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Population demography and genetic diversity in the Pleistocene cave lion
Stockholm University, Faculty of Science, Department of Zoology. Swedish Museum of Natural History, Sweden.
Stockholm University, Faculty of Science, Department of Zoology. Swedish Museum of Natural History, Sweden.
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2015 (English)In: Open Quaternary, ISSN 2055-298X, Vol. 1, no 1, 4Article in journal (Refereed) Published
Abstract [en]

With a range that covered most of northern Eurasia and parts of North America, the cave lion (Panthera spelaea) was one of the most widespread carnivores of the Late Pleistocene. Earlier ancient DNA analyses have shown that it is distinct from modern lions, and have suggested a demographic decline in Beringia during marine isotope stage 3 (MIS 3). Here, we further investigate the Late Pleistocene population dynamics in more detail by combining a powerful algorithm that couples MCMC with coalescent simulations under an approximate Bayesian computation framework. We use an ancient DNA dataset of previously published (n = 34) and new radiocarbon dated specimens (n = 14). Phylogenetic and network analyses based on the mitochondrial control region and the ATP8 gene identified two major haplogroups, one of which appears to vanish around 41,000 cal a BP. The approximate Bayesian computation analysis suggested a decline in effective population size (Ne) in Beringia of at least a 2-fold magnitude that began approximately 47,000 cal a BP, followed by an increase in Ne, most likely around 18,000 cal a BP. The cave lion went through a demographic bottleneck during MIS 3, which may have lasted for several tens of thousands of years, and only recovered shortly before the species' extinction. Several other large mammal species display similar declines in genetic diversity in Beringia during MIS 3, suggesting that major environmental changes might have affected megafaunal populations during this time period.

Place, publisher, year, edition, pages
2015. Vol. 1, no 1, 4
Keyword [en]
Panthera spelaea, Beringia, bottleneck, Quaternary, haplogroup, Megafauna
National Category
Evolutionary Biology
Research subject
Systematic Zoology
Identifiers
URN: urn:nbn:se:su:diva-127825DOI: 10.5334/oq.aaOAI: oai:DiVA.org:su-127825DiVA: diva2:911417
Available from: 2016-03-11 Created: 2016-03-11 Last updated: 2016-03-14Bibliographically approved
In thesis
1. Large carnivore population turnover and ecological change during the Late Quaternary
Open this publication in new window or tab >>Large carnivore population turnover and ecological change during the Late Quaternary
2016 (English)Doctoral thesis, comprehensive summary (Other academic)
Abstract [en]

The cave lion (Panthera spelaea), the grey wolf (Canis lupus) and the brown bear (Ursus arctos) all shared an intercontinental distribution across the northern hemisphere during most of the Late Quaternary, and experienced repeated events of climate change. The cave lion went extinct at the end of the Pleistocene and although the wolf and the bear have survived until present day, recent human persecution has caused demographic bottlenecks and local extinctions. In this thesis, mitochondrial and nuclear DNA was analyzed from ancient and modern samples in order to study spatiotemporal changes in genetic diversity in the three species. Mitochondrial sequences analyzed from 48 radiocarbon dated cave lion remains revealed two haplogroups, of which the more genetically diverse seemingly disappeared around 41,000 years BP. Serial coalescent simulations on the data supported a population bottleneck in Beringia between roughly 47-18,000 years BP. Its long duration prevents a specific causal factor to be singled out, but the early onset and overlapping declines of other large mammals in the region suggests that major environmental changes greatly impacted the fauna of Beringia during this time. Using a similar genetic marker, a set of 126 modern wolves and two Siberian wolf remains of Late Pleistocene age were analyzed. The sequences yielded from the latter samples pertained to a basal haplogroup, which contained all Late Pleistocene wolves from previous studies. As data from both modern and ancient wolves were combined, a pattern of decreasing genetic diversity was identified around the Pleistocene-Holocene transition. This decrease was further tested by serial coalescent simulations, which supported a bottleneck in northern North America around this time. Further analyses were applied to one of the ancient wolf remains from Siberia, producing a draft genome sequence and a complete mitochondrial genome. Given the radiocarbon date of the Siberian wolf, a slower mutation rate could be inferred, which pushed back the split between the lineages leading to modern wolves and dogs to at least 27,000 years BP. The Siberian wolf was positioned close to the split but basal to these lineages. A global comparison with modern dogs indicated a closer genetic affiliation between the Siberian wolf and some arctic breeds. For the brown bear, phylogeographic changes in Europe were studied over the last 50,000 years, using radiocarbon dating and mitochondrial sequences. When concatenated and compared with published data, the mtDNA revealed a turnover event just before the LGM, while the dating confirmed a presence of brown bears at relatively high latitudes during this period. Marked shifts in population size were also inferred. Furthermore, data of stable isotope levels confirmed a dietary shift to increasing herbivory around the LGM. Finally, a recent anthropogenic bottleneck among Scandinavian brown bears was studied. While no change in genetic structure could be detected, mitochondrial and microsatellite markers showed a decline in genetic diversity, especially pronounced in the southern subpopulation. ABC simulations supported a bottleneck taking place across all of Scandinavia. Taken together, this thesis have identified and elucidated several impacts on genetic diversity in the past populations of large carnivores. The use of different genetic markers has enabled comparisons with published data, but also revealed their comparatively different benefits and limitations. Overall, the presented studies compose a synthesis of past population dynamics in large carnivores, uniquely revealed by ancient DNA.

Place, publisher, year, edition, pages
Stockholm: Department of Zoology, Stockholm University, 2016
National Category
Evolutionary Biology
Research subject
Systematic Zoology
Identifiers
urn:nbn:se:su:diva-127845 (URN)978-91-7649-380-9 (ISBN)
Public defence
2016-04-29, De Geersalen, Geovetenskapens hus, Svante Arrhenius väg 14, Stockholm, 13:00 (English)
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Supervisors
Note

At the time of the doctoral defense, the following papers were unpublished and had a status as follows: Paper 2: Manuscript. Paper 4: Manuscript.

Available from: 2016-04-06 Created: 2016-03-13 Last updated: 2016-04-05Bibliographically approved

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