Molecular phylogeny of the extinct giant deer, Megaloceros giganteus (original) (raw)
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The phylogenetic position of the 'giant deer' Megaloceros giganteus
Nature, 2005
Nature Publishing Group substitution types), incorporating site-specific rates for each of the four site categories (first, second, third and non-coding). For maximum-likelihood analyses, heuristic searches were conducted with starting trees generated by ten randomly derived stepwise addition sequences, with branch swapping by tree bisection-reconnection (TBR) and re-estimation of parameters. The maximumlikelihood topology was also recovered by using both maximum parsimony and neighbour-joining with the HKY85 substitution model. Bootstrap support values were obtained by an analysis of 1,000 replicate data sets, with the use of maximum-likelihood analysis under a GTR þ SS model with reestimation of parameters at each step. Replicate data sets that maintained proportionality of each site type were generated with PAML v3.14 (ref. 29). Bayesian analyses of the morphological, molecular and combined data sets were conducted with MrBayes v3.1. Topology searches were initiated from random starting trees, with molecular data assigned a GTR þ SS model, and morphological data analysed with distributed rates and likelihoods corrected for scoring bias caused by the presence of only variable characters in the data set. Both combined and molecular analyses were run for 5,000,000 generations, and the morphology-only analysis was run for 2,500,000 generations. Trees were sampled every 100 generations, with the first 25% discarded as burn-in 30 .
The giant deer Megaloceros giganteus is among the most fascinating Late Pleistocene Eurasian megafauna that became extinct at the end of the last ice age. Important questions persist regarding its phylogenetic relationship to contemporary taxa and the reasons for its extinction. We analyzed two large ancient cervid bone fragments recovered from cave sites in the Swabian Jura (Baden- Württemberg, Germany) dated to 12,000 years ago. Using hybridization capture in combination with next generation sequencing, we were able to reconstruct nearly complete mitochondrial genomes from both specimens. Both mtDNAs cluster phylogenetically with fallow deer and show high similarity to previously studied partial Megaloceros giganteus DNA from Kamyshlov in western Siberia and Killavullen in Ireland. The unexpected presence of Megaloceros giganteus in Southern Germany after the Ice Age suggests a later survival in Central Europe than previously proposed. The complete mtDNAs provide strong phylogenetic support for a Dama-Megaloceros clade. Furthermore, isotope analyses support an increasing competition between giant deer, red deer, and reindeer after the Last Glacial Maximum, which might have contributed to the extinction of Megaloceros in Central Europe.
Mitochondrial Genomes of Giant Deers Suggest their Late Survival in Central Europe
2015
The giant deer Megaloceros giganteus is among the most fascinating Late Pleistocene Eurasian megafauna that became extinct at the end of the last ice age. Important questions persist regarding its phylogenetic relationship to contemporary taxa and the reasons for its extinction. We analyzed two large ancient cervid bone fragments recovered from cave sites in the Swabian Jura (Baden-Württemberg, Germany) dated to 12,000 years ago. Using hybridization capture in combination with next generation sequencing, we were able to reconstruct nearly complete mitochondrial genomes from both specimens. Both mtDNAs cluster phylogenetically with fallow deer and show high similarity to previously studied partial Megaloceros giganteus DNA from Kamyshlov in western Siberia and Killavullen in Ireland. The unexpected presence of Megaloceros giganteus in Southern Germany after the Ice Age suggests a later survival in Central Europe than previously proposed. The complete mtDNAs provide strong phylogenetic support for a Dama-Megaloceros clade. Furthermore, isotope analyses support an increasing competition between giant deer, red deer, and reindeer after the Last Glacial Maximum, which might have contributed to the extinction of Megaloceros in Central Europe.