The radiation of macaques out of Africa: Evidence from mitogenome divergence times and the fossil record.

Fossil evidence indicates that numerous catarrhine clades of African origin expanded or shifted their ranges into Eurasia, among them macaques Macaca Lacépède, 1799. Macaques represent the sister taxon of African papionins and can thus be used as a model comparing an 'out-of-Africa' with an intra-African, e.g., baboons-Papio Erxleben, 1777 evolutionary history. The first step for such a comparison is to establish a well-resolved phylogeny of macaques with reliably estimated divergence times and to compare it with that of baboons and the fossil record. Therefore, we used mitochondrial (mtDNA) genome data deposited in GenBank of 16 out of 23 extant macaque species and of all six baboon taxa. We reconstructed phylogenetic trees using maximum-likelihood and Bayesian inferences and dated differentiation events using three fossil-based calibration sets. The obtained tree topology is in agreement with findings from earlier mtDNA studies, but yielded stronger nodal supports. We observed some para- and polyphylies in macaques and baboons, suggesting that ancient gene flow among divergent lineages has been common in both genera. Our divergence time estimates are in broad agreement with earlier findings and with the fossil record. Macaques started to diversify 7.0-6.7 Ma, followed by a stepwise radiation into several species groups in Asia, whereas baboons commenced diversification around 2.2 Ma. Accordingly, divergence of species groups and species in macaques clearly predates divergences in baboons. Based on our phylogenetic results with estimated divergence times and the recorded chronostratigraphic ranges of extinct macaque and baboon taxa, we compare the evolutionary radiations of both genera from paleobiogeographic and adaptive viewpoints.

Alu SINE analyses of 3,000-year-old human skeletal remains: a pilot study.

BACKGROUND: As Short Interspersed Elements (SINEs), human-specific Alu elements can be used for population genetic studies. Very recent inserts are polymorphic within and between human populations. In a sample of 30 elements originating from three different Alu subfamilies, we investigated whether they are preserved in prehistorical skeletal human remains from the Bronze Age Lichtenstein cave in Lower Saxony, Germany. In the present study, we examined a prehistoric triad of father, mother and daughter. RESULTS: For 26 of the 30 Alu loci investigated, definite results were obtained. We were able to demonstrate that presence/absence analyses of Alu elements can be conducted on individuals who lived 3,000 years ago. The preservation of the ancient DNA (aDNA) is good enough in two out of three ancient individuals to routinely allow the amplification of 500 bp fragments. The third individual revealed less well-preserved DNA, which results in allelic dropout or complete amplification failures. We here present an alternative molecular approach to deal with these degradation phenomena by using internal Alu subfamily specific primers producing short fragments of approximately 150 bp. CONCLUSIONS: Our data clearly show the possibility of presence/absence analyses of Alu elements in individuals from the Lichtenstein cave. Thus, we demonstrate that our method is reliably applicable for aDNA samples with good or moderate DNA preservation. This method will be very useful for further investigations with more Alu loci and larger datasets. Human population genetic studies and other large-scale investigations would provide insight into Alu SINE-based microevolutionary processes in humans during the last few thousand years and help us comprehend the evolutionary dynamics of our genome.