Chromosome studies in the orangutan (Pongo pygmaeus): Practical applications for breeding and conservation

The unequivocal identification of Bornean, Sumatran, and first-generation hybrid orangutans can be carried out by chromosome analysis, a procedure that is more reliable than any other so far used to distinguish between orangutan subspecies. Chromosome differences between subspecies have been compared with protein and DNA studies, and these have shown that Bornean and Sumatran orangutans are more different from each other than we originally thought. Chromosome studies in the orangutan have shown variant chromosome types that are not subspecies-specific. One of these variant types is a product of a complex double inversion rearrangement and is a polymorphic trait in both subspecies. In view of our findings, specific guidelines have been recommended for evaluating the fertility of hybrid specimens and maintaining purebred orangutan stocks.     

Fertility and mortality patterns of captive Bornean and Sumatran orangutans: is there a species difference in life history?

Across broad taxonomic groups, life history models predict that increased ecological predictability will lead to conservative investment in reproductive effort. Within species, however, organisms are predicted to have increased reproductive rates under improved environmental conditions. It is not clear how these models apply to closely-related species. In this paper, we examine predictions from these models as applied to variability in reproductive rates between the two species of orangutans, Pongo pygmaeus (Bornean) and Pongo abelii (Sumatran). Orangutans exhibit characteristics of a "slow" life history strategy with large bodies, late age at maturity, low reproductive rates, and long lifespan. Recently, researchers proposed that Sumatran orangutans may have an even slower life history than Bornean orangutans as a result of ecological and genetic differences (Wich et al., 2004). We examined this hypothesis by studying important aspects of life history of both species under conditions of relative ecological stability, in captivity. In this large dataset, there were no significant species differences in age of first or last reproduction, completed fertility, perinatal and postnatal mortality, or female longevity. Bornean orangutans in captivity did have significantly longer interbirth intervals, and male Bornean orangutans had higher survival past maturity. Our results do not support the hypothesis that selection has led to decreased reproductive effort under conditions of increased habitat quality in Sumatra (Wich et al., 2004), and instead suggest that phenotypic flexibility may be particularly important in explaining differences between closely related species.     

Plasticity of human chromosome 3 during primate evolution

Comparative mapping of more than 100 region-specific clones from human chromosome 3 in Bornean and Sumatran orangutans, siamang gibbon, and Old and New World monkeys allowed us to reconstruct ancestral simian and hominoid chromosomes. A single paracentric inversion derives chromosome 1 of the Old World monkey Presbytis cristata from the simian ancestor. In the New World monkey Callithrix geoffroyi and siamang, the ancestor diverged on multiple chromosomes, through utilizing different breakpoints. One shared and two independent inversions derive Bornean orangutan 2 and human 3, implying that neither Bornean orangutans nor humans have conserved the ancestral chromosome form. The inversions, fissions, and translocations in the five species analyzed involve at least 14 different evolutionary breakpoints along the entire length of human 3; however, particular regions appear to be more susceptible to chromosome reshuffling. The ancestral pericentromeric region has promoted both large-scale and micro-rearrangements. Small segments homologous to human 3q11.2 and 3q21.2 were repositioned intrachromosomally independent of the surrounding markers in the orangutan lineage. Breakage and rearrangement of the human 3p12.3 region were associated with extensive intragenomic duplications at multiple orangutan and gibbon subtelomeric sites. We propose that new chromosomes and genomes arise through large-scale rearrangements of evolutionarily conserved genomic building blocks and additional duplication, amplification, and/or repositioning of inherently unstable smaller DNA segments contained within them.     

Chromosome and C-heterochromatin polymorphisms in the Italian newt,Triturus italicus

A combined chromosome and C-heterochromatin polymorphism in pair 12 in the complement of the newt species, T. italicus is described. The C-heterochromatin polymorphism is presumably due to a loss in the proximal C-band, whereas the chromosomal polymorphism has its origin in two different independent pericentric inversions both including the centromere and the proximal C-band of chromosome 12. The double-inversion polymorphism has a wide distribution over the range and follows a clear bipolarity between a northern area where the karyotype is homomorphic for the standard type of pair 12 (ST/ST) and an opposite area where the ST type is completely replaced by variant M₁ and M₂ metacentric chromosomes 12. Various karyophylogenies are possible, but the simplest and the most probable presumes an ancestral karyotype of ST/ST and a mechanism of gradual replacement of the heterobrachial chromosome ST by two independent pericentric inversions. The present data are discussed in relation to existing theories on karyological evolution of Urodeles and the functional significance of telocentric chromosomes suggested by Sessions et al. (1982).     

Speciation and intrasubspecific variation of Bornean orangutans, Pongo pygmaeus pygmaeus

Mitochondrial DNA control region sequences of orangutans (Pongo pygmaeus) from six different populations on the island of Borneo were determined and analyzed for evidence of regional diversity and were compared separately with orangutans from the island of Sumatra. Within the Bornean population, four distinct subpopulations were identified. Furthermore, the results of this study revealed marked divergence, supportive evidence of speciation between Sumatran and Bornean orangutans. This study demonstrates that, as an entire population, Bornean orangutans have not experienced a serious genetic bottleneck, which has been suggested as the cause of low diversity in humans and east African chimpanzees. Based on these new data, it is estimated that Bornean and Sumatran orangutans diverged approximately 1.1 MYA and that the four distinct Bornean populations diverged 860,000 years ago. These findings have important implications for management, breeding, and reintroduction practices in orangutan conservation efforts.     

Molecular genetic divergence of orang utan (Pongo pygmaeus) subspecies based on isozyme and two-dimensional gel electrophoresis

The orang utan (Pongo pygmaeus), as currently recognized, includes two geographically separated subspecies: Pongo pygmaeus pygmaeus, which resides on Borneo, and P. p. abelii, which inhabits Sumatra. At present, there is no known route of gene flow between the two populations except through captive individuals which have been released back into the wild over the last several decades. The two subspecies are differentiated by morphological and behavioral characters, and they can be distinguished by a subspecies specific pericentric chromosomal inversion. Nei-genetic distances were estimated between orang utan subspecies, gorilla, chimpanzee and humans using 44 isozyme loci and using 458 soluble fibroblast proteins which were resolved by two-dimensional gel electrophoresis. Phenetic analysis of both data sets supports the following conclusions: the orang utan subspecies distances are approximately 10 times closer to each other than they are to the African apes, and the orang utan subspecies are approximately as divergent as are the two chimpanzee species. Comparison of the genetic distances to genetic distance estimates done in the same laboratory under identical conditions reveals that the distance between Bornean vs. Sumatran orang utans is 5-10 times the distance measured between several pairs of subspecies including lions, cheetahs, and tigers. Near species level molecular genetic distances between orang utan subspecies would support the separate management of Bornean and Sumatran orang utans as evolutionary significant units (Ryder 1987). Evolutionary topologies were constructed from the distance data using both cladistic and phenetic methods. The majority of resulting trees affirmed previous molecular evolutionary studies that indicated that man and chimpanzee diverged from a common ancestor subsequent to the divergence of gorilla from the common ancestor.     

Chromosome rearrangement patterns of an SD chromosome (SDKona-2) in Drosophila melanogaster caused by hybrid dysgenesis.

The types and frequencies of spontaneous chromosome rearrangements caused by hybrid dysgenesis were studied in a second chromosome autosome of Drosophila melanogaster. This second chromosome, being an SD chromosome, had two important advantages over other autosomes for this study: (i) it had the two inversions characteristic of a standard SD-72 chromosome type, which distinguished it from its homolog in polytene chromosome spreads, and (ii) because of the meiotic drive associated with the segregation distorter system, it was preferentially transmitted to the next generation. The chromosome mutation frequency of this chromosome (given the name SDKona-2) was 8.3 and 11.7% in the F2 and F3 generations, respectively. The types of new chromosome rearrangements observed in the first four generations included paracentric inversions, pericentric inversions, duplications, deletions, reciprocal translocations (involving the third chromosome), and transpositions. Small paracentric inversions were the most common type of new rearrangement. Later, over 35 generations, some of these new rearrangements changed, either by becoming more complex or by being replaced with yet another new chromosome rearrangement. Duplications were unstable and were replaced by paracentric inversions whose breakpoints were on either side of the duplication. Transpositions arose both from a single multibreak event and from a series of two-break events.     

Slow loris (Nycticebus borneanus) consumption by a wild Bornean orangutan (Pongo pygmaeus wurmbii)

Primates - Vertebrate predation and consumption by wild Bornean orangutans (Pongo pygmaeus spp.) is rare. In contrast to recorded observations of slow loris consumption by Sumatran orangutans...     

New karyotypes and somatic and germ-cell banding in Akodon arviculoides (Rodentia, Cricetidae).

Chromosomal polymorphism resulting from three autosomal pericentric inversions and a complex rearrangement involving the largest chromosome of the complement (pair 1) in Akodon arviculoides (2n= 14, 15) is reported. G- and C-banding patterns in somatic and meiotic cells allowed the precise identification of all chromosomes and rearrangements. In meiosis of male specimens with 2n = 15, a large trivalent reflecting the complex rearrangement in autosomal pair 1 was observed. Two possible explanations for it are discussed. G- and C-bands in diplotene cells in heterozygotes for the inversions showed different configurations depending on the pairing in the inverted segments. Chiasma frequency data fro three specimens are analyzed.     

Inferring Pongo conservation units: a perspective based on microsatellite and mitochondrial DNA analyses

In order to define evolutionarily significant and management units (ESUs and MUs) among subpopulations of Sumatran (Pongo pygmaeus abelii) and Bornean (P. p. pygmaeus) orangutans we determined their genetic relationships. We analyzed partial sequences of four mitochondrial genes and nine autosomal microsatellite loci of 70 orangutans to test two hypotheses regarding the population structure within Borneo and the genetic distinction between Bornean and Sumatran orangutans. Our data show Bornean orangutans consist of two genetic clusters—the western and eastern clades. Each taxon exhibits relatively distinct mtDNA and nuclear genetic distributions that are likely attributable to genetic drift. These groups, however, do not warrant designations as separate conservation MUs because they demonstrate no demographic independence and only moderate genetic differentiation. Our findings also indicate relatively high levels of overall genetic diversity within Borneo, suggesting that observed habitat fragmentation and erosion during the last three decades had limited influence on genetic variability. Because the mtDNA of Bornean and Sumatran orangutans are not strictly reciprocally monophyletic, we recommend treating these populations as separate MUs and discontinuing inter-island translocation of animals unless absolutely necessary.     

Geographical variation in and evolutionary history of the Sunda clouded leopard (Neofelis diardi) (Mammalia: Carnivora: Felidae) with the description of a new subspecies from Borneo

Recent morphological and molecular studies led to the recognition of two extant species of clouded leopards; Neofelis nebulosa from mainland southeast Asia and Neofelis diardi from the Sunda Islands of Borneo and Sumatra, including the Batu Islands. In addition to these new species-level distinctions, preliminary molecular data suggested a genetic substructure that separates Bornean and Sumatran clouded leopards, indicating the possibility of two subspecies of N. diardi. This suggestion was based on an analysis of only three Sumatran and seven Bornean individuals. Accordingly, in this study we re-evaluated this proposed subspecies differentiation using additional molecular (mainly historical) samples of eight Bornean and 13 Sumatran clouded leopards; a craniometric analysis of 28 specimens; and examination of pelage morphology of 20 museum specimens and of photographs of 12 wild camera-trapped animals. Molecular (mtDNA and microsatellite loci), craniomandibular and dental analyses strongly support the differentiation of Bornean and Sumatran clouded leopards, but pelage characteristics fail to separate them completely, most probably owing to small sample sizes, but it may also reflect habitat similarities between the two islands and their recent divergence. However, some provisional discriminating pelage characters are presented that need further testing. According to our estimates both populations diverged from each other during the Middle to Late Pleistocene (between 400 and 120 kyr). We present a discussion on the evolutionary history of Neofelis diardi sspp. on the Sunda Shelf, a revised taxonomy for the Sunda clouded leopard, N. diardi, and formally describe the Bornean subspecies, Neofelis diardi borneensis, including the designation of a holotype (BM.3.4.9.2 from Baram, Sarawak) in accordance with the rules of the International Code of Zoological Nomenclature.     

The mitochondrial DNA molecule of sumatran orangutan and a molecular proposal for two (Bornean and Sumatran) species of orangutan

The complete mitochondrial DNA (mtDNA) molecule of Sumatran orangutan, plus the complete mitochondrial control region of another Sumatran specimen and the control regions and five protein-coding genes of two specimens of Bornean orangutan were sequenced and compared with a previously reported complete mtDNA of Bornean orangutan. The two orangutans are presently separated at the subspecies level. Comparison with five different species pairs—namely, harbor seal/grey seal, horse/donkey, fin whale/blue whale, common chimpanzee/pygmy chimpanzee, and Homo/common chimpanzee—showed that the molecular difference between Sumatran and Bornean orangutan is much greater than that between the seals, and greater than that between the two chimpanzees, but similar to that between the horse and the donkey and the fin and blue whales. Considering their limited morphological distinction the comparison revealed unexpectedly great molecular difference between the two orangutans. The nucleotide difference between the orangutans is about 75% of that between Homo and the common chimpanzee, whereas the amino acid difference exceeds that between Homo and the common chimpanzee. On the basis of their molecular distinction we propose that the two orangutans should be recognized as different species, Pongo pygmaeus, Bornean orangutan, and P. abelii, Sumatran orangutan. Received: 15 May 1996 / Accepted: 21 June 1996     

A model for the evolution of developmental arrest in male orangutans

Male Sumatran orangutans (Pongo abelii) may delay for many years the acquisition of the full array of secondary sexual traits, including their characteristic cheek flanges. Such flexible developmental arrest is unique among male primates. Among male Bornean orangutans (Pongo pygmaeus) such long delays appear less common. Here, we develop a simple model to identify the conditions under which developmental arrest can be adaptive. We show that the baseline strategy (i.e., males are not susceptible to arrest) cannot be invaded by the flexible strategy (i.e., males can arrest their development when the conditions are unfavorable) when the potential for high‐ranking unflanged or flanged males to monopolize sexual access to females is low. In contrast, at high monopolization potential, the flexible strategy is the evolutionarily stable strategy. We also derive the proportion of flanged males in the population for each combination of monopolization values. This model concurs with field data that found a different monopolization potential between Bornean and Sumatran flanged males and a lower proportion of flanged males in the population in Sumatran orangutans. Pronounced developmental arrest is linked to very low adult mortality, which explains why it is so limited in its taxonomic distribution. Am J Phys Anthropol 2012. © 2012 Wiley Periodicals, Inc.     

Upper respiratory tract disease in captive orangutans (Pongo sp.): prevalence in 20 European zoos and predisposing factors

Background Upper respiratory tract disease (URTD) is a significant cause of morbidity in captive orangutans (Pongo abelii, Pongo pygmaeus), and the pathogenesis is often unknown. Methods The prevalence of respiratory disease in captive European orangutans (201 animals; 20 zoos) and possible predisposing factors were investigated. Results Bornean orangutans (P. pygmaeus) showed chronic respiratory signs significantly more often (13.8%) than Sumatran (P. abelii; 3.6%), and males (15.8%) were more often afflicted than females (3.9%). Hand‐reared animals (21%) developed air sacculitis more often than parent‐reared animals (5%). Diseased animals were more often genetically related to animals with respiratory diseases (93%) than to healthy animals (54%). None of the environmental conditions investigated had a significant effect on disease prevalence. Conclusion Results suggest a higher importance of individual factors for the development of URTD than environmental conditions. Bornean, male and hand‐reared orangutans and animals related to diseased animals need increased medical surveillance for early detection of respiratory disease.     

Evidence of species specific pericentric inversion in the karyotype of the midge Chironomus balatonicus

Pericentric inversions do not play any important role in chromosomal rearrangements in the karyotype evolution of the genus Chironomus. However, a unique case of the fixed pericentric inversion was discovered in chromosome 2 of Chironomus balatonicus--one of the members of plumosus-species group (Kikhadze et al., 1996a; Golygina et al., 1996). According to morphological criteria, a centromere band on chromosome 2 changed its position in Ch. balatonicus. The cloned H3-SauDNA, specific for centromeres in plumosus group, was in situ hybridized with Ch. balatonicus polytene chromosomes, and thus a real change in the centromere position was proved to be a result of pericentric inversion. This was also confirmed after differential C-staining.     

Molecular Definition of Pericentric Inversion Breakpoints Occurring during the Evolution of Humans and Chimpanzees

High-resolution G-banding analysis has demonstrated remarkable morphological conservation of the chromosomes of the Hominidae family members (humans, chimpanzees, gorillas, and orangutans), with the most notable differences between the genomes appearing as changes in heterochromatin distribution and pericentric inversions. Pericentric inversions may have been important for the establishment of reproductive isolation and speciation of the hominoids as they diverged from a common ancestor. Here the previously published primate karyotype comparisons, coupled with the resources of the Human Genome Project, have been used to identify pericentric inversion breakpoints seen when comparing the human karyotype to that of chimpanzee. Yeast artificial chromosome (YAC) clones were used to detect, by fluorescencein situhybridization, five evolutionary pericentric inversion breakpoints present on the chimpanzee chromosome equivalents of human chromosomes 4, 9, and 12. In addition, two YACs from human 12p that detect a breakpoint in chimpanzee detect a similar rearrangement in gorilla.     

Sex-biased dispersal and volcanic activities shaped phylogeographic patterns of extant Orangutans (genus: Pongo)

The Southeast Asian Sunda archipelago harbors a rich biodiversity with a substantial proportion of endemic species. The evolutionary history of these species has been drastically influenced by environmental forces, such as fluctuating sea levels, climatic changes, and severe volcanic activities. Orangutans (genus: Pongo), the only Asian great apes, are well suited to study the relative impact of these forces due to their well-documented behavioral ecology, strict habitat requirements, and exceptionally slow life history. We investigated the phylogeographic patterns and evolutionary history of orangutans in the light of the complex geological and climatic history of the Sunda archipelago. Our study is based on the most extensive genetic sampling to date, covering the entire range of extant orangutan populations. Using data from three mitochondrial DNA (mtDNA) genes from 112 wild orangutans, we show that Sumatran orangutans, Pongo abelii, are paraphyletic with respect to Bornean orangutans (P. pygmaeus), the only other currently recognized species within this genus. The deepest split in the mtDNA phylogeny of orangutans occurs across the Toba caldera in northern Sumatra and, not as expected, between both islands. Until the recent past, the Toba region has experienced extensive volcanic activity, which has shaped the current phylogeographic patterns. Like their Bornean counterparts, Sumatran orangutans exhibit a strong, yet previously undocumented structuring into four geographical clusters. However, with 3.50 Ma, the Sumatran haplotypes have a much older coalescence than their Bornean counterparts (178 kya). In sharp contrast to the mtDNA data, 18 Y-chromosomal polymorphisms show a much more recent coalescence within Sumatra compared with Borneo. Moreover, the deep geographic structure evident in mtDNA is not reflected in the male population history, strongly suggesting male-biased dispersal. We conclude that volcanic activities have played an important role in the evolutionary history of orangutans and potentially of many other forest-dwelling Sundaland species. Furthermore, we demonstrate that a strong sex bias in dispersal can lead to conflicting patterns in uniparentally inherited markers even at a genus-wide scale, highlighting the need for a combined usage of maternally and paternally inherited marker systems in phylogenetic studies.     

Comparative analysis of karyotypes in European shrew species. I. The sibling species Sorex araneus and S. gemellus: Q-bands, G-bands, and position of NORs

The karyotypes of two closely related species of the genus Sorex (Mammalia, Insectivora) were compared with each other by G- and Q-banding techniques and by Ag-AS staining (GOODPASTURE and BLOOM, 1975). By comparing the G-banded karyotypes, it could be ascertained that the basic differences in karyotype between the two species lie in three pericentric inversions, three paracentric inversions, and one reciprocal translocation. This is in near agreement with FORD and HAMERTON (1970), who assumed that both species differ by three pericentric inversions and one tandem translocation. Furthermore, the karyotype of S. araneus (race C) presented by HALKKA et al. (1974) has been compared with the S. araneus of the present report. Considering the species with respect to karyotypic evolution, it is supposed that S. araneus and S. gemellus derive from a common ancestor.     

The genomic sequence for Prader-Willi/Angelman syndromes' loci of human is apparently conserved in the great apes

Chromosomal changes through pericentric inversions play an important role in the origin of species. Certain pericentric inversions are too minute to be detected cytogenetically, thus hindering the complete reconstruction of hominoid phylogeny. The advent of the fluorescence in situ hybridization (FISH) technique has facilitated the identification of many chromosomal segments, even at the single gene level. Therefore the cosmid probe for Prader-Willi (PWS)/Angelman syndrome to the loci on human chromosome 15 [ql 1-12] is being used as a marker to highlight the complementary sequence in higher primates. We hybridized metaphase chromosomes of chimpanzee (PTR), gorilla (GGO), and orangutan (PPY) with this probe (Oncor) to characterize the chromosomal segments because the nature of these pericentric inversions remains relatively unknown. Our observations suggest that a pericentric inversion has occurred in chimpanzee chromosome (PTR 16) which corresponds to human chromosome 15 at PTR 16 band pl 112, while in gorilla (GGO 15) and orangutan (PPY 16) the bands q11-12 complemented to human chromosome 15 band q11-12. This approach has proven to be a better avenue to characterize the pericentric inversions which have apparently occurred during human evolution. Genetic divergence in the speciation process which occurs through chromosomal rearrangement needs to be reevaluated and further explored using newer techniques.Correspondence to: R.S. Verma     

Molecular cytogenetic characterization of breakpoints involving pericentric inversions of human chromosome 9

Pericentric inversions involving the secondary constriction (qh) region of chromosome 9 are considered to be normal variants. The evolutionary mechanisms and conservation of these inversions via Mendelian fashion have been investigated since the advent of banding techniques. Routine cytogenetic techniques cannot provide the fine characterization necessary to determine the type of genetic material involved in these rearrangements. Therefore, the fluorescence in situ hybridization technique with the human centromere-specific alpha satellite and the beta satellite (D9Z5) and classical satellite (D9Z1) human DNA probes were used to identify the breakpoints of chromosome 9 pericentric inversions. Four unique types of pericentric inversions involving the 9qh region were observed, and the mechanism may be due to breakage and reunion at the proposed breakpoints. They are: type A inversions consist of breakpoints within the alpha and beta satellite DNA regions; type B consist of breakpoints within the beta satellite DNA region and band 9q13; type C involve breakage within the beta and classical satellite DNA regions, and type D have breakpoints within the alpha and classical satellite DNA regions. Obviously, reshuffling of satellite DNA sequences has occurred, which has given rise to a variety of heteromorphisms whose clinical significance remains obscure. Received: 21 December 1995 / Revised: 30 May 1996