• Change: Risks and predictability

      Hobohm, Carsten; Vanderplank, Sula E.; Hobohm, Carsten; Cabin, Robert J. (Springer International PublishingCham, Switzerland, 2021)
      ...This study deals with the question of how stochastic effects, changing ecological conditions, the introduction of alien species, and dramatic events in general, can be characterized and quantified. We propose some initial ideas for the establishment of an indicator system for constancy and change through time, with respect to the effect size....
    • Comparative and demographic analysis of orang-utan genomes

      Locke, Devin P.; Hillier, LaDeana W.; Warren, Wesley C.; Worley, Kim C.; Nazareth, Lynne V.; Muzny, Donna M.; Yang, Shiaw-Pyng; Wang, Zhengyuan; Chinwalla, Asif T.; Minx, Pat; et al. (2011)
      ‘Orang-utan’ is derived from a Malay term meaning ‘man of the forest’ and aptly describes the southeast Asian great apes native to Sumatra and Borneo. The orang-utan species, Pongo abelii (Sumatran) and Pongo pygmaeus (Bornean), are the most phylogenetically distant great apes from humans, thereby providing an informative perspective on hominid evolution. Here we present a Sumatran orang-utan draft genome assembly and short read sequence data from five Sumatran and five Bornean orang-utan genomes. Our analyses reveal that, compared to other primates, the orang-utan genome has many unique features. Structural evolution of the orang-utan genome has proceeded much more slowly than other great apes, evidenced by fewer rearrangements, less segmental duplication, a lower rate of gene family turnover and surprisingly quiescent Alu repeats, which have played a major role in restructuring other primate genomes. We also describe a primate polymorphic neocentromere, found in both Pongo species, emphasizing the gradual evolution of orang-utan genome structure. Orang-utans have extremely low energy usage for a eutherian mammal1, far lower than their hominid relatives. Adding their genome to the repertoire of sequenced primates illuminates new signals of positive selection in several pathways including glycolipid metabolism. From the population perspective, both Pongo species are deeply diverse; however, Sumatran individuals possess greater diversity than their Bornean counterparts, and more species-specific variation. Our estimate of Bornean/Sumatran speciation time, 400,000 years ago, is more recent than most previous studies and underscores the complexity of the orang-utan speciation process. Despite a smaller modern census population size, the Sumatran effective population size (Ne) expanded exponentially relative to the ancestral Ne after the split, while Bornean Ne declined over the same period. Overall, the resources and analyses presented here offer new opportunities in evolutionary genomics, insights into hominid biology, and an extensive database of variation for conservation efforts.
    • Copy number variation analysis in the great apes reveals species-specific patterns of structural variation

      Gazave, E.; Darre, F.; Morcillo-Suarez, C.; Petit-Marty, N.; Carreno, A.; Marigorta, U. M.; Ryder, Oliver A.; Blancher, A.; Rocchi, M.; Bosch, E.; et al. (2011)
      ...We performed intraspecific comparative genomic hybridizations to identify loci harboring copy number variants in each of the four great apes: bonobos, chimpanzees, gorillas, and orangutans. For the first time, we could analyze differences in CNV location and frequency in these four species, and compare them with human CNVs and primate segmental duplication (SD) maps....
    • Disorders of sexual development in wild and captive exotic animals

      Mastromonaco, G. F.; Houck, Marlys L.; Bergfelt, D. R. (2012)
      ...Compared to the wealth of information available on humans and domestic species, a better understanding of the factors influencing sexual development in wildlife is essential for developing and improving population management or conservation plans. This review attempts to bring together the different facets of DSDs as studied in the fields of reproductive physiology, endocrinology, ecotoxicology, wildlife biology, and environmental health.
    • Environmental violence and the socio-environmental (de)evolution of a landscape in the San Quintín Valley.

      Narchi, Nemer E.; Vanderplank, Sula E.; Medina-Rodríguez, Jesús; Alfaro-Mercado, Enrique (2020)
      The social and environmental effects of industrial agriculture in the San Quintín Valley of Baja California are closely related. An environmental history of the...
    • Human and great ape red blood cells differ in plasmalogen levels and composition

      Moser, A.B.; Steinberg, S.J.; Watkins, P.A.; Moser, H.W.; Ramaswamy, K.; Siegmund, K.D.; Lee, D.R.; Ely, J.J.; Ryder, Oliver A.; Hacia, J.G. (2011)
      Plasmalogens are ether phospholipids required for normal mammalian developmental, physiological, and cognitive functions. They have been proposed to act as membrane antioxidants and reservoirs of polyunsaturated fatty acids as well as influence intracellular signaling and membrane dynamics. Plasmalogens are particularly enriched in cells and tissues of the human nervous, immune, and cardiovascular systems. Humans with severely reduced plasmalogen levels have reduced life spans, abnormal neurological development, skeletal dysplasia, impaired respiration, and cataracts. Plasmalogen deficiency is also found in the brain tissue of individuals with Alzheimer disease.
    • Identification of differences in human and great ape phytanic acid metabolism that could influence gene expression profiles and physiological functions

      Watkins, Paul A.; Moser, Ann B.; Toomer, Cicely B.; Steinberg, Steven J.; Moser, Hugo W.; Karaman, Mazen W.; Ramaswamy, Krishna; Siegmund, Kimberly D.; Lee, D. Rick; Ely, John J.; et al. (2010)
      It has been proposed that anatomical differences in human and great ape guts arose in response to species-specific diets and energy demands. To investigate functional genomic consequences of these differences, we compared their physiological levels of phytanic acid, a branched chain fatty acid that can be derived from the microbial degradation of chlorophyll in ruminant guts. Humans who accumulate large stores of phytanic acid commonly develop cerebellar ataxia, peripheral polyneuropathy, and retinitis pigmentosa in addition to other medical conditions. Furthermore, phytanic acid is an activator of the PPAR-alpha transcription factor that influences the expression of genes relevant to lipid metabolism.
    • Land use change and the future of biodiversity

      Hobohm, Carsten; Beierkuhnlein, Carl; Börtitz, Christine; Ralph Clark, V.; El Balti, Nadja; Fichtner, Andreas; Franklin, Scott; Gaens, Thomas; Härdtle, Werner; Hansen, Andreas Skriver; et al. (Springer International PublishingCham, Switzerland, 2021)
      This synthesis report is a meta-analysis of perspectives for biodiversity and ecosystems, with a strong focus on human impacts on the environment, and a work order to enable and manage the protection, survival and evolution of all species on Earth. The goal is to protect nature without any further species loss (Zero Extinction)....
    • Resources for humans, plants and animals: Who is the ruler of the driver? And: Can resource use explain everything?

      Hobohm, Carsten; Vanderplank, Sula E.; Hobohm, Carsten; Cabin, Robert J. (Springer International PublishingCham, Switzerland, 2021)
      ...We ask the question “is it possible to estimate the effects of human exploitation of ecosystems?” Under changing conditions the ecosystem is adapting the resource use permanently by adjusting the combination of its features. Productivity is the driver of recent conditions and biomass is storage; the existence of each is a precondition for the other. Species diversity can increase by immigration and evolution and decrease by emigration and extinction.....