TY - JOUR A1 - Meyer, Matthias A1 - Palkopoulou, Eleftheria A1 - Baleka, Sina Isabelle A1 - Stiller, Mathias A1 - Penkman, Kirsty E. H. A1 - Alt, Kurt W. A1 - Ishida, Yasuko A1 - Mania, Dietrich A1 - Mallick, Swapan A1 - Meijer, Tom A1 - Meller, Harald A1 - Nagel, Sarah A1 - Nickel, Birgit A1 - Ostritz, Sven A1 - Rohland, Nadin A1 - Schauer, Karol A1 - Schueler, Tim A1 - Roca, Alfred L. A1 - Reich, David A1 - Shapiro, Beth A1 - Hofreiter, Michael T1 - Palaeogenomes of Eurasian straight-tusked elephants challenge the current view of elephant evolution JF - eLife N2 - The straight-tusked elephants Palaeoloxodon spp. were widespread across Eurasia during the Pleistocene. Phylogenetic reconstructions using morphological traits have grouped them with Asian elephants (Elephas maximus), and many paleontologists place Palaeoloxodon within Elephas. Here, we report the recovery of full mitochondrial genomes from four and partial nuclear genomes from two P. antiquus fossils. These fossils were collected at two sites in Germany, Neumark-Nord and Weimar-Ehringsdorf, and likely date to interglacial periods similar to 120 and similar to 244 thousand years ago, respectively. Unexpectedly, nuclear and mitochondrial DNA analyses suggest that P. antiquus was a close relative of extant African forest elephants (Loxodonta cyclotis). Species previously referred to Palaeoloxodon are thus most parsimoniously explained as having diverged from the lineage of Loxodonta, indicating that Loxodonta has not been constrained to Africa. Our results demonstrate that the current picture of elephant evolution is in need of substantial revision. Y1 - 2017 U6 - https://doi.org/10.7554/eLife.25413 SN - 2050-084X VL - 6 PB - eLife Sciences Publications CY - Cambridge ER - TY - JOUR A1 - Alter, S. Elizabeth A1 - Meyer, Matthias A1 - Post, Klaas A1 - Czechowski, Paul A1 - Gravlund, Peter A1 - Gaines, Cork A1 - Rosenbaum, Howard C. A1 - Kaschner, Kristin A1 - Turvey, Samuel T. A1 - van der Plicht, Johannes A1 - Shapiro, Beth A1 - Hofreiter, Michael T1 - Climate impacts on transocean dispersal and habitat in gray whales from the Pleistocene to 2100 JF - Molecular ecology N2 - Arctic animals face dramatic habitat alteration due to ongoing climate change. Understanding how such species have responded to past glacial cycles can help us forecast their response to today's changing climate. Gray whales are among those marine species likely to be strongly affected by Arctic climate change, but a thorough analysis of past climate impacts on this species has been complicated by lack of information about an extinct population in the Atlantic. While little is known about the history of Atlantic gray whales or their relationship to the extant Pacific population, the extirpation of the Atlantic population during historical times has been attributed to whaling. We used a combination of ancient and modern DNA, radiocarbon dating and predictive habitat modelling to better understand the distribution of gray whales during the Pleistocene and Holocene. Our results reveal that dispersal between the Pacific and Atlantic was climate dependent and occurred both during the Pleistocene prior to the last glacial period and the early Holocene immediately following the opening of the Bering Strait. Genetic diversity in the Atlantic declined over an extended interval that predates the period of intensive commercial whaling, indicating this decline may have been precipitated by Holocene climate or other ecological causes. These first genetic data for Atlantic gray whales, particularly when combined with predictive habitat models for the year 2100, suggest that two recent sightings of gray whales in the Atlantic may represent the beginning of the expansion of this species' habitat beyond its currently realized range. KW - ancient DNA KW - climate change KW - last glacial maximum KW - marine mammal Y1 - 2015 U6 - https://doi.org/10.1111/mec.13121 SN - 0962-1083 SN - 1365-294X VL - 24 IS - 7 SP - 1510 EP - 1522 PB - Wiley-Blackwell CY - Hoboken ER - TY - JOUR A1 - Hartmann, Stefanie A1 - Helm, Conrad A1 - Nickel, Birgit A1 - Meyer, Matthias A1 - Struck, Torsten H. A1 - Tiedemann, Ralph A1 - Selbig, Joachim A1 - Bleidorn, Christoph T1 - Exploiting gene families for phylogenomic analysis of myzostomid transcriptome data JF - PLoS one N2 - Background: In trying to understand the evolutionary relationships of organisms, the current flood of sequence data offers great opportunities, but also reveals new challenges with regard to data quality, the selection of data for subsequent analysis, and the automation of steps that were once done manually for single-gene analyses. Even though genome or transcriptome data is available for representatives of most bilaterian phyla, some enigmatic taxa still have an uncertain position in the animal tree of life. This is especially true for myzostomids, a group of symbiotic ( or parasitic) protostomes that are either placed with annelids or flatworms. Methodology: Based on similarity criteria, Illumina-based transcriptome sequences of one myzostomid were compared to protein sequences of one additional myzostomid and 29 reference metazoa and clustered into gene families. These families were then used to investigate the phylogenetic position of Myzostomida using different approaches: Alignments of 989 sequence families were concatenated, and the resulting superalignment was analyzed under a Maximum Likelihood criterion. We also used all 1,878 gene trees with at least one myzostomid sequence for a supertree approach: the individual gene trees were computed and then reconciled into a species tree using gene tree parsimony. Conclusions: Superalignments require strictly orthologous genes, and both the gene selection and the widely varying amount of data available for different taxa in our dataset may cause anomalous placements and low bootstrap support. In contrast, gene tree parsimony is designed to accommodate multilocus gene families and therefore allows a much more comprehensive data set to be analyzed. Results of this supertree approach showed a well-resolved phylogeny, in which myzostomids were part of the annelid radiation, and major bilaterian taxa were found to be monophyletic. Y1 - 2012 U6 - https://doi.org/10.1371/journal.pone.0029843 SN - 1932-6203 VL - 7 IS - 1 PB - PLoS CY - San Fransisco ER -