Species‐level view of population structure and gene flow for a critically endangered primate (<i><scp>V</scp>arecia variegata</i>)

<jats:title>Abstract</jats:title><jats:p>Lemurs are among the world's most threatened mammals. The critically endangered black‐and‐white ruffed lemur (<jats:italic><jats:styled-content style="fixed-case">V</jats:styled-content>arecia variegata</jats:italic>), in particular, has recently experienced rapid population declines due to habitat loss, ecological sensitivities to habitat degradation, and extensive human hunting pressure. Despite this, a recent study indicates that ruffed lemurs retain among the highest levels of genetic diversity for primates. Identifying how this diversity is apportioned and whether gene flow is maintained among remnant populations will help to diagnose and target conservation priorities. We sampled 209 individuals from 19 sites throughout the remaining <jats:italic><jats:styled-content style="fixed-case">V</jats:styled-content>. variegata</jats:italic> range. We used 10 polymorphic microsatellite loci and ~550 bp of mt<jats:styled-content style="fixed-case">DNA</jats:styled-content> sequence data to evaluate genetic structure and population dynamics, including dispersal patterns and recent population declines. Bayesian cluster analyses identified two distinct genetic clusters, which optimally partitioned data into populations occurring on either side of the <jats:styled-content style="fixed-case">M</jats:styled-content>angoro River. Localities north of the Mangoro were characterized by greater genetic diversity, greater gene flow (lower genetic differentiation) and higher mt<jats:styled-content style="fixed-case">DNA</jats:styled-content> haplotype and nucleotide diversity than those in the south. Despite this, genetic differentiation across all sites was high, as indicated by high average <jats:italic>F</jats:italic><jats:sub>ST</jats:sub> (0.247) and Φ<jats:styled-content style="fixed-case"><jats:sub>ST</jats:sub></jats:styled-content> (0.544), and followed a pattern of isolation‐by‐distance. We use these results to suggest future conservation strategies that include an effort to maintain genetic diversity in the north and restore connectivity in the south. We also note the discordance between patterns of genetic differentiation and current subspecies taxonomy, and encourage a re‐evaluation of conservation management units moving forward.</jats:p>