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

Abstract

Capuchins are platyrrhines (monkeys found in the Americas) within the Cebidae family. For most of their taxonomic history, the two main morphological types of capuchins, gracile (untufted) and robust (tufted), were assigned to a single genus, Cebus. Further, all tufted capuchins were assigned to a single species, Cebus apella, despite broad geographic ranges spanning Central and northern South America. In 2012, tufted capuchins were assigned to their genus, Sapajus, with eight currently recognized species and five Cebus species, although these numbers are still under debate. Alu retrotransposons are a class of mobile element insertion (MEI) widely used to study primate phylogenetics. However, Alu elements have rarely been used to study capuchins. Recent genome-level assemblies for capuchins (Cebus imitator; [Cebus_imitator_1.0] and Sapajus apella [GSC_monkey_1.0]) facilitated large scale ascertainment of young lineage-specific Alu insertions. Reported here are 1607 capuchin specific and 678 Sapajus specific Alu insertions along with candidate oligonucleotides for locus-specific PCR assays for many elements. PCR analyses identified 104 genus level and 51 species level Alu insertion polymorphisms. The Alu datasets reported in this study provide a valuable resource that will assist in the classification of archival samples lacking phenotypic data and for the study of capuchin phylogenetic relationships.

Keywords: Alu; Cebidae; Cebus; Sapajus; capuchin; phylogeny; platyrrhine.

Figure 1

Photographs representative of untufted and tufted capuchins. (A) C. imitator, an untufted, adult male Panamanian white-faced capuchin. Photograph by Amanda Melin. (B) S. apella, a tufted, brown capuchin [14].

Figure 2

C. imitator genomic Alu insertion polymorphisms. Lanes: 1 100 bp DNA ladder, 2 TLE (negative control), 3 Human (HeLa), 4 Callithrix jacchus (Common marmoset), 5 Saimiri s. sciureus (Common squirrel monkey), 6 Aotus trivirgatus (Three striped owl monkey), 7 C. imitator, 8–9 C. capucinus, 10–11 C. albifrons, 12 C. a. albifrons, 13–20 S. apella. (A) Locus #69, Alu is present in all Cebus species individuals (~693 bp DNA fragment lanes 7–12) and absent in all Sapajus samples (~381 bp DNA fragment lanes 13–20); (B) Locus #49, Alu is polymorphic among Cebus individuals (~580 bp fragment present, ~275 bp fragment absent) and absent in all Sapajus samples; (C) Locus #9, Alu is present in Cebus individuals (~653 bp fragment) and polymorphic among Sapajus individuals (~653 bp, and ~340 bp DNA fragments). Blue lines superimposed on gel images visually separate Cebus, Sapajus, and outgroups.

Figure 3

S. apella genomic Alu insertion polymorphisms. Lanes: 1 100 bp DNA ladder, 2 TLE (negative control), 3 Human (HeLa), 4 C. jacchus (Common marmoset), 5 S. s. sciureus (Common squirrel monkey), 6 A. trivirgatus (Three striped owl monkey), 7–17 S. apella, 18 C. imitator, 19–20 C. capucinus, 21–22 C. albifrons, 23 C. a. albifrons. (A) Locus # 984.99, the Alu element is present in all Sapajus individuals (~528 bp) and absent in all Cebus samples (~227 bp fragment); (B) Locus #978.25, the Alu element is polymorphic among Sapajus individuals (~604 bp and ~292 bp DNA fragments) and absent in Cebus samples; (C) Locus #944.49, the Alu element is present in all Sapajus individuals (~671 bp fragment), and heterozygous present (~671 bp and ~341 bp DNA fragments) in individual KB-4207, C. a. albifrons. Blue lines superimposed on gel images visually separate Cebus, Sapajus and outgroups.