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Alfred Russell Wallace's The Malay Archipelago, published in 1869, is a classic text in natural history and the theory of evolution. Amidst heroic hunting narratives and picturesque descriptions of local fauna and flora, stands out a curious episode in which Wallace describes adopting a baby orangutan, whose mother he had killed. Wallace, a British naturalist and collector, cultivated an affectionate relationship with the orphaned orangutan, often referring to her as his "baby." This paper examines how the orangutan was transformed from being a moving target for museum display, to a beloved companion but also a scientific specimen. In this process, Wallace redesigned his colonial bungalow to a space that combined domestic settings with engineered nature-like environments, a familiar construction in later primate research. I use Wallace's adoption episode to discuss how affect and care were interwoven into the exploitative relations of British naturalists and physiologists and the animals they studied. The account of Wallace's idiosyncratic relationship with the orangutan is augmented with additional documentation of the close relationships of scientists with research animals, staged as familial kinship. The emergence of the "laboratory pet" demonstrates how the production of knowledge, the sharing of households, and human-animal emotional ties were interwoven in early biomedical research. [ABSTRACT FROM AUTHOR]

As peat-swamp forests in Borneo become progressively more fragmented, the species that inhabit them are increasingly threatened, notably the Endangered Bornean orang-utan Pongo pygmaeus. The area of a failed agricultural project known as the Mega Rice Project in Central Kalimantan, Indonesia, is composed of fragments of peat-swamp forest that are reported to contain orang-utans, although no comprehensive survey has previously been conducted. In a portion of this area we identified remaining forest fragments, using satellite imagery, and surveyed line transects for orang-utan sleeping nests to determine the density, abundance and distribution of the species. The total area of peat-swamp forest in the study area is 76,755 ha, 59,948 ha of which comprises patches at least as large as the home range of a female orang-utan (250 ha). We estimate a mean population density of 2.48 ± SE 0.32 individuals km−2 and a population of 1,700 ± SE 220 or 1,507 ± SE 195 individuals, based on a 25 and 250 ha minimum patch size threshold, respectively. This is c. 40–45% of the original population, and the fragmented population is unlikely to be viable in terms of long-term demographic and genetic stability. To ensure persistence of this population of orang-utans, direct conservation action to connect forest fragments and prevent further loss of peat-swamp forest will be required, including re-establishing the hydrological regime, reforesting barren areas and fighting fires. [ABSTRACT FROM PUBLISHER]

Investigating how different evolutionary forces have shaped patterns of DNA variation within and among species requires detailed knowledge of their demographic history. Orang-utans, whose distribution is currently restricted to the South- East Asian islands of Borneo ( Pongo pygmaeus) and Sumatra ( Pongo abelii), have likely experienced a complex demographic history, influenced by recurrent changes in climate and sea levels, volcanic activities and anthropogenic pressures. Using the most extensive sample set of wild orang-utans to date, we employed an Approximate Bayesian Computation ( ABC) approach to test the fit of 12 different demographic scenarios to the observed patterns of variation in autosomal, X-chromosomal, mitochondrial and Y-chromosomal markers. In the best-fitting model, Sumatran orang-utans exhibit a deep split of populations north and south of Lake Toba, probably caused by multiple eruptions of the Toba volcano. In addition, we found signals for a strong decline in all Sumatran populations ~24 ka, probably associated with hunting by human colonizers. In contrast, Bornean orang-utans experienced a severe bottleneck ~135 ka, followed by a population expansion and substructuring starting ~82 ka, which we link to an expansion from a glacial refugium. We showed that orang-utans went through drastic changes in population size and connectedness, caused by recurrent contraction and expansion of rainforest habitat during Pleistocene glaciations and probably hunting by early humans. Our findings emphasize the fact that important aspects of the evolutionary past of species with complex demographic histories might remain obscured when applying overly simplified models. [ABSTRACT FROM AUTHOR]

Background High-throughput sequencing has opened up exciting possibilities in population and conservation genetics by enabling the assessment of genetic variation at genome-wide scales. One approach to reduce genome complexity, i.e. investigating only parts of the genome, is reduced-representation library (RRL) sequencing. Like similar approaches, RRL sequencing reduces ascertainment bias due to simultaneous discovery and genotyping of singlenucleotide polymorphisms (SNPs) and does not require reference genomes. Yet, generating such datasets remains challenging due to laboratory and bioinformatical issues. In the laboratory, current protocols require improvements with regards to sequencing homologous fragments to reduce the number of missing genotypes. From the bioinformatical perspective, the reliance of most studies on a single SNP caller disregards the possibility that different algorithms may produce disparate SNP datasets. Results We present an improved RRL (iRRL) protocol that maximizes the generation of homologous DNA sequences, thus achieving improved genotyping-by-sequencing efficiency. Our modifications facilitate generation of single-sample libraries, enabling individual genotype assignments instead of pooled-sample analysis. We sequenced ~1% of the orangutan genome with 41-fold median coverage in 31 wild-born individuals from two populations. SNPs and genotypes were called using three different algorithms. We obtained substantially different SNP datasets depending on the SNP caller. Genotype validations revealed that the Unified Genotyper of the Genome Analysis Toolkit and SAMtools performed significantly better than a caller from CLC Genomics Workbench (CLC). Of all conflicting genotype calls, CLC was only correct in 17% of the cases. Furthermore, conflicting genotypes between two algorithms showed a systematic bias in that one caller almost exclusively assigned heterozygotes, while the other one almost exclusively assigned homozygotes. Conclusions Our enhanced iRRL approach greatly facilitates genotyping-by-sequencing and thus direct estimates of allele frequencies. Our direct comparison of three commonly used SNP callers emphasizes the need to question the accuracy of SNP and genotype calling, as we obtained considerably different SNP datasets depending on caller algorithms, sequencing depths and filtering criteria. These differences affected scans for signatures of natural selection, but will also exert undue influences on demographic inferences. This study presents the first effort to generate a population genomic dataset for wild-born orangutans with known population provenance. [ABSTRACT FROM AUTHOR]

The article reflects on the utility of Arthrobacter luteus (Alu) element, a short stretch of DNA, to study short interspersed nuclear elements (SINEs). It further discusses the importance of the ORF2 capsid protein slippage in maintaining active SINE source elements in primate lineages. It suggests that the A-tail expansion of Alu elements may explain the appearance of Alu stealth-driver elements in the orangutan genome.

The heritability of human personality is well-established. Recent research indicates that nonadditive genetic effects, such as dominance and epistasis, play a large role in personality variation. One possible explanation for the latter finding is that there has been recent selection on human personality. To test this possibility, we estimated additive and nonadditive genetic variance in personality and subjective well-being of zoo-housed orangutans. More than half of the genetic variance in these traits could be attributed to nonadditive genetic effects, modeled as dominance. Subjective well-being had genetic overlap with personality, though less so than has been found in humans or chimpanzees. Since a large portion of nonadditive genetic variance in personality is not unique to humans, the nonadditivity of human personality is not sufficient evidence for recent selection of personality in humans. Nonadditive genetic variance may be a general feature of the genetic structure of personality in primates and other animals. [ABSTRACT FROM AUTHOR]

We demonstrate that much of the morphological and metrical data Lehtonen et al. ( Journal of Biogeography, 2011, 38, 805-808) present in support of a closer relationship between humans and chimpanzees than between humans and orangutans are faulty. When the numerous invalid features and suggested character states are excluded, as they should be, the most robust theory of relationship that can be generated is between humans and orangutans. With regard to the direct optimization method (DOM) resolving problems in analysing molecular (sequence) data, the method, if valid, requires that demonstration of sequence similarity is per force a demonstration of synapomorphy. In brief, DOM fails both to test theories of relatedness and to take into account the fact that identification of shared similarity does not translate into demonstration of synapomorphy. [ABSTRACT FROM AUTHOR]

Natural selection has a critical role in the diversity of morphological traits. However, the genetic basis underlying the evolution and diversity of morphological characteristics, particularly in the context an organism's behavior, lifestyle, and environment, is not well understood. The discovery of nasal chemoreceptors in mammals provided an opportunity to address this question. Here, we identify 4 nasal chemoreceptor gene families (V1R, V2R, OR, and TAAR) from horse, guinea pig, marmoset and orangutan genome sequences, respectively. Together with previously described mammalian nasal chemoreceptor gene repertoires, we found a significant positive correlation between functional gene number and morphological complexity, both in the main olfactory system and the vomeronasal system. The combined analysis of morphological data, behavioral data, and gene repertoires suggests that nocturnal mammals tend to possess more species-specific chemoreceptor genes and more complicated olfactory organs than diurnal mammals. Moreover, analysis of evolutionary forces revealed the existence of positive selection on the species-specific genes, likely reflecting the species-specific detection of odors and pheromones. Taken together, these results reflect a rare case of adaptation to circadian rhythm activity at the genome scale, and strongly suggest that the complexity of morphological olfactory organs and the diversification of nasal chemoreceptors in nocturnal mammals are under selection for the ability to perceive the variety of odors that nocturnal mammals may encounter in their particular dark environments. [ABSTRACT FROM AUTHOR]

The article discusses genetic research on orangutans native to the island of Sumatra, and examines its application to conservation efforts. The harmful effects of habitat destruction on the orangutans are commented on, and the necessity of maintaining genetic diversity for the species' survival is emphasized.

In this article the author discusses the research that claims that humans are more closely related to orangutans than chimpanzees. He outlines the study in which he mentions important points such as the criticism of the molecular genetic analyses of the relationships between human and chimpanzee. Also investigated are the Short INterspersed Elements (SINEs) of the three creatures, the humans, orangutans, and chimpanzees.

The article presents a summary of an article found online at http://dx.doi.org/10.1126/science.aar6343 about an analysis of the great ape genomes. It states chimpanzee and orangutan genomes were sequenced and assembled using high-coverage single-molecule real-time long-read sequencing methods. It comments the genome assemblies provides a comprehensive view of intermediate-size structural genetic variations and will provide greater understanding of genetic differences between apes and humans.

We search the complete orangutan genome for regions where humans are more closely related to orangutans than to chimpanzees due to incomplete lineage sorting (ILS) in the ancestor of human and chimpanzees. The search uses our recently developed coalescent hidden Markov model (HMM) framework. We find ILS present in ⇔1/41% of the genome, and that the ancestral species of human and chimpanzees never experienced a severe population bottleneck. The existence of ILS is validated with simulations, site pattern analysis, and analysis of rare genomic events. The existence of ILS allows us to disentangle the time of isolation of humans and orangutans (the speciation time) from the genetic divergence time, and we find speciation to be as recent as 9-13 million years ago (Mya; contingent on the calibration point). The analyses provide further support for a recent speciation of human and chimpanzee at ⇔1/44 Mya and a diverse ancestor of human and chimpanzee with an effective population size of about 50,000 individuals. Posterior decoding infers ILS for each nucleotide in the genome, and we use this to deduce patterns of selection in the ancestral species. We demonstrate the effect of background selection in the common ancestor of humans and chimpanzees. In agreement with predictions from population genetics, ILS was found to be reduced in exons and gene-dense regions when we control for confounding factors such as GC content and recombination rate. Finally, we find the broad-scale recombination rate to be conserved through the complete ape phylogeny. [ABSTRACT FROM AUTHOR]