Sensitivity of the polyDetect computational pipeline for phylogenetic analyses

Rockwell

et al. 2022

Genes

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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. There 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.

Section: Resultsmentioning

confidence: 99%

Section: Lineage-specific Alu Elementsmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

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

Rockwell

et al. 2022

Genes

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“…Alu element detection methods based on Alu -genome junctions, such as the polyDetect program [ 10 ] have been applied to the Cebidae lineage of platyrrhine phylogeny [ 11 ]. However, the short reads did not allow for sufficient homology to accurately predict shared Alu insertions across genera diverged by ~20 my [ 3 , 12 ].…”

Section: Introductionmentioning

confidence: 99%

“…To overcome the impact of evolutionary random genomic decay across lineages, the current study uses the full-length Alu sequences extracted from the assembled genomes along with 600 bp of flanking unique DNA sequence. The genomes of the same four cebid species used in Storer et al (2020) [ 11 ] (marmoset, squirrel monkey, capuchin monkey and owl monkey), were used to computationally ascertain all possible Alu insertions from the available genome assemblies and align them to the other three genomes. Full-length Alu sequence and a combined total of 1200 bp of flanking sequence provides adequate homology for accurate multiple sequence alignments.…”

Section: Introductionmentioning

confidence: 99%

Cebidae Alu Element Alignments and a Complex Non-Human Primate Radiation

Brown

et al. 2022

Life

Phylogenetic relationships among Cebidae species of platyrrhine primates are presently under debate. Studies prior to whole genome sequence (WGS) availability utilizing unidirectional Alu repeats linked Callithrix and Saguinus as sister taxa, based on a limited number of genetic markers and specimens, while the relative positions of Cebus, Saimiri and Aotus remained controversial. Multiple WGS allowed computational detection of Alu-genome junctions, however random mutation and evolutionary decay of these short-read segments prevented phylogenetic resolution. In this study, WGS for four Cebidae genomes of marmoset, squirrel monkey, owl monkey and capuchin were analyzed for full-length Alu elements and each locus was compared to the other three genomes in all possible combinations using orthologous region sequence alignments. Over 2000 candidates were aligned and subjected to visual inspection. Approximately 34% passed inspection and were considered shared in their respective category, 48% failed due to the target being present in all four genomes, having N’s in the sequence or other sequence quality anomalies, and 18% were determined to represent near parallel insertions (NP). Wet bench locus specific PCR confirmed the presence of shared Alu insertions in all phylogenetically informative categories, providing evidence of extensive incomplete lineage sorting (ILS) and an abundance of Alu proliferation during the complex radiation of Cebidae taxa.

Owl Monkey Alu Insertion Polymorphisms and Aotus Phylogenetics

Rewerts

et al. 2022

Genes

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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.