The mitochondrial genome of a 130 000 year old polar bear from Svalbard

The polar bear has become the flagship species in the climate-change discussion. However, little is known about how past climate impacted its evolution and persistence, given an extremely poor fossil record. Although it is undisputed from analyses of mitochondrial (mt) DNA that polar bears constitute a lineage within the genetic diversity of brown bears, timing estimates of their divergence have differed considerably. Using next-generation sequencing technology, we have generated a complete, high-quality mt genome from a stratigraphically validated 130,000- to 110,000-year-old polar bear jawbone. In addition, six mt genomes were generated of extant polar bears from Alaska and brown bears from the Admiralty and Baranof islands of the Alexander Archipelago of southeastern Alaska and Kodiak Island. We show that the phylogenetic position of the ancient polar bear lies almost directly at the branching point between polar bears and brown bears, elucidating a unique morphologically and molecularly documented fossil link between living mammal species. Molecular dating and stable isotope analyses also show that by very early in their evolutionary history, polar bears were already inhabitants of the Artic sea ice and had adapted very rapidly to their current and unique ecology at the top of the Arctic marine food chain. As such, polar bears provide an excellent example of evolutionary opportunism within a widespread mammalian lineage.

Reference: Lindqvist, Schuster, Sun, Talbot, Qi, Tomsho, Kasson, Zeyl, Aass, Miller, Ingolfsson, Bachmann, Wiig. 2010. Complete mitochondrial genome of a Pleistocene jawbone unveils the origin of polar bears.
Proceedings of the National Academy of Sciences USA, 107, 5053-5057.

 

The nuclear genome of the polar bear fossil from Poolepynten, Svalbard

Polar bears (PBs) are superbly adapted to the extreme Arctic environment and have become emblematic of the threat to biodiversity from global climate change. Their divergence from the lower-latitude brown bear provides a textbook example of rapid evolution of distinct phenotypes. However, limited mitochondrial and nuclear DNA evidence conflicts in the timing of PB origin as well as placement of the species within versus sister to the brown bear lineage. We gathered extensive genomic sequence data from contemporary polar, brown, and American black bear samples, in addition to a 130,000- to 110,000-y old PB, to examine this problem from a genome-wide perspective. Nuclear DNA markers reflect a species tree consistent with expectation, showing polar and brown bears to be sister species. However, for the enigmatic brown bears native to Alaska’s Alexander Archipelago, we estimate that not only their mitochondrial genome, but also 5–10% of their nuclear genome, is most closely related to PBs, indicating ancient admixture between the two species. Explicit admixture analyses are consistent with ancient splits among PBs, brown bears and black bears that were later followed by occasional admixture. We also provide paleodemographic estimates that suggest bear evolution has tracked key climate events, and that PB in particular experienced a prolonged and dramatic decline in its effective population size during the last ca. 500,000 years. We demonstrate that brown bears and PBs have had sufficiently independent evolutionary histories over the last 4–5 million years to leave imprints in the PB nuclear genome that likely are associated with ecological adaptation to the Arctic environment.

Reference: Miller, Schuster, Welch, Ratan, Bedoya-Reina, Zhao, Kim, Burhans, Drautz, Wittekindt, Tomsho, Ibarra-Laclette, Herrera-Estrella, Peacock, Farley, Sage, Rode, Obbard, Montiel, Bachmann, Ingólfsson, Aars, Mailund, Wiig, Talbot, Lindqvist. 2012. Polar and brown bear genomes reveal ancient admixture and demographic footprints of past climate change.
Proceedings of the National Academy of Sciences USA 109, E2382–E2390.

Mycobacterium tuberculosis in historic human long bone remains from 18th century burials in Kaiserebersdorf, Austria

The project targets historic human bone remains from a 18th century cemetry related to a poor house established by the Habsburg empress Maria Theresia in Kaiserebersdorf, Austria. Many inmates of the poorhouse are expected to have suffered from tuberculosis. We intended to diagnose tuberculosis by molecular means. DNA extracts from several bones were subjected to PCR amplfications targeting a repetitive insertion sequence (IS 6110) in the genome of Mycobaterium tuberculosis. This marker has been applied successfully in earlier studies on molecular diagnostics of tuberculosis. Unfortunately, ribs and vertebrae that are suited best for diagnosis of tuberculosis were preserved poorly. Therefore, we targeted long bones such as e.g., femurs. It turned out that such bones from Kaiserebersdorf, Austria are not suitable for the purpose; all attempts to detect tuberculosis were negative

The project was funded by the SYNTHESYS (Synthesis of Systematic Resources) program to LB in 2006 (AT-TAF-2968) for working at the NHM, Vienna, Austria.

The project was conducted in co-operation with the Molecular Systematics and the Anthropological collection of the Natural History Museum, Vienna, Austria

Reference: Bachmann, L., Daeubl, B., Lindqvist, C., Kruckenhauser, L., Teschler-Nicola, M., Haring, E. 2008. PCR diagnostics of Mycobacterium tuberculosis in historic human long bone remains from 18th century burials in Kaiserebersdorf, Austria.
BMC Research Notes 1, 83.

The paper was marked "highly accessed article" by the publishers.