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<p>Recent discovery of two lineage-specific Platy-1 SINE (Short INterspersed Element) subfamilies, active within the genome of mantled howler monkey (<i>Alouatta palliata</i>) [AloPal_v1], prompted analyses by polymerase chain reaction (PCR) to evaluate their utility for population genetics. A polymorphism rate of 30% was detected by comparison to DNA from a <i>cis</i>-Andean species, <i>A. sara</i>. Concurrently, six new genome assemblies were released for <i>Alouatta</i> species from the <i>cis</i>-Andean clade for comparison. <i>A. palliata</i> also has a more robust amplification of young <i>Alu</i> SINEs, as compared to other Atelidae species, including a limited number of pre-<i>Alu</i>Ta15 derived insertions. While <i>Alu</i> mobile element insertions (MEIs), have been widely used to study primate phylogenetics, SINEs have not yet been utilized in the study of howler monkey (<i>Alouatta</i>) relationships. This study reports phylogenetically informative presence / absence data and candidate oligonucleotides for locus-specific PCR for 335 young <i>Alu</i> elements from <i>A. palliata</i> as well as over 600 Platy-1 MEIs representing <i>A. palliata</i>, <i>A. caraya</i>, <i>A. belzebul</i>,<i> A. discolor</i>, <i>A. seniculus puruensis</i>, <i>A. s. juara</i> and <i>A. macconnelli</i>. These datasets provide a valuable resource of ‘identical by descent’ MEIs for the study of howler monkey phylogenetics, population genetics and conservation strategies for application to wild populations.</p>

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Howler monkey Platy-1 and Alu SINEs: a resource for Alouatta genomics

  • 期刊论文

  • 出版模式：

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  • 发表日期：

    2026年4月29日

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  • Jerilyn A. Walker,
  • Jessica M. Storer,
  • Sarah O. Massey,
  • Thomas O. Beckstrom,
  • David A. Ray,
  • Mark A. Batzer

摘要

Recent discovery of two lineage-specific Platy-1 SINE (Short INterspersed Element) subfamilies, active within the genome of mantled howler monkey (Alouatta palliata) [AloPal_v1], prompted analyses by polymerase chain reaction (PCR) to evaluate their utility for population genetics. A polymorphism rate of 30% was detected by comparison to DNA from a cis-Andean species, A. sara. Concurrently, six new genome assemblies were released for Alouatta species from the cis-Andean clade for comparison. A. palliata also has a more robust amplification of young Alu SINEs, as compared to other Atelidae species, including a limited number of pre-AluTa15 derived insertions. While Alu mobile element insertions (MEIs), have been widely used to study primate phylogenetics, SINEs have not yet been utilized in the study of howler monkey (Alouatta) relationships. This study reports phylogenetically informative presence / absence data and candidate oligonucleotides for locus-specific PCR for 335 young Alu elements from A. palliata as well as over 600 Platy-1 MEIs representing A. palliata, A. caraya, A. belzebul, A. discolor, A. seniculus puruensis, A. s. juara and A. macconnelli. These datasets provide a valuable resource of ‘identical by descent’ MEIs for the study of howler monkey phylogenetics, population genetics and conservation strategies for application to wild populations.