to obtain an overall estimate of the species tree.

An important cause of gene tree conflict is the population effect of *incomplete lineage sorting*, in which gene lineages coalesce in ancestral populations earlier than the time these lineages first enter a common ancestral population. The *multispecies coalescent model* [@pamilo1988; @rosenberg2002; @rannala2003; @degnan2005; @degnan2009] is commonly used to model this process, producing a distribution of rooted gene trees given a rooted species tree topology and branch lengths (a measure of time and population size on each edge of the species tree). The multispecies coalescent provides a natural framework for incorporating population effects, allowing gene trees to possibly be discordant with the species tree (see Fig. \[F:partition\]), a phenomenon that is very common in multilocus studies [@rokas2003; @ebersberger2007; @cranston2009].

(100,1204)(0,0) (-1000,200)

(2436.0, 0.0)\[l\]

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

(-100,650)

(2436.0,0.0)\[l\]

${\operatorname{MRCA}}(\{a,b,c\})$

(-1250,0)[ ![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 