Genus-wide paleogenetic analysis of Middle to Late Pleistocene extinct straight-tusked elephants (Palaeoloxodon) to infer phylogeography and patterns of admixture
Systematics and Morphology (Zoology)
Final Report Abstract
The aim of this project was the expansion of available genetic data for Palaeoloxodon, the genus of the extinct straight-tusked elephant. Straight-tusked elephants are challenging for ancient DNA (aDNA) research has they were distributed in temperate to tropical climates and the majority of specimens discovered are 100,000 years old or older. The combination of a warm climate and high age lead to highly degraded DNA, to the point were no DNA can be recovered, although aDNA laboratory methods have improved considerably in recent years. The five available mitochondrial genomes and one high coverage genome from Palaeoloxodon specimens from Germany and Italy show a complex evolutionary history including several hybridization events. The project analyzed 97 samples covering a large part of the distribution of Palaeoloxodon and successfully recovered two complete mitochondrial genomes: one from the Upper Rhine Valley, Germany, the other from the province of Hebei, China. Additionally, another 13 samples showed low amount of endogenous DNA, meaning that the success rate was only ~15%. The mitochondrial genome from Germany clustered with previously identified P. antiquus specimens from Neumark-Nord (Germany, ~120,000 years old), suggesting a relatively homogeneous population in Central Europe during the last interglacial. Surprisingly, the Chinese specimen grouped together with a sample from Weimar- Ehringsdorf (Germany, ~240,000 years old), suggesting a wide geographical distribution for this clade and raising questions about species delineation, as no Palaeoloxodon species was previously believed to inhabit both Europe and Eastern Asia. Although mitochondrial genomes were successfully recovered, nuclear genomic data is needed to fully understand the complex history of Palaeoloxodon in Eurasia. The currently available data suggests complex migration and hybridization dynamics, including the possibility of multiple hybridization events with the African Forest elephant and more than one migration from Africa into Eurasia. Future research should focus on recovering nuclear DNA to clarify these relationships and further explore the genetic diversity of Palaeoloxodon across its range.
Publications
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A genetic glimpse of the Chinese straight-tusked elephants. Biology Letters, 19(7).
Lin, Haifeng; Hu, Jiaming; Baleka, Sina; Yuan, Junxia; Chen, Xi; Xiao, Bo; Song, Shiwen; Du, Zhicheng; Lai, Xulong; Hofreiter, Michael & Sheng, Guilian
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A female woolly mammoth’s lifetime movements end in an ancient Alaskan hunter-gatherer camp. Science Advances, 10(3).
Rowe, Audrey G.; Bataille, Clement P.; Baleka, Sina; Combs, Evelynn A.; Crass, Barbara A.; Fisher, Daniel C.; Ghosh, Sambit; Holmes, Charles E.; Krasinski, Kathryn E.; Lanoë, François; Murchie, Tyler J.; Poinar, Hendrik; Potter, Ben; Rasic, Jeffrey T.; Reuther, Joshua; Smith, Gerad M.; Spaleta, Karen J.; Wygal, Brian T. & Wooller, Matthew J.
