---
title: "Chapter 3"
---

Figure 3.5

Pueblo lineage 
```{r}
```

A simple model for allel fixation

Figure 3.13
```{r}
# drift vs selection
set.seed(1)
N <- 10000          # population size
gens <- 200       # generations
p0 <- 0.2         # initial allele frequency
s <- .1            # selection advantage (fitness of A is 1+s, a is 1)

drift <- sel <- numeric(gens + 1)
drift[1] <- p0
sel[1] <- p0

for (g in 1:gens) {
  # neutral drift
  drift[g + 1] <- rbinom(1, N, drift[g]) / N
  
  # selection then drift (haploid fitness model)
  p_after_sel <- (1 + s) * sel[g] / ((1 + s) * sel[g] + (1 - sel[g]))
  sel[g + 1] <- rbinom(1, N, p_after_sel) / N
}
aá
matplot(
  cbind(0:gens, 0:gens),
  cbind(drift, sel),
  type = "l", lty = 1, lwd = 4, xlab = "Generation", ylab = "Allele A frequency",
  col = c("grey50", "firebrick"), main = "Neutral drift vs. positive selection"
)
abline(h = c(0, 1), lty = 2, col = "gray70")
legend("topright", c("drift", "selected"), col = c("grey50", "firebrick"), lwd = 2, bty = "n")
```

We will see later how this can be adapte to represent change in frequency of cultural traits under different cultrural transmission regimes