Owl Monkey Alu Insertion Polymorphisms and Aotus Phylogenetics

Abstract

Owl monkeys (genus Aotus), or “night monkeys” are platyrrhine primates in the Aotidae family. Early taxonomy only recognized one species, Aotus trivirgatus, until 1983, when Hershkovitz proposed nine unique species designations, classified into red-necked and gray-necked species groups based predominately on pelage coloration. Recent studies questioned this conventional separation of the genus and proposed designations based on the geographical location of wild populations. Alu retrotransposons are a class of mobile element insertion (MEI) widely used to study primate phylogenetics. A scaffold-level genome assembly for one Aotus species, Aotus nancymaae [Anan_2.0], facilitated large-scale ascertainment of nearly 2000 young lineage-specific Alu insertions. This study provides candidate oligonucleotides for locus-specific PCR assays for over 1350 of these elements. For 314 Alu elements across four taxa with multiple specimens, PCR analyses identified 159 insertion polymorphisms, including 21 grouping A. nancymaae and Aotus azarae (red-necked species) as sister taxa, with Aotus vociferans and A. trivirgatus (gray-necked) being more basal. DNA sequencing identified five novel Alu elements from three different taxa. The Alu datasets reported in this study will assist in species identification and provide a valuable resource for Aotus phylogenetics, population genetics and conservation strategies when applied to wild populations.

Extensive Independent Amplification of Platy-1 Retroposons in Tamarins, Genus Saguinus

“…Platy-1 elements mobilize via TPRT and therefore compete for the same LINE (L1) enzymatic machinery that Alu elements do to achieve successful propagation. Alu content has not yet been characterized in tamarins specifically, to determine if Alu amplification rates are lower due to the vast expansion of Platy-1 elements, as compared to other reported platyrrhine genomes [22][23][24][25][26]. However, we have observed that Platy-1 elements in tamarins and other genomes [5] are often flanked by one or more Alu elements.…”

Framework of the Alu Subfamily Evolution in the Platyrrhine Three-Family Clade of Cebidae, Callithrichidae, and Aotidae

“…Four high-quality platyrrhine genomes (common marmoset; C. jacchus [caljac3], capuchin monkey; Cebus imitator [Cebus_imitator-1.0], squirrel monkey; S. boliviensis [SaiBol1] and owl monkey; Aotus nancymaae [Anan_2.0]) were obtained from the National Center for Biotechnology Information (NCBI) and analyzed for their Alu content using RepeatMasker (RepeatMasker-Open-4.0). Ascertainment of lineage-specific or recently integrated Alu insertions from the owl monkey genome [Anan_2.0] and from the C. imitator genome [Cebus_imitator-1.0] [25] were performed as described previously [26][27][28][29]. Briefly, fulllength Alu elements were extracted from the RepeatMasker output using a custom python script (described at link https://github.com/t-beck; accessed on 19 December 2022).…”

“…We found approximately 12,089 owl monkey lineage-specific Alu insertions in the [Anan_2.0] genome, from a total of 658,009 full-length insertions [27,28], and approximately 9602 capuchin lineage-specific Alu insertions in the [Cebus_imitator-1.0] genome, from a total of 617,132 full-length insertions [29]. An initial COSEG analysis of the lineage-specific Alu elements in the capuchin genome indicated that there were 16 subfamilies present.…”