Correction: An Alu-Based Phylogeny of Lemurs (Infraorder: Lemuriformes)

Abstract

Lemurs (infraorder: Lemuriformes) are a radiation of strepsirrhine primates endemic to the island of Madagascar. As of 2012, 101 lemur species, divided among five families, have been described. Genetic and morphological evidence indicates all species are descended from a common ancestor that arrived in Madagascar ,55-60 million years ago (mya). Phylogenetic relationships in this species-rich infraorder have been the subject of debate. Here we use Alu elements, a family of primatespecific Short INterspersed Elements (SINEs), to construct a phylogeny of infraorder Lemuriformes. Alu elements are particularly useful SINEs for the purpose of phylogeny reconstruction because they are identical by descent and confounding events between loci are easily resolved by sequencing. The genome of the grey mouse lemur (Microcebus murinus) was computationally assayed for synapomorphic Alu elements. Those that were identified as Lemuriformes-specific were analyzed against other available primate genomes for orthologous sequence in which to design primers for PCR (polymerase chain reaction) verification. A primate phylogenetic panel of 24 species, including 22 lemur species from all five families, was examined for the presence/absence of 138 Alu elements via PCR to establish relationships among species. Of these, 111 were phylogenetically informative. A phylogenetic tree was generated based on the results of this analysis. We demonstrate strong support for the monophyly of Lemuriformes to the exclusion of other primates, with Daubentoniidae, the aye-aye, as the basal lineage within the infraorder. Our results also suggest Lepilemuridae as a sister lineage to Cheirogaleidae, and Indriidae as sister to Lemuridae. Among the Cheirogaleidae, we show strong support for Microcebus and Mirza as sister genera, with Cheirogaleus the sister lineage to both. Our results also support the monophyly of the Lemuridae. Within Lemuridae we place Lemur and Hapalemur together to the exclusion of Eulemur and Varecia, with Varecia the sister lineage to the other three genera.

Recently Integrated Alu Elements in Capuchin Monkeys: A Resource for Cebus/Sapajus Genomics

“…A recent study conducted on populations of S. libidinosus, a species considered "Near Threatened" [12], emphasized that there is currently a lack of developed genetic systems available to study capuchin population and conservation genetics [13]. Primate specific Alu retrotransposons are well-established diagnostic genetic markers for the study of population genetic and phylogenetic relationships [15][16][17][18][19][20][21][22][23][24][25][26][27][28][29][30][31]. Nonautonomous Alu elements mobilize via a "copy and paste" mechanism through an RNA intermediate, utilizing the enzymatic machinery of autonomous LINE (L1) elements.…”

Owl Monkey Alu Insertion Polymorphisms and Aotus Phylogenetics

“…The TPRT mechanism is considered unidirectional such that the absence of insertion is, by default, the ancestral state; conversely, shared insertions with matching TSDs are accepted as being inherited from a common ancestor. These unique attributes have made Alu elements well-established diagnostic molecular markers for the study of primate population genetic and phylogenetic relationships [ 16 , 17 , 18 , 19 , 20 , 21 , 22 , 23 , 24 , 25 , 26 , 27 , 28 , 29 , 30 , 31 ].…”