Graham L Banes

University of Wisconsin–Madison | UW · Wisconsin National Primate Research Center

Male orangutans (Pongo spp.) exhibit bimaturism, an alternative reproductive tactic, with flanged and unflanged males displaying two distinct morphological and behavioral phenotypes. Flanged males are larger than unflanged males and display secondary sexual characteristics which unflanged males lack. The evolutionary explanation for alternative rep...

Various global-scale proposals exist to reduce the loss of biological diversity. These include the Half-Earth and Whole-Earth visions that respectively seek to set aside half the planet for wildlife conservation or to diversify conservation practices fundamentally and change the economic systems that determine environmental harm. Here we assess the...

The Sumatran orang-utan (Pongo abelii) reference genome was first published in 2011, in conjunction with ten re-sequenced genomes from unrelated wild-caught individuals. Together, these published data have been utilized in almost all great ape genomic studies, plus in much broader comparative genomic research. Here, we report that the original sequ...

Conservation strategies are rarely systematically evaluated, which reduces transparency, hinders the cost-effective deployment of resources, and hides what works best in different contexts. Using data on the iconic and critically endangered orangutan (Pongo spp.), we developed a novel spatiotemporal framework for evaluating conservation investments...

Despite long being considered as “junk”, transposable elements (TEs) are now accepted as catalysts of evolution. One example is Mutator -like elements (MULEs, one type of terminal inverted repeat DNA TEs, or TIR TEs) capturing sequences as Pack-MULEs in plants. However, their origination mechanism remains perplexing, and whether TIR TEs mediate dup...

Microarrays can be a cost-effective alternative to high-throughput sequencing for discovering novel single-nucleotide polymorphisms (SNPs). Illumina’s iScan platform dominates the market, but their commercial microarray products are designed for model organisms. Further, the platform outputs data in a proprietary format. This cannot be easily conve...

The human genome harbors 14,000 duplicated or retroposed pseudogenes. Given their functionality as regulatory RNAs and low conservation, we hypothesized that pseudogenes could shape human-specific phenotypes. To test this, we performed co-expression analyses and found that pseudogene exhibited tissue-specific expression, especially in the bone marr...

Using data on the iconic orangutan (Pongo spp.), we developed a novel spatiotemporal framework for evaluating conservation investments. We show that around USD 1 billion was invested between 1999 and 2019 into orangutan conservation by governments, non-governmental organizations, companies and communities. Broken down by allocation to different con...

Background Orang-utans comprise three critically endangered species endemic to the islands of Borneo and Sumatra. Though whole-genome sequencing has recently accelerated our understanding of their evolutionary history, the costs of implementing routine genome screening and diagnostics remain prohibitive. Capitalizing on a tri-fold locus discovery a...

Bornean orang-utans Pongo pygmaeus sspp and Sumatran orang-utans Pongo abelii are Critically Endangered species, in rapid decline throughout their ranges in Indonesia and Malaysia. Although substantial populations are well documented in Western zoos, comparatively little is known about those in the East, despite their endemism to the region. Here,...

Unsustainable exploitation of natural resources is increasingly affecting the highly biodiverse tropics [1, 2]. Although rapid developments in remote sensing technology have permitted more precise estimates of land-cover change over large spatial scales [3, 4, 5], our knowledge about the effects of these changes on wildlife is much more sparse [6,...

For many threatened species the rate and drivers of population decline are difficult to assess accurately: species' surveys are typically restricted to small geographic areas, are conducted over short time periods, and employ a wide range of survey protocols. We addressed methodological challenges for assessing change in the abundance of an endange...

The hypervariable region I (HVRI) is persistently used to discern haplotypes, to distinguish geographic subpopulations, and to infer taxonomy in a range of organisms. Numerous studies have highlighted greater heterogeneity elsewhere in the mitochondrial DNA control region, however–particularly, in some species, in other understudied hypervariable r...

Accession codes of published sequences used in phylogenetic analyses. (DOCX)

Confiscated and displaced mammals are often taken to sanctuaries, where the explicit goal may be reintroduction to the wild. By inadvertently collecting animals from different source populations, however, such efforts risk reintroducing individuals that have not been in genetic contact for significant periods of time. Using genetic analyses and 44...

Unlike most mammals, male orang-utans exhibit bimaturism, in that mature individuals express one of two distinct morphological forms. Socially subordinate, ‘unflanged’ males are comparable to females in their size and facial morphology, while socially dominant ‘flanged’ males exhibit extreme sexual dimorphism and secondary sexual characteristics, p...

This study investigated the reproductive parameters of free-ranging rehabilitant female orangutans. We aimed to assess the factors that influence these parameters and provide information that could assist with the management of orangutan reintroduction programs. We analyzed the birth records of free-ranging female rehabilitants at Bukit Lawang, Buk...