Molecular Genetics Laboratory

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Molecular Genetics Laboratory

photo from the DNA-labor A genetics laboratory is an integral part of the Primatology department, providing the facilities for genetic investigations of wild primate populations. Genetic data can be combined with information on behavior, group structure or range, or geographic distribution to yield insights into the evolution of the living primates. Genetic analysis can be done at various levels, and the methods used vary depending upon the questions of interest. Some of the questions we are currently interested in answering using genetic approaches are:

Kinship and social behavior
Do kin relationships affect how individuals interact with one another? Are maternal or paternal kin preferred?

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These questions are particularly interesting to address in chimpanzees because male chimpanzees are philopatric and thus spend their entire lives in the same group and engage in extensive affiliative and cooperative behavior. We have determined that in wild chimpanzee communities, the majority of adult individuals are unrelated to one another (Lukas et al., 2005; Langergraber et al., 2007). Furthermore, while maternal brothers cooperate at high rates, unrelated males also form close bonds, while paternal brothers exhibit no preference for one another (Langergraber et al., 2007). Similarly, although female chimpanzee also form social bonds with one another, pairs of close kin are rare (Langergraber et al., 2009). This suggests that like humans, chimpanzees are quite flexible in their choice of cooperative partners. Wild white-faced capuchin females typically have several maternal and paternal female relatives in the group, but only exhibit preferences for maternal kin (Perry et al., 2008) and along with the evidence from chimpanzees this suggests that preferences for paternal kin may not be widespread in primates. Both male and female gorillas disperse and thus are not expected to be in groups with their relatives. However, analysis of multiple groups of western gorillas suggested that male silverback gorillas may range near relatives, and suggested that this may account for the somewhat puzzling accounts of reduced aggression observed (Bradley et al., 2005). Despite dispersing one or more times, female gorillas also have the potential for interactions with kin, as they often end up in a group containing a female relative (Bradley et al., 2007).
Paternity and behavior
In group-living primates, which individuals father the offspring? How does lifetime reproductive success vary among individuals, between sexes, and among species?

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Primate males compete for reproductive opportunities, and genetic analysis is necessary to determine who has succeeded in fathering offspring. In chimpanzees, males with high social rank generally have higher reproductive success (Vigilant et al., 2001; Boesch et al., 2006) although this advantage varies with group size and other factors (Inoue et al., 2008; Langergraber et al., in prep). In mountain gorilla groups containing more than one male, the dominant male sires the majority of the offspring but apparently cannot prevent subordinates from also achieving some reproductive success (Bradley et al., 2005; Nsubuga et al., 2008). In primate groups in which the dominant male sires the majority of the offspring, he is usually deposed before his daughters reach breeding age and so inbreeding is avoided. In some groups of wild white-faced capuchin monkeys, males may have lengthy tenures as the alpha male. We found that fathers and daughters avoided breeding in such groups, even though the alpha was otherwise reproductively dominant (Muniz et al., 2005). In ongoing work, we are investigating whether cooperative relationships among male Assamese macaques influences the distribution of paternities in the group (Ostner et al., in prep.).
Dispersal and landscape genetics
Do discontinuous habitats hinder dispersal among population fragments? In continuous habitats, does the environment play any role in structuring dispersal movements?

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Gorillas exhibit both male and female dispersal, and so are especially interesting for the study of dispersal dynamics. In a study of the highly endangered Cross River gorillas, we showed that dispersal among fragments appears to be ongoing, which is encouraging for efforts to protect their habitat and dispersal corridors (Bergl and Vigilant, 2007). In contrast to the Cross River gorillas, the mountain gorillas in Bwindi Impenetrable National Park, Uganda live in a continuous habitat with abundant edible vegetation. However, genetic analysis of the entire ~300 gorilla population revealed structuring of the population genetic variation in females, but not in males. By incorporating information on diet differences of groups at two ends of the park, vegetation sampling data, and altitudinal differences, we interpreted our results as suggesting that females prefer to disperse to nearby groups that have diet choices similar to those they are accustomed to, and thus that these female mountain gorillas are potentially exhibiting a previously unsuspected natal habitat bias (Guschanski et al., 2008). Genetic analysis of multiple groups of wild black and white colobus monkeys, together with observational data, suggested that a pattern of genetic structure consistent with female dispersal was more likely the outcome of an unobserved group dissolution (Harris et al., 2009).
Evolutionary histories of primate populations
When did different populations of widespread primates, such as eastern and western gorillas, become separate and was this a gradual or sudden process?

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We generated ~ 15 kb of autosomal DNA sequence data from representatives of western and eastern gorillas and used coalescent modeling approaches to infer that the two populations split about 1 million years ago but continued to exchange migrants until perhaps as recently as 80,000 years ago (Thalmann et al., 2007). We are also anticipating complicated population histories in an ongoing study of multiple species of gibbons (Chan et al., in prep). With the increasing availability of high-throughput sequencing approaches we expect this to be promising area for further research (Vigilant, 2009).
Censusing and tracking
How many individuals occupy a given area, and how are they distributed into groups?

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It takes years to habituate a chimpanzee or gorilla group to human observation, and there is a limit to the number of groups that can be simultaneously monitored. We analyzed samples collected during a field census of the entire Bwindi mountain gorilla population to estimate the minimum number of individuals and find potential sources of error in field-based estimation approaches (Guschanski et al., 2009). In ongoing work, we compare genotypes derived from hundreds of samples collected over several years in Loango, Gabon and derive estimates of the numbers of gorillas and chimpanzees using the area, group compositions, and minimum ranging patterns (Arandjelovic et al., in preparation). Genetic analysis was also used to support the suggestion that lethal aggression between chimpanzees at this site occurred between groups rather than within a group (Boesch et al., 2007). In collaborative work with the Chinese Academy of Sciences (Zoology, Beijing) we are assessing the population size, structure and genetic diversity of an important population of Sichuan snub-nosed monkeys (Chang et al., in prep.).
Genetic analysis of noninvasive samples
How should noninvasive samples be preserved, and how can one avoid errors arising from the use of the low concentration DNAs derived from such samples? How can genotyping be made more efficient?

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Noninvasive sources of DNA, such as feces, chewed fruit or hair, contain very small amounts of DNA as compared to DNA sources such as blood, so appropriate collection and analysis techniques are needed to efficiently obtain reliable results. The amount of DNA surviving in feces varies with storage conditions, and we found that storing feces overnight in ethanol and subsequently drying the material using silica gel produces the best results (Nsububa et al., 2004). We devised a quantitative PCR assay to estimate the concentration of the donor’s DNA in extracts from feces, and use this information to make sure the results are replicated an appropriate number of times (Morin et al., 2001). Recently we demonstrated that a two-step multiplex PCR approach increases the speed and accuracy of genotyping using DNA from noninvasive samples, thus saving time, money and DNA (Arandjelovic et al., 2009).

Technical aspects include

Use of noninvasively-collected samples (feces, shed hairs) as sources of DNA for genetic analysis.

Approaches commonly used are

1. Examination of sequence variation in the first hypervariable region of the control region of the maternally-inherited mitochondrial DNA (mtDNA) molecule

2. Construction of individually distinctive high-resolution genotypes at multiple loci in the nuclear genome using microsatellite markers

3. Analysis of sequence variation at nuclear loci by either direct sequencing, or by sequencing of cloned PCR products.

Equipment and facilities available include

ABI 3100 Genetic Analyzer for high-throughput microsatellite analysis
ABI 310 Genetic Analyzers for microsatellite analysis
ABI 3730 DNA Analyzer for high-throughput sequencing
ABI 7700 Sequence Detection System for quantitative PCR
Numerous PCR machines, with gradient capability
Laminar flow hood, to reduce risk of contamination to low endogenous DNA content samples
Separate dedicated room for DNA extraction from noninvasive samples
Separate dedicated room for PCR set-up
Separate dedicated room for work with museum specimens