David S. Woodruff

Estimating population sizes for elusive animals: the forest elephants of Kakum National Park, Ghana

African forest elephants are difficult to observe in the dense vegetation, and previous studies have relied upon indirect methods to estimate population sizes. Using multilocus genotyping of noninvasively collected samples, we performed a genetic survey of the forest elephant population at Kakum National Park, Ghana. We estimated population size, sex ratio and genetic variability from our data, then combined this information with field observations to divide the population into age groups. Our population size estimate was very close to that obtained using dung counts, the most commonly used indirect method of estimating the population sizes of forest elephant populations. As their habitat is fragmented by expanding human populations, management will be increasingly important to the persistence of forest elephant populations. The data that can be obtained from noninvasively collected samples will help managers plan for the conservation of this keystone species.

Female reproductive strategies, paternity and community structure in wild West African chimpanzees

Although the variability and complexity of chimpanzee behaviour frustrates generalization, it is widely believed that social evolution in this species occurs in the context of the recognizable social group or community. We used a combination of field observations and noninvasive genotyping to study the genetic structure of a habituated community of 55 wild chimpanzees, Pan troglodytes verus, in the Taï Forest, Côte dIvoire. Pedigree relationships in that community show that female mate choice strategies are more variable than previously supposed and that the observed social groups are not the exclusive reproductive units. Genetic evidence based on nuclear microsatellite markers and behavioural obser-vations reveal that females in the Taï forest actively seek mating partners outside their social unit; noncommunity males accounted for half the paternities over 5 years. This female mating strategy increases male gene flow between communities despite male philopatry, and negates the predicted higher relatedness among community males. Kin selection seems unlikely to explain the frequent cooperation and sharing observed among group males in this population. Similarly, inbreeding avoidance is probably not the sole cause of permanent adolescent female dispersal as a combination of extragroup mating and avoidance of incest with home group males would allow females to avoid inbreeding without the hazards associated with immigration into a new community. Extragroup mating as part of chimpanzee females reproductive strategy may allow them to choose from a wider variety and number of males, without losing the resources and support provided by their male social group partners. Copyright 1999 The Association for the Study of Animal Behaviour.

Paternity exclusion in a community of wild chimpanzees using hypervariable simple sequence repeats

We report the use of hypervariable simple sequence repeat (SSR) nuclear loci to study paternity in a community of wild chimpanzees (Pan troglodytes schweinfurthii) in Gombe National Park, Tanzania. All 43 living members of a habituated community were sampled and 35 were genotyped at 8 SSR loci using DNA amplified from hair. Paternity exclusions were performed for 25 chimpanzees including 10 for whom the mother was also genotyped. In each case 12–20 males were potential fathers based on their age and/ or direct observation of sexual behaviour. 179 tests involving potential father/offspring combinations were performed. In four cases the data permit the probable identification of the previously undetermined father; these are the first such determinations for free‐ranging chimpanzees, and the first based on non‐invasive sampling. In another four cases we were able to exclude all but two to five potential fathers, and in the remaining cases we were able to exclude all living males. For molecular ecologists SSR genotype databases offer important advantages over currently popular minisatellite DNA fingerprinting: they can be analysed unequivocally using traditional population genetics techniques and they can be expanded through time and space by other researchers.

Genetic Analysis of Group Composition and Breeding System in a Wild Common Marmoset (Callithrix jacchus) Population

We established pedigree relations in three wild common marmoset social groups for which observational data were available, together with genotypes of some individuals from neighboring groups. Relatedness of 40 individuals were based on 11 microsatellite loci amplified from nDNA obtained noninvasively from plucked hair. The wild marmosets were only half as variable as a captive population characterized previously: 2–6 alleles/locus; HO = 0.41 and HE = 0.35. Parentage exclusion probabilities were 61.8% for an offspring and one alleged parent and 90.7% for an offspring with one confirmed and one alleged parent. Each group (n = 5–14 individuals) had two breeding females and ≥2 adult males. Within each group the infants and reproductively inactive adults were closely related to at least the breeding females; the latter were related to each other as closely as mother/infant pairs or sisters. Relatedness of adult males was lower, indicating recent intergroup dispersal. Genetic data confirm Callithrix jacchus live in relatively stable extended family groups of closely related individuals. Matings occurred preferentially among the least related adults and most infants were fathered by the dominant male. The genetic data are consistent with polygynmonandry as are the field observations. Callithrix have variable mating systems, ranging from monogamy to polyandry to polygyny within social groups plus extragroup copulations; our data provide no evidence for polyandry and are inconclusive with respect to extragroup paternity. Nevertheless, noninvasive multilocus genotyping methods will resolve these questions when longer-term studies of entire populations are undertaken.

Non-invasive sampling and DNA amplification for paternity exclusion, community structure, and phylogeography in wild chimpanzees

Genetic studies of free-ranging primates have been seriously impeded by difficulties of sampling tissues, including the undesirability of bleeding habituated animals, of transporting frozen samples to the laboratory, and of the inherent inadequacies of accessible variation including allozymes, mtDNA RFLP patterns and DNA fingerprints. We have developed methods of non-invasive DNA sampling and DNA-level genotyping which, when combined with a hierarchical analysis of mtDNA sequences and hypervariable nDNA simple sequence repeat (microsatellite) loci size length polymorphisms, facilitate the resolution of most questions at the individual, social group (community), population, and species (phylogenetic) levels. This approach, based on DNA amplified from shed hair, represents an important new tool for the acquisition of genetic information and will facilitate the study and management of both captive and free-ranging chimpanzees (Pan troglodytes). Our hierarchical analysis of population genetics of chimpanzees has revealed high historical levels of gene flow and large effective population sizes, as well as substantial divergence between the West African subspecies and chimpanzees from central and East Africa. At the community level, closer relatedness among philopatric males than among females supports the view that kin selection has been an evolutionary force shaping male-male cooperation in this species. Results from our study of the now relatively isolated Gombe community suggest that habitat fragmentation affects population genetic structure and possibly population viability.

Identification of Chimpanzee Subspecies with DNA from Hair and Allele-Specific Probes

We describe a non-invasive method of determining the subspecies identity of common chimpanzees (Pan troglodytes), based on subspecies-specific sequence differences in the mitochondrial genome. This procedure involves the extraction of DNA from hair, the amplification of a short (410 base pair b. p. )) segment of the non-coding displacement loop (D-loop) by the polymerase chain reaction (PCR), and subspecies identification based on rapid allele-specific oligonucleotide (ASO) probe dot-blot typing. This approach will contribute to : (i) the colony-level management of captive chimpanzees by enabling managers to recognize hybrids between subspecies and minimize outbreeding depression; (ii) the recognition of inappropriately matched individuals in comparative behavioural and experimental studies; and (iii) forensic questions surrounding the origin of illegally traded animals.