Alu insertion loci and platyrrhine primate phylogeny

TLDR: One of the largest applications of SINE elements to phylogenetic analysis to date is reported, and the results provide a robust molecular phylogeny for platyrrhine primates.

About: This article is published in Molecular Phylogenetics and Evolution.The article was published on 2005-04-01 and is currently open access. It has received 137 citations till now. The article focuses on the topics: Atelidae & Alu element.

Figures

Fig. 1. Illustration of the protocol used to identify NWM-speciWc Alu insertions. Red lines indicate linker fragments ligated to digested genomic DNA (blue/black). Blue lines indicate Alu elements in genomic DNA fragments.

Table 2 Linker sequencesa for Alu detection protocol

Table 3 Alu selection primers

Fig. 2. Results of primate phylogenetic panel PCR ampliWcation for four loci. Locus names and template DNA are indicated.

Fig. 4. The Alu insertion pattern exhibited at locus 58. Four distinct Alu insertions occurred along several lineages. Element “a” inserted in the Callitrichine common ancestor. A second Alu, “c,” inserted in the common ancestor of macaques and green monkeys. A truncated Alu element, “b,” inserted in the owl monkey lineage (Aotus) after the divergence from squirrel monkeys. Finally, a fourth, full-length insertion, “d,” occurred in the lineage leading to Saimiri sciureus.

Fig. 3. The most parsimonious tree generated from analysis of 189 Alu insertions for nine platyrrhine primates and three outgroup taxa. Numbers with arrows indicate the number of unambiguous insertions supporting that node.

Frequently asked questions

Q1. What are the contributions in "Alu insertion loci and platyrrhine primate phylogeny" ?

The authors used these loci to investigate branching order and have produced a cladogram that supports a sister relationship between Atelidae ( spider, woolly, and howler monkeys ) and Cebidae ( marmosets, tamarins, and owl monkeys ) and then the joining of this two family clade to Pitheciidae ( titi and saki monkeys ). In this study, the authors report one of the largest applications of SINE elements to phylogenetic analysis to date, and the results provide a robust molecular phylogeny for platyrrhine primates. 

Q2. What is the way to interpret the results of a phylogenetic analysis?

Alu insertions within a single ampliWed locus in taxa can lead to problems interpreting results in phylogenetic analyses that use SINE insertions. 

Q3. What is the reason for the success of SINEs as phylogenetic markers?

One reason for the success of SINEs as phylogenetic and population genetic markers is that their mode of evolution is unidirectional (Hillis, 1999). 

Q4. What was the ampliWcation of each locus?

Oligonucleotide primers for polymerase chain reaction (PCR) ampliWcation of each locus were designed for the young or lineage-speciWc Alu insertions using Primer3 (Rozen and Skaletsky, 1998). 

Q5. Why did the authors remove P. paniscus from the analysis?

Because of these observations and because PAUP* allows a maximum of 12 taxa when performing an exhaustive search of all possible trees, the authors removed P. paniscus and Lemur from the analysis. 

Q6. Where was the secondary Alu insertion found?

DNA sequence analysis of the locus revealed that a secondary Alu insertion was present in Pithecia downstream of the originally identiWed insertion, which was present only in the atelids. 

Q7. What is the significance of the Alu elements in the human genome?

These elements have been extremely successful at propagating in primate genomes as evidenced by the fact that they make up »10% of the human genome by mass (Batzer and Deininger, 2002; Lander et al., 2001). 

Q8. What taxa were included in the study?

The taxa included were Aotus trivirgatus (owl monkey), Saguinus labiatus (red-bellied tamarin), Lagothrix lagotricha (woolly monkey), Ateles geoVroyi (black-handed spider monkey), Callithrix pygmaea (pygmy marmoset), Pithecia p. pithecia (northern white-faced saki), Callicebus d. donacophilus (Bolivian gray titi), Saimiri s. sciureus (squirrel monkey), and Alouatta sara (Bolivian red howler). 

Q9. How many Alu insertion loci were found to be useful for phylogenetic?

By the criteria described above, 92 computationally derived and 85 experimentally derived Alu insertion loci were found to be potentially useful for phylogenetic analysis of New World primates.