Comparison of vitamin D metabolites in wild and captive baboons

Vitamin D adequacy is essential for multiple physiologic processes. With limited exposure to sunlight for vitamin D3 synthesis, captive primates are supplemented with vitamin D3 (cholecalciferol). Vitamin D metabolite data from wild primates living indigenously could suggest optimum levels. The purpose of this study was to: 1) to explore whether baboons, a speciose genus whose members have significant exposed skin, coat color variation and wide geographical distribution, mirrors the skin pigmentation-vitamin D relationship found in humans; 2) compare vitamin D metabolite levels in wild and captive members of the same or similar baboon species; and 3) apply a recently developed method currently used in humans for measuring multiple vitamin D metabolites as a panel to explore if/how these metabolites can inform us on vitamin D sufficiency. Serum samples from males of three baboon species in the wild: Papio anubis (olive baboon, dark exposed skin), P. cynocephalus (yellow baboon, brown exposed skin), and P. hamadryas (hamadryas baboon, pink exposed skin), were compared with vitamin D supplemented captive olive baboons with sun exposure. Liquid chromatography/tandem mass spectrometry (LC/MS/MS) measured vitamin D and its main metabolites. Cholecalciferol, 25 hydroxyvitamin D2&3 (25(OH)D2&3 ), and 24,25 dihydroxyvitamin D2&3 (24,25(OH)2 D2&3 ), showed significant differences by species. The levels of cholecalciferol due to supplements in the captive olive baboons did not convert to higher 25(OH)D3 while the wild olive baboons exhibited the lowest levels for both cholecalciferol and 25(OH)D3 . Further metabolic conversion of 25(OH)D3 to 24,25(OH)2 D3 indicated that all baboons had more similar conversion ratios and these were within the same range found for humans that are depicted as having adequate vitamin D levels. This study provided evidence that exposed skin color does influence vitamin D3 levels, with lower levels in darker skinned species, but these differences are eliminated in the downstream metabolite conversion indicating strong regulatory control.

Romain CP, Bennett EC, Robichaux A, Clement BN, Raveendran M, Worley KC, Phillips-Conroy J, Jolly CJ, Rogers J, Konkel MK, Batzer MA. Alu Insertion Polymorphisms as Evidence for Population Structure in Baboons

Male dispersal from the natal group at or near maturity is a feature of most baboon (Papio) species. It potentially has profound effects upon population structure and evolutionary processes, but dispersal, especially for unusually long distances, is not readily documented by direct field observation. In this pilot study, we investigate the possibility of retrieving baboon population structure in yellow (Papio cynocephalus) and kinda (Papio kindae) baboons from the distribution of variation in a genome-wide set of 494 Alu insertion polymorphisms, made available via the recently completed Baboon Genome Analysis Consortium. Alu insertion variation in a mixed population derived from yellow and olive (Papio anubis) baboons identified each individual's proportion of heritage from either parental species. In an unmixed yellow baboon population, our analysis showed greater similarity between neighboring than between more distantly situated groups, suggesting structuring of the population by male dispersal distance. Finally (and very provisionally), an unexpectedly sharp difference in Alu insertion frequencies between members of neighboring social groups of kinda baboons suggests that intergroup migration may be more rare than predicted in this little known species.

Mutation rates and the evolution of germline structure

Genome sequencing studies of de novo mutations in humans have revealed surprising incongruities in our understanding of human germline mutation. In particular, the mutation rate observed in modern humans is substantially lower than that estimated from calibration against the fossil record, and the paternal age effect in mutations transmitted to offspring is much weaker than expected from our long-standing model of spermatogenesis. I consider possible explanations for these discrepancies, including evolutionary changes in life-history parameters such as generation time and the age of puberty, a possible contribution from undetected post-zygotic mutations early in embryo development, and changes in cellular mutation processes at different stages of the germline. I suggest a revised model of stem-cell state transitions during spermatogenesis, in which 'dark' gonial stem cells play a more active role than hitherto envisaged, with a long cycle time undetected in experimental observations. More generally, I argue that the mutation rate and its evolution depend intimately on the structure of the germline in humans and other primates.This article is part of the themed issue 'Dating species divergences using rocks and clocks'.

Out of Africa, but how and when? The case of hamadryas baboons (Papio hamadryas)

Many species of Arabian mammals are considered to be of Afrotropical origin and for most of them the Red Sea has constituted an obstacle for dispersal since the Miocene-Pliocene transition. There are two possible routes, the 'northern' and the 'southern', for terrestrial mammals (including humans) to move between Africa and Arabia. The 'northern route', crossing the Sinai Peninsula, is confirmed for several taxa by an extensive fossil record, especially from northern Egypt and the Levant, whereas the 'southern route', across the Bab-el-Mandab Strait, which links the Red Sea with the Gulf of Aden, is more controversial, although post-Pliocene terrestrial crossings of the Red Sea might have been possible during glacial maxima when sea levels were low. Hamadryas baboons (Papio hamadryas) are the only baboon taxon to disperse out of Africa and still inhabit Arabia. In this study, we investigate the origin of Arabian hamadryas baboons using mitochondrial sequence data from 294 samples collected in Arabia and Northeast Africa. Through the analysis of the geographic distribution of genetic diversity, the timing of population expansions, and divergence time estimates combined with palaeoecological data, we test: (i) if Arabian and African hamadryas baboons are genetically distinct; (ii) if Arabian baboons exhibit population substructure; and (iii) when, and via which route, baboons colonized Arabia. Our results suggest that hamadryas baboons colonized Arabia during the Late Pleistocene (130-12 kya [thousands of years ago]) and also moved back to Africa. We reject the hypothesis that hamadryas baboons were introduced to Arabia by humans, because the initial colonization considerably predates the earliest records of human seafaring in this region. Our results strongly suggest that the 'southern route' from Africa to Arabia could have been used by hamadryas baboons during the same time period as proposed for modern humans.

Genetic evidence reveals temporal change in hybridization patterns in a wild baboon population

The process and consequences of hybridization are of interest to evolutionary biologists because of the importance of hybridization in understanding reproductive isolation, speciation, and the influence of introgression on population genetic structure. Recent studies of hybridization have been enhanced by the advent of sensitive, genetic marker-based techniques for inferring the degree of admixture occurring within individuals. Here we present a genetic marker-based analysis of hybridization in a large-bodied, long-lived mammal over multiple generations. We analysed patterns of hybridization between yellow baboons (Papio cynocephalus) and anubis baboons (Papio anubis) in a well-studied natural population in Amboseli National Park, Kenya, using genetic samples from 450 individuals born over the last 36 years. We assigned genetic hybrid scores based on genotypes at 14 microsatellite loci using the clustering algorithm implemented in STRUCTURE 2.0, and assessed the robustness of these scores by comparison to pedigree information and through simulation. The genetic hybrid scores showed generally good agreement with previous morphological assessments of hybridity, but suggest that genetic methods may be more sensitive for identification of low levels of hybridity. The results of our analysis indicate that the proportion of hybrids in the Amboseli population has grown over time, but that the average proportion of anubis ancestry within hybrids is gradually decreasing. We argue that these patterns are probably a result of both selective and nonselective processes, including differences in the timing of life-history events for hybrid males relative to yellow baboon males, and stochasticity in long-distance dispersal from the source anubis population into Amboseli.

Interpreting genetic variability: the effects of shared evolutionary history

Data from different individuals at a single locus are positively correlated because of the shared genealogy of the sampled genes. This paper illustrates the qualitative effects on genealogical trees of assumptions about population demography, and it considers the consequences for genetic variability. An understanding of these effects is invaluable in the interpretation of data and for inferences about population history. In contrast, traditional genetic measures of diversity and approximation methods do not seem well suited for addressing the problem.

Heterogeneous genomic molecular clocks in primates

Using data from primates, we show that molecular clocks in sites that have been part of a CpG dinucleotide in recent past (CpG sites) and non-CpG sites are of markedly different nature, reflecting differences in their molecular origins. Notably, single nucleotide substitutions at non-CpG sites show clear generation-time dependency, indicating that most of these substitutions occur by errors during DNA replication. On the other hand, substitutions at CpG sites occur relatively constantly over time, as expected from their primary origin due to methylation. Therefore, molecular clocks are heterogeneous even within a genome. Furthermore, we propose that varying frequencies of CpG dinucleotides in different genomic regions may have contributed significantly to conflicting earlier results on rate constancy of mammalian molecular clock. Our conclusion that different regions of genomes follow different molecular clocks should be considered when inferring divergence times using molecular data and in phylogenetic analysis.

Nucleotide diversity in populations of balitorid cave fishes from Thailand

Genetic variabilities in four cave and eight surface species of balitorid freshwater fishes from Thailand were assessed using random amplified polymorphic DNA (RAPD). Cave species have consistently lower RAPD variation than surface species and it is hypothesized that this difference is a function of reduced population size in cave fishes. Indices of nucleotide diversity (pi) were calculated from the RAPD data and are four to five times higher for the surface species than the cave species: 6.4 x 10-3 vs. 1.4 x 10-3. The pi-values for cave fishes are significantly lower than those for surface balitorids and those measured in other species using RAPD/amplified fragment length polymorphism data.

Microsatellite polymorphisms in Bolivian squirrel monkeys (Saimiri boliviensis)

Two different approaches were used to identify new microsatellite polymorphisms among captive Bolivian squirrel monkeys (Saimiri boliviensis). In the first case, PCR primers for published human microsatellite loci were screened using genomic DNA from squirrel monkeys. Six polymorphic loci were identified using DNA samples from 19 unrelated individuals. The average heterozygosity among these six loci is 0.73. In the second set of experiments, a DNA library was created from Saimiri genomic DNA, and clones were selected from that library by screening with probes containing di-, tri-, and tetranucleotide repeats. Six novel microsatellites were identified this way, with an average heterozygosity of 0.59. Primer pairs for these six cloned microsatellites were also screened using a series of DNA samples from ten other platyrrhine species to assess the potential utility of these loci in other taxa. This study provides 12 new DNA polymorphisms that will be useful for various studies of this genus and demonstrates that both approaches can be used to develop new DNA polymorphisms in platyrrhine species.

Simian T-lymphotropic virus type 1 (STLV-1) infection in wild yellow baboons (Papio hamadryas cynocephalus) from Mikumi National Park, Tanzania

Serum and peripheral blood leukocytes from wild yellow baboons (Papio hamadryas cynocephalus) were tested for the presence of STLV-1-specific antibodies and proviral DNA. Fourteen of 30 sera tested positive by radioimmunoprecipitation assay (RIPA) with HTLV-1. Among 36 DNA samples tested by PCR 15 were positive by double nested PCR for a fragment of the STLV-1 env gene, the most sensitive assay among PCR tests employed. Of 30 animals that were tested both serologically and by PCR in only 1 case were the results discordant (PCR-positive, antibody-negative). The DNA sequences from env (378 bp), pol (212 bp), and LTR (705 bp) were determined for 5, 5, and 2 Mikumi STLV-1 isolates, respectively. The DNA sequences of Mikumi STLV-1 isolates were virtually identical and phylogenetic analysis revealed that they were clearly distinct from previously published baboon STLV-1 sequences, including those STLV-1 isolates presumed to be from yellow baboons. The results of this study suggest that reliable placement of individual STLV-1 within the PTLV-1 phylogeny requires genomic sequences of STLV-1 isolates from wild animals whose taxonomic identity and geographical origin are firmly established and that the LTR is the genomic region of STLV-1 which is the most informative for cladistic analysis of these viruses.