Hypotheses about chimpanzee social behavior, phylogeography, and evolution were evaluated by noninvasive genotyping of free-ranging individuals from 20 African sites. Degrees of relatedness among individuals in one community were inferred from allele-sharing at eight nuclear simple sequence repeat (SSR) loci. Males are related on the order of half-siblings, and homozygosity is significantly increased at several SSR loci compared to Hardy-Weinberg expectations. These data support the kin-selection hypothesis for the evolution of cooperation among males. Sequence variation patterns at two mitochondrial loci indicate historically high long-distance gene flow and clarify the relationships among three allopatric subspecies. The unexpectedly large genetic distance between the western subspecies, Pan troglodytes verus, and the other two subspecies suggests a divergence time of about 1.58 million years. This result, if confirmed at nuclear loci and supported by eco-behavioral data, implies that P. t. verus should be elevated to full species rank.

Understanding the historical biogeography of this global biodiversity hotspot is as important to long-term conservation goals as ecology and evolution are to understanding current patterns and processes. Today's geography is, however, misleading and typical of only *2% of the last million years; [90% of that time the region's land area was 1.5-2.0 times larger as mean sea levels were 62 m below today's, climates were cooler, and extensive forests and savanna covered the emerged Sunda plains. The region's land area varied two-fold as sea levels fluctuated up to ±50 m with each of *50 Pleistocene glacial cycles, and forests expanded and contracted with oscillations in land area and seasonality. This dynamic geographic history is relevant to the development of biogeographic regionalism and shows that it is today's forests that are refugial, not those of the Last Glacial Maximum. This history affects how species will adapt or shift their ranges in response to global warming and further decreases in land area (submergence of low-lying coastal areas) during the 21st century. The alternative is mass species extinction. The biota is also threatened by the continued destruction of forest, destruction of Mekong River flood-pulse based ecosystems, and continued human population growth. Human biogeography will become more important in conservation planning as tens of millions of people who depend on protected area forests, riverine ecosystems, and coastal habitats become environmental refugees. Conservation scientists need to become more involved in regional ecological education, environmental stewardship, and ecosystem-based adaptation to sustain as much as possible of this rich biota and the ecological services it provides.

In the context of a study of wild chimpanzees, Pan troglodytes verus, we found that genotypes based on single PCR amplifications of microsatellite loci from single shed hair have a high error rate. We quantified error rates using the comparable results of 791 single shed hair PCR amplifications of 11 microsatellite loci of 18 known individuals. The most frequent error was the amplification of only one of the two alleles present at a heterozygous locus. This phenomenon, called allelic dropout, produced false homozygotes in 31% of single-hair amplifications. There was no difference in the probability of preferential amplification between longer and shorter alleles. The probability of scoring false homozygotes can be reduced to below 0.05 by three separate amplifications from single hairs of the same individual or by pooling hair samples from the same individual. In this study an additional 5.6% of the amplifications gave wrong genotypes because of contamination, labelling and loading errors, and possibly amplification artefacts. In contrast, amplifications from plucked hair taken from four dead individuals gave consistent results (error rate < 0.01%, n = 120). Allelic dropout becomes a problem when the DNA concentration falls below 0.05 ng/10 microL in the template as it can with shed hair, and extracts from faeces and masticated plant matter.

Tropical forests continue to be felled and fragmented around the world. A key question is how rapidly species disappear from forest fragments and how quickly humans must restore forest connectivity to minimize extinctions. We surveyed small mammals on forest islands in Chiew Larn Reservoir in Thailand 5 to 7 and 25 to 26 years after isolation and observed the near-total loss of native small mammals within 5 years from <10-hectare (ha) fragments and within 25 years from 10- to 56-ha fragments. Based on our results, we developed an island biogeographic model and estimated mean extinction half-life (50% of resident species disappearing) to be 13.9 years. These catastrophic extinctions were probably partly driven by an invasive rat species; such biotic invasions are becoming increasingly common in human-modified landscapes. Our results are thus particularly relevant to other fragmented forest landscapes and suggest that small fragments are potentially even more vulnerable to biodiversity loss than previously thought.

Phylogenetic trees for the four extant species of African hominoids are presented, based on mtDNA control region-1 sequences from 1,158 unique haplotypes. We include 83 new haplotypes of western chimpanzees and bonobos. Phylogenetic analysis of this enlarged database, which takes intraspecific geographic variability into account, reveals different patterns of evolution among species and great heterogeneity in species-level variation. Several chimpanzee and bonobo clades (and even single social groups) have retained substantially more mitochondrial variation than is seen in the entire human species. Among the 811 human haplotypes, those that branch off early are predominantly but not exclusively African. Neighbor joining trees provide strong evidence that eastern chimpanzee and human clades have experienced reduced effective population sizes, the latter apparently since the Homo sapiens-neanderthalensis split. Application of topiary pruning resolves ambiguities in the phylogenetic tree that are attributable to homoplasies in the data set. The diverse patterns of mtDNA sequence variation seen in today's hominoid taxa probably ref lect historical differences in ecological plasticity, female-biased dispersal, range fragmentation over differing periods of time, and competition among social groups. These results are relevant to the origin of zoonotic diseases, including HIV-1, and call into question some aspects of the current taxonomic treatment and conservation management of gorillas and chimpanzees.In spite of the absence of relevant fossils, studies of genetic variation have settled the question of whether humans are more closely related to gorillas or chimpanzees in favor of the latter (1). However, most such comparative studies have been based on no more than six individuals of each taxon with the exception of humans (2-9). Furthermore, the individual apes used in these comparisons are typically of unknown geographic origin, and there has been a tendency to treat all chimpanzees as a homogeneous group. Advances in DNA sequencing technology and noninvasive genotyping (10-13) now permit a more thorough analysis of the geographic variation within and among mitochondrial DNA (mtDNA) sequences in each of the living African hominoids. The noncoding control region 1 (CR1) was selected for analysis because it is hypervariable and was thought to be relatively free from direct natural selection and therefore was thought to provide a less ambiguous record of mutational change and phylogenetic relationships (9).Here we present a comparison of genetic variation in all nine recognized taxa of African or African-derived hominoid: (i) western lowland gorilla (Gorilla g. gorilla); (ii) eastern moun- (14). We also include three other groups in our analyses: a Neandertal (Homo s. neanderthalensis) and Bornean and Sumatran orangutans (Pongo p. pygmaeus and Pongo p. abelii, respectively). Using common names except when ambiguous, we show that these taxa have very different amounts and patterns of genetic variation, with hum...