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

Area of Science:

• Genomics
• Molecular Evolution
• Population Genetics

Background:

• Two lineage-specific Platy-1 SINE subfamilies were recently discovered in the mantled howler monkey (Alouatta palliata).
• Short INterspersed Elements (SINEs) have not been extensively used for studying howler monkey (Alouatta) evolutionary history.
• Alu mobile element insertions (MEIs) are widely used in primate phylogenetics.

Purpose of the Study:

• To evaluate the utility of Platy-1 SINEs and Alu elements for population genetics in howler monkeys.
• To identify phylogenetically informative markers for Alouatta species.
• To provide a resource for howler monkey phylogenetics, population genetics, and conservation.

Main Methods:

• Polymerase chain reaction (PCR) was used to analyze DNA from Alouatta species.
• Presence/absence data for 335 young Alu elements and over 600 Platy-1 MEIs were collected.
• Comparative analysis with six new genome assemblies from cis-Andean Alouatta species was performed.

Main Results:

• A polymorphism rate of 30% was detected between Alouatta palliata and Alouatta sara.
• A. palliata showed more robust amplification of young Alu SINEs compared to other Atelidae species.
• Phylogenetically informative presence/absence data for numerous Alu and Platy-1 elements were generated across multiple Alouatta species.

Conclusions:

• Platy-1 SINEs and Alu elements represent a valuable resource for 'identical by descent' MEIs in howler monkeys.
• These genetic markers can be applied to study howler monkey phylogenetics and population genetics.
• The data can inform conservation strategies for wild howler monkey populations.