species tree topology. Using upper case letters for gene lineages sampled from their corresponding species, failure of the $A$ and $B$ lineages to coalesce in their MRCA population makes any of the $\binom{3}{2}$ coalescences between $A$, $B$, and $C$ equally likely under the model in the MRCA population of $a$, $b$, and $c$. (a) The gene tree is $((((B,C),A),D,E)$. (b) The gene tree is $(((B,C),A),(D,E))$.[]{data-label="F:partition"}](partitionA.eps "fig:"){width=".48\textwidth"}]{}

(100,1204)(0,0) (300,200)

(2436.0, 0.0)\[l\]

$a$ $b$ $c$ $d$ $e$

(50,0)[ ![Gene trees within a species tree. In the multispecies coalescent, gene lineages sampled from species are assumed to coalesce (form nodes in the gene tree) no more recently than their most recent common ancestor (MRCA) in the species tree. Coalescence of lineages in populations more ancient than their MRCA can lead to gene tree topologies that are discordant with the species tree topology. Using upper case letters for gene lineages sampled from their corresponding species, failure of the $A$ and $B$ lineages to coalesce in their MRCA population makes any of the $\binom{3}{2}$ coalescences between $A$, $B$, and $C$ equally likely under the model in the MRCA population of $a$, $b$, and $c$. (a) The gene tree is $((((B,C),A),D,E)$. (b) The gene tree is 