 7D). The small haplotypic ancestry shared between São Vicente-born individuals and West Central and/or South West Central African population may stem from illegal slave-trade known to have surged during this period. Nevertheless, the poor performances of our parameter inference for the other parameters of this recurring admixture period may indicate that more complex admixture scenarios than the ones considered occurred in this island, thus begging for future work further complexifying admixture histories to be reconstructed with ABC.

Interestingly, historical data show that São Vicente census only very recently started to increase, with newly available water sources and a protected deep-water harbor in the bay of Mindelo, unique in Cabo Verde, which favored the massive economic expansion of the island in the late 19th century and throughout the 20th century (Figure 7—source data 1, Duarte et al., 2015<sup>p.36</sup>). Furthermore, the end of the agro-slavery system and end of plantation economy in Cabo Verde at the end of the 18th century and beginning of the 19th century are known historically to have triggered emigration from Santo Antão and rural-urban migrations during the 19th and 20th century, essential for São Vicente perennial peopling (Albuquerque and Santos, 2007; Patterson, 1988). This is further consistent with extensive familial grand-parental birth-places in Santo Antão and extensive familial relationships reported by São Vicente-born individuals in our familial anthropology interviews.

Altogether, these historical, economic, and demographic processes may well explain the onset of the large reproductive population increase identified in our analyses (Figure 7C), as well as haplotypic local ancestry patterns largely resembling those obtained for Santo Antão (Figure 3). Furthermore, they are consistent with the substantial European admixture pulse identified at the turn of the 19th and 20th century with our analyses. Reflecting the historical small population size, São Vicente had high total levels of ROH (Figure 4). Interestingly, individuals from this island, on average, show more African ancestry in ROH compared to the remainder of the genome. This could possibly reflect historical marriage prohibitions or the historically high levels of recurrent African admixture, or both.

## Admixture history of Sal (First official settlement 1529; Perennial settlement: 1841)

### *MetHis-ABC inferences detailed results for Sal*

Finally, the admixture history of individuals born on Sal inferred with NN-ABC is overall ambiguous a posteriori (Figure 7, Figure 7—figure supplements 1-3, Appendix 5—table 9). Indeed, while our RF-ABC scenario-choice leaned towards a complex admixture history with a period of recurring admixture from Europe and two African admixture pulses after the initial founding admixture event for the population of Sal, the duration and intensity of the European admixture period, as well as the first African admixture pulse, all showed posterior parameter distributions seldom departing from their priors. Nevertheless, we clearly identify a recent African admixture pulse of moderate intensity (median = 0.2401, mode = 0.1780, 95%CI=[0.0197-0.6590]), which likely occurred at the end of the 19th century (generation median = 17.6 after the founding of Cabo Verde at generation 0, mode = 17.9, 95%CI=[12.5-19.0]). Furthermore, our results indicate a strong and very recent effective size expansion in Sal, up to 63,289 individuals (median, mode = 88,248, 95%CI=[5689-98,181]).

### Discussion for the admixture history of Sal

Sal was among the early Cabo Verdean islands to be officially settled and exploited, in 1529 (Figure 7—source data 1), as a source of sea-salt both exported and employed locally in the free-range herding meat-production and tannery industry at the historical root of Cabo Verde economy with Europe and Africa (Albuquerque and Santos, 1991; Patterson, 1988). However, its perennial peopling dated only from 1841, the last perennially peopled island of Cabo Verde, as water sources and agricultural surfaces are scarce on this island. This slow demographic expansion is well captured by our inference showing a reduced population size during most Cabo Verde history on Sal, followed very recently by a strong reproductive size increase (Figure 7C). Furthermore, in this context, our results clearly identifying only a recent admixture pulse of African origin at the beginning of the
**Appendix 5—table 9.** Sal NN-ABC posterior parameter estimations for Sal island, cross-validation posterior parameter errors, and cross-validation 95% Credibility Interval accuracies.

Cross-validation errors and 95% CI accuracies are based on 1000 NN-ABC posterior parameter inferences using, in turn, each one of the 1000 simulations closest to the observed data used as pseudo-observed data, and the remaining 99,999 simulations as the reference table. Error calculations are based on the mode and, separately, the median point estimate for each 1000 pseudo-observed simulations posterior parameter estimation, compared to the known parameter used for simulation. We considered 11 neurons in the hidden layer and a tolerance level of 0.01 (1000 simulations) for all posterior parameter estimation in this analysis as identified in

**Appendix 1—table 1.** Plotted distributions for posterior parameter estimations can be found in **Figure 7—figure supplements 1–3**.

<table><thead><tr><th rowspan="2">SAL<br>Afr2P-EurRec.<br>scenario<br>parameters</th><th colspan="4">Parameter posterior estimation</th><th colspan="3">1000 cross-validation errors</th></tr><tr><th>Mode</th><th>Median</th><th>50% Credibility<br>Interval</th><th>95% Credibility<br>Interval</th><th>Mode<br>mean<br>absolute<br>error</th><th>Median<br>mean<br>absolute<br>error</th><th>95% CI<br>length<br>accuracy</th></tr></thead><tbody><tr><td>Ne.0</td><td>525</td><td>518</td><td>[285 - 745]</td><td>[41 - 966]</td><td>306</td><td>250</td><td>0.061</td></tr><tr><td>Ne.20</td><td>88248</td><td>63289</td><td>[36457 - 82778]</td><td>[5689 - 98181]</td><td>30007</td><td>24554</td><td>0.058</td></tr><tr><td>u.Ne</td><td>0.038</td><td>0.076</td><td>[0.035 - 0.155]</td><td>[0.005 - 0.399]</td><td>0.112</td><td>0.102</td><td>0.056</td></tr><tr><td>sAfr,0</td><td>0.8853</td><td>0.5820</td><td>[0.3164 - 0.8077]</td><td>[0.0247 - 0.9820]</td><td>0.3039</td><td>0.2508</td><td>0.060</td></tr><tr><td>tAfr,p1</td><td>3.2</td><td>9.0</td><td>[4.8 - 13.1]</td><td>[1.8 - 16.8]</td><td>4.9</td><td>4.1</td><td>0.122</td></tr><tr><td>sAfr,tAfr,p1</td><td>0.7261</td><td>0.5166</td><td>[0.2893 - 0.7374]</td><td>[0.0302 - 0.9626]</td><td>0.2667</td><td>0.2275</td><td>0.063</td></tr><tr><td>tAfr,p2</td><td>17.9</td><td>17.6</td><td>[16.3 - 18.0]</td><td>[12.5 - 19.0]</td><td>1.3</td><td>1.2</td><td>0.212</td></tr><tr><td>sAfr,tAfr,p2</td><td>0.1780</td><td>0.2401</td><td>[0.1374 - 0.3655]</td><td>[0.0197 - 0.6590]</td><td>0.1588</td><td>0.1462</td><td>0.071</td></tr><tr><td>tEur,p1</td><td>3.9</td><td>9.3</td><td>[5.3 - 12.6]</td><td>[3.3 - 16.8]</td><td>4.2</td><td>3.4</td><td>0.180</td></tr><tr><td>tEur,p2</td><td>17.8</td><td>16.2</td><td>[13.9 - 17.8]</td><td>[6.8 - 19.4]</td><td>3.7</td><td>3.5</td><td>0.102</td></tr><tr><td>sEur,tEur,p1</td><td>0.4931</td><td>0.5657</td><td>[0.3810 - 0.7810]</td><td>[0.1100 - 0.9754]</td><td>0.2585</td><td>0.2183</td><td>0.072</td></tr><tr><td>sEur,tEur,p2</td><td>0.0730</td><td>0.2061</td><td>[0.0842 - 0.4034]</td><td>[0.0113 - 0.7804]</td><td>0.1926</td><td>0.1734</td><td>0.076</td></tr><tr><td>u.sEur</td><td>0.137</td><td>0.207</td><td>[0.102 - 0.346]</td><td>[0.011 - 0.486]</td><td>0.156</td><td>0.128</td><td>0.061</td></tr></tbody></table>

20th century could reflect the recent economic migrations of Western African populations to this island, during the development of its salt mining activities and its travel and tourism activities since then. Nevertheless, our scenario-choice results suggested the occurrence of a period of recurrent European admixture in Sal, which our posterior parameter inference largely failed to identify. This is possibly due to the complex recent peopling history of Sal that we fail to capture with genetic data, which will need to be clarified in the future in particular with additional samples from this island. Nevertheless, reflecting the historical small population size, Sal has high total levels of ROH (Figure 4).
**Appendix 5—table 10.** Cabo Verde NN-ABC posterior parameter estimations for 225 Cabo Verde-born individuals considered as a single random-mating population, cross-validation posterior parameter errors, and cross-validation 95% Credibility Interval accuracies.

Cross-validation errors and 95% CI accuracies are based on 1000 NN-ABC posterior parameter inferences using, in turn, each one of the 1000 simulations closest to the observed data used as pseudo-observed data, and the remaining 99,999 simulations as the reference table. Error calculations are based on the mode and, separately, the median point estimate for each 1000 pseudo-observed simulations posterior parameter estimation, compared to the known parameter used for simulation. We considered five neurons in the hidden layer and a tolerance level of 0.01 (1000 simulations) for all posterior parameter estimation in this analysis as identified in

**Appendix 1—table 1.** Plotted distributions for posterior parameter estimations can be found in **Figure 7—figure supplements 1–3**.

<table><caption>CABO VERDE Parameter posterior estimation</caption><thead><tr><th rowspan="2">Afr2P-Eur2P scenario parameters</th><th rowspan="2">Mode</th><th rowspan="2">Median</th><th rowspan="2">50% Credibility Interval</th><th rowspan="2">95% Credibility Interval</th><th colspan="3">1000 cross-validation errors</th></tr><tr><th>Mode mean absolute error</th><th>Median mean absolute error</th><th>95% CI length accuracy</th></tr></thead><tbody><tr><td>Ne.0</td><td>343</td><td>490</td><td>[267 - 726]</td><td>[34 - 968]</td><td>296</td><td>238</td><td>0.058</td></tr><tr><td>Ne.20</td><td>86901</td><td>61995</td><td>[36958-82637]</td><td>[8050-98176]</td><td>26496</td><td>23321</td><td>0.047</td></tr><tr><td>u.Ne</td><td>0.469</td><td>0.400</td><td>[0.310-0.463]</td><td>[0.172-0.497]</td><td>0.118</td><td>0.107</td><td>0.041</td></tr><tr><td>sAfr,0</td><td>0.5801</td><td>0.5015</td><td>[0.2560-0.7308]</td><td>[0.0271-0.9794]</td><td>0.3000</td><td>0.2464</td><td>0.057</td></tr><tr><td>tAfr,p1</td><td>3.1</td><td>9.0</td><td>[5.0-13.0]</td><td>[2.0-18.0]</td><td>5.7</td><td>4.2</td><td>0.090</td></tr><tr><td>sAfr,tAfr,p1</td><td>0.4597</td><td>0.4831</td><td>[0.2575-0.7249]</td><td>[0.0263-0.9644]</td><td>0.2556</td><td>0.2310</td><td>0.049</td></tr><tr><td>tAfr,p2</td><td>19.2</td><td>18.6</td><td>[17.2-19.3]</td><td>[11.9-19.3]</td><td>1.3</td><td>1.2</td><td>0.153</td></tr><tr><td>sAfr,tAfr,p2</td><td>0.7056</td><td>0.6224</td><td>[0.4317-0.7576]</td><td>[0.1164-0.9303]</td><td>0.1483</td><td>0.1379</td><td>0.037</td></tr><tr><td>tEur,p1</td><td>2.4</td><td>6.1</td><td>[3.0-9.3]</td><td>[2.0-16.1]</td><td>4.4</td><td>3.4</td><td>0.146</td></tr><tr><td>sEur,tEur,p1</td><td>0.1193</td><td>0.4300</td><td>[0.2038-0.7022]</td><td>[0.0216-0.9718]</td><td>0.3006</td><td>0.2487</td><td>0.056</td></tr><tr><td>tEur,p2</td><td>18.2</td><td>15.1</td><td>[11.2-17.9]</td><td>[4.1-19.0]</td><td>3.1</td><td>2.7</td><td>0.086</td></tr><tr><td>sEur,tEur,p2</td><td>0.1882</td><td>0.4150</td><td>[0.2029-0.6780]</td><td>[0.0313-0.9647]</td><td>0.2471</td><td>0.2115</td><td>0.051</td></tr></tbody></table>