International Journal of Primatology

, Volume 34, Issue 2, pp 303–314

A New Method for Genome-wide Marker Development and Genotyping Holds Great Promise for Molecular Primatology

  • Christina M. Bergey
  • Luca Pozzi
  • Todd R. Disotell
  • Andrew S. Burrell
Article

DOI: 10.1007/s10764-013-9663-2

Cite this article as:
Bergey, C.M., Pozzi, L., Disotell, T.R. et al. Int J Primatol (2013) 34: 303. doi:10.1007/s10764-013-9663-2

Abstract

Over the last two decades primatologists have benefited from the use of numerous molecular markers to study various aspects of primate behavior and evolutionary history. However, most of the studies to date have been based on a single locus, usually mitochondrial DNA, or a few nuclear markers, e.g., microsatellites. Unfortunately, the use of such markers not only is unable to address successfully important questions in primate population genetics and phylogenetics (mainly because of the discordance between gene tree and species tree), but also their development is often a time-consuming and expensive task. The advent of next-generation sequencing allows researchers to generate large amounts of genomic data for nonmodel organisms. However, whole genome sequencing is still cost prohibitive for most primate species. We here introduce a second-generation sequencing technique for genotyping thousands of genome-wide markers for nonmodel organisms. Restriction site–associated DNA sequencing (RAD-seq) reduces the complexity of the genome and allows inexpensive and fast discovery of thousands of markers in many individuals. Here, we describe the principles of this technique and we demonstrate its application in five primates, Microcebus sp., Cebus sp., Theropithecus gelada, Pan troglodytes, and Homo sapiens, representing some of the major lineages within the order. Despite technical and bioinformatic challenges, RAD-seq is a promising method for multilocus phylogenetic and population genetic studies in primates, particularly in young clades in which a high number of orthologous regions are likely to be found across populations or species.

Keywords

Genotyping Nonmodel organisms Phylogenetics Population genetics Restriction site–associated DNA sequencing Second-generation DNA sequencing Single-nucleotide polymorphisms 

Copyright information

© Springer Science+Business Media New York 2013

Authors and Affiliations

  • Christina M. Bergey
    • 1
    • 2
  • Luca Pozzi
    • 1
    • 2
  • Todd R. Disotell
    • 1
    • 2
  • Andrew S. Burrell
    • 1
  1. 1.Department of AnthropologyNew York UniversityNew YorkUSA
  2. 2.New York Consortium in Evolutionary PrimatologyNew YorkUSA