Cebidae <i>Alu</i> Element Alignments and a Complex Non-Human Primate Radiation
Phylogenetic relationships among Cebidae species of platyrrhine primates are presently under debate. Studies prior to whole genome sequence (WGS) availability utilizing unidirectional <i>Alu</i> repeats linked <i>Callithrix</i> and <i>Saguinus</i> as sister taxa,...
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MDPI AG
2022-10-01
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| Series: | Life |
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| Online Access: | https://www.mdpi.com/2075-1729/12/10/1655 |
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| author | Jessica M. Storer Jerilyn A. Walker Morgan A. Brown Mark A. Batzer |
| author_facet | Jessica M. Storer Jerilyn A. Walker Morgan A. Brown Mark A. Batzer |
| author_sort | Jessica M. Storer |
| collection | DOAJ |
| description | Phylogenetic relationships among Cebidae species of platyrrhine primates are presently under debate. Studies prior to whole genome sequence (WGS) availability utilizing unidirectional <i>Alu</i> repeats linked <i>Callithrix</i> and <i>Saguinus</i> as sister taxa, based on a limited number of genetic markers and specimens, while the relative positions of <i>Cebus</i>, <i>Saimiri</i> and <i>Aotus</i> remained controversial. Multiple WGS allowed computational detection of <i>Alu</i>-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 <i>Alu</i> 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 <i>Alu</i> insertions in all phylogenetically informative categories, providing evidence of extensive incomplete lineage sorting (ILS) and an abundance of <i>Alu</i> proliferation during the complex radiation of Cebidae taxa. |
| first_indexed | 2024-03-09T19:55:58Z |
| format | Article |
| id | doaj.art-684eaf0a217a4cb9b9fe77951dd3aec7 |
| institution | Directory Open Access Journal |
| issn | 2075-1729 |
| language | English |
| last_indexed | 2024-03-09T19:55:58Z |
| publishDate | 2022-10-01 |
| publisher | MDPI AG |
| record_format | Article |
| series | Life |
| spelling | doaj.art-684eaf0a217a4cb9b9fe77951dd3aec72023-11-24T00:57:58ZengMDPI AGLife2075-17292022-10-011210165510.3390/life12101655Cebidae <i>Alu</i> Element Alignments and a Complex Non-Human Primate RadiationJessica M. Storer0Jerilyn A. Walker1Morgan A. Brown2Mark A. Batzer3Department of Biological Sciences, Louisiana State University, 202 Life Sciences Building, Baton Rouge, LA 70803, USADepartment of Biological Sciences, Louisiana State University, 202 Life Sciences Building, Baton Rouge, LA 70803, USADepartment of Biological Sciences, Louisiana State University, 202 Life Sciences Building, Baton Rouge, LA 70803, USADepartment of Biological Sciences, Louisiana State University, 202 Life Sciences Building, Baton Rouge, LA 70803, USAPhylogenetic relationships among Cebidae species of platyrrhine primates are presently under debate. Studies prior to whole genome sequence (WGS) availability utilizing unidirectional <i>Alu</i> repeats linked <i>Callithrix</i> and <i>Saguinus</i> as sister taxa, based on a limited number of genetic markers and specimens, while the relative positions of <i>Cebus</i>, <i>Saimiri</i> and <i>Aotus</i> remained controversial. Multiple WGS allowed computational detection of <i>Alu</i>-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 <i>Alu</i> 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 <i>Alu</i> insertions in all phylogenetically informative categories, providing evidence of extensive incomplete lineage sorting (ILS) and an abundance of <i>Alu</i> proliferation during the complex radiation of Cebidae taxa.https://www.mdpi.com/2075-1729/12/10/1655Cebidae<i>Alu</i>phylogenyplatyrrhine |
| spellingShingle | Jessica M. Storer Jerilyn A. Walker Morgan A. Brown Mark A. Batzer Cebidae <i>Alu</i> Element Alignments and a Complex Non-Human Primate Radiation Life Cebidae <i>Alu</i> phylogeny platyrrhine |
| title | Cebidae <i>Alu</i> Element Alignments and a Complex Non-Human Primate Radiation |
| title_full | Cebidae <i>Alu</i> Element Alignments and a Complex Non-Human Primate Radiation |
| title_fullStr | Cebidae <i>Alu</i> Element Alignments and a Complex Non-Human Primate Radiation |
| title_full_unstemmed | Cebidae <i>Alu</i> Element Alignments and a Complex Non-Human Primate Radiation |
| title_short | Cebidae <i>Alu</i> Element Alignments and a Complex Non-Human Primate Radiation |
| title_sort | cebidae i alu i element alignments and a complex non human primate radiation |
| topic | Cebidae <i>Alu</i> phylogeny platyrrhine |
| url | https://www.mdpi.com/2075-1729/12/10/1655 |
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