@article{ThomasCarvalhoHaileetal.2019, author = {Thomas, Jessica E. and Carvalho, Gary R. and Haile, James and Rawlence, Nicolas J. and Martin, Michael D. and Ho, Simon Y. W. and Sigfusson, Arnor P. and Josefsson, Vigfus A. and Frederiksen, Morten and Linnebjerg, Jannie F. and Castruita, Jose A. Samaniego and Niemann, Jonas and Sinding, Mikkel-Holger S. and Sandoval-Velasco, Marcela and Soares, Andre E. R. and Lacy, Robert and Barilaro, Christina and Best, Juila and Brandis, Dirk and Cavallo, Chiara and Elorza, Mikelo and Garrett, Kimball L. and Groot, Maaike and Johansson, Friederike and Lifjeld, Jan T. and Nilson, Goran and Serjeanston, Dale and Sweet, Paul and Fuller, Errol and Hufthammer, Anne Karin and Meldgaard, Morten and Fjeldsa, Jon and Shapiro, Beth and Hofreiter, Michael and Stewart, John R. and Gilbert, M. Thomas P. and Knapp, Michael}, title = {Demographic reconstruction from ancient DNA supports rapid extinction of the great auk}, series = {eLife}, volume = {8}, journal = {eLife}, publisher = {eLife Sciences Publications}, address = {Cambridge}, issn = {2050-084X}, doi = {10.7554/eLife.47509}, pages = {35}, year = {2019}, abstract = {The great auk was once abundant and distributed across the North Atlantic. It is now extinct, having been heavily exploited for its eggs, meat, and feathers. We investigated the impact of human hunting on its demise by integrating genetic data, GPS-based ocean current data, and analyses of population viability. We sequenced complete mitochondrial genomes of 41 individuals from across the species' geographic range and reconstructed population structure and population dynamics throughout the Holocene. Taken together, our data do not provide any evidence that great auks were at risk of extinction prior to the onset of intensive human hunting in the early 16th century. In addition, our population viability analyses reveal that even if the great auk had not been under threat by environmental change, human hunting alone could have been sufficient to cause its extinction. Our results emphasise the vulnerability of even abundant and widespread species to intense and localised exploitation.}, language = {en} } @article{ChenLiZhangetal.2019, author = {Chen, Shun-Gang and Li, Ji and Zhang, Fan and Xiao, Bo and Hu, Jia-Ming and Cui, Yin-Qiu and Hofreiter, Michael and Hou, Xin-Dong and Sheng, Gui-Lian and Lai, Xu-Long and Yuan, Jun-Xia}, title = {Different maternal lineages revealed by ancient mitochondrial genome of Camelus bactrianus from China}, series = {Mitochondrial DNA Part A}, volume = {30}, journal = {Mitochondrial DNA Part A}, number = {7}, publisher = {Routledge, Taylor \& Francis Group}, address = {Abingdon}, issn = {2470-1394}, doi = {10.1080/24701394.2019.1659250}, pages = {786 -- 793}, year = {2019}, abstract = {Domestic Bactrian camel (Camelus bactrianus) used to be one of the most important livestock species in Chinese history, as well as the major transport carrier on the ancient Silk Road. However, archeological studies on Chinese C. bactrianus are still limited, and molecular biology research on this species is mainly focused on modern specimens. In this study, we retrieved the complete mitochondrial genome from a C. bactrianus specimen, which was excavated from northwestern China and dated at 1290-1180 cal. Phylogenetic analyses using 18 mitochondrial genomes indicated that the C. bactrianus clade was divided into two maternal lineages. The majority of samples originating from Iran to Japan and Mongolia belong to subclade A1, while our sample together with two Mongolian individuals formed the much smaller subclade A2. Furthermore, the divergence time of these two maternal lineages was estimated as 165 Kya (95\% credibility interval 117-222 Kya), this might indicate that several different evolutionary lineages were incorporated into the domestic gene pool during the initial domestication process. Bayesian skyline plot (BSP) analysis a slow increase in female effective population size of C. bactrianus from 5000 years ago, which to the beginning of domestication of C. bactrianus. The present study also revealed that there were extensive exchanges of genetic information among C. bactrianus populations in regions along the Silk Road.}, language = {en} } @article{PalkopoulouLipsonMallicketal.2018, author = {Palkopoulou, Eleftheria and Lipson, Mark and Mallick, Swapan and Nielsen, Svend and Rohland, Nadin and Baleka, Sina Isabelle and Karpinski, Emil and Ivancevici, Atma M. and Thu-Hien To, and Kortschak, Daniel and Raison, Joy M. and Qu, Zhipeng and Chin, Tat-Jun and Alt, Kurt W. and Claesson, Stefan and Dalen, Love and MacPhee, Ross D. E. and Meller, Harald and Rocar, Alfred L. and Ryder, Oliver A. and Heiman, David and Young, Sarah and Breen, Matthew and Williams, Christina and Aken, Bronwen L. and Ruffier, Magali and Karlsson, Elinor and Johnson, Jeremy and Di Palma, Federica and Alfoldi, Jessica and Adelsoni, David L. and Mailund, Thomas and Munch, Kasper and Lindblad-Toh, Kerstin and Hofreiter, Michael and Poinar, Hendrik and Reich, David}, title = {A comprehensive genomic history of extinct and living elephants}, series = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {115}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, number = {11}, publisher = {National Acad. of Sciences}, address = {Washington}, issn = {0027-8424}, doi = {10.1073/pnas.1720554115}, pages = {E2566 -- E2574}, year = {2018}, language = {en} } @article{WutkeSandovalCastellanosBeneckeetal.2018, author = {Wutke, Saskia and Sandoval-Castellanos, Edson and Benecke, Norbert and D{\"o}hle, Hans-J{\"u}rgen and Friederich, Susanne and Gonzalez, Javier and Hofreiter, Michael and Lougas, Lembi and Magnell, Ola and Malaspinas, Anna-Sapfo and Morales-Muniz, Arturo and Orlando, Ludovic and Reissmann, Monika and Trinks, Alexandra and Ludwig, Arne}, title = {Decline of genetic diversity in ancient domestic stallions in Europe}, series = {Science Advances}, volume = {4}, journal = {Science Advances}, number = {4}, publisher = {American Assoc. for the Advancement of Science}, address = {Washington}, issn = {2375-2548}, doi = {10.1126/sciadv.aap9691}, pages = {7}, year = {2018}, abstract = {Present-day domestic horses are immensely diverse in their maternally inherited mitochondrial DNA, yet they show very little variation on their paternally inherited Y chromosome. Although it has recently been shown that Y chromosomal diversity in domestic horses was higher at least until the Iron Age, when and why this diversity disappeared remain controversial questions. We genotyped 16 recently discovered Y chromosomal single-nucleotide polymorphisms in 96 ancient Eurasian stallions spanning the early domestication stages (Copper and Bronze Age) to the Middle Ages. Using this Y chromosomal time series, which covers nearly the entire history of horse domestication, we reveal how Y chromosomal diversity changed over time. Our results also show that the lack of multiple stallion lineages in the extant domestic population is caused by neither a founder effect nor random demographic effects but instead is the result of artificial selection-initially during the Iron Age by nomadic people from the Eurasian steppes and later during the Roman period. Moreover, the modern domestic haplotype probably derived from another, already advantageous, haplotype, most likely after the beginning of the domestication. In line with recent findings indicating that the Przewalski and domestic horse lineages remained connected by gene flow after they diverged about 45,000 years ago, we present evidence for Y chromosomal introgression of Przewalski horses into the gene pool of European domestic horses at least until medieval times.}, language = {en} } @article{DolotovskayaBordalloHausetal.2020, author = {Dolotovskaya, Sofya and Bordallo, Juan Torroba and Haus, Tanja and Noll, Angela and Hofreiter, Michael and Zinner, Dietmar and Roos, Christian}, title = {Comparing mitogenomic timetrees for two African savannah primate genera (Chlorocebus and Papio)}, series = {Zoological journal of the Linnean Society}, volume = {190}, journal = {Zoological journal of the Linnean Society}, number = {3}, publisher = {Oxford Univ. Press}, address = {Oxford}, issn = {0024-4082}, doi = {10.1093/zoolinnean/zlaa026}, pages = {1071 -- 1073}, year = {2020}, language = {en} } @article{ThomasCarvalhoHaileetal.2017, author = {Thomas, Jessica E. and Carvalho, Gary R. and Haile, James and Martin, Michael D. and Castruita, Jose A. Samaniego and Niemann, Jonas and Sinding, Mikkel-Holger S. and Sandoval-Velasco, Marcela and Rawlence, Nicolas J. and Fuller, Errol and Fjeldsa, Jon and Hofreiter, Michael and Stewart, John R. and Gilbert, M. Thomas P. and Knapp, Michael}, title = {An ‛Aukward' tale}, series = {Genes}, volume = {8}, journal = {Genes}, number = {6}, publisher = {MDPI}, address = {Basel}, issn = {2073-4425}, doi = {10.3390/genes8060164}, pages = {164}, year = {2017}, abstract = {One hundred and seventy-three years ago, the last two Great Auks, Pinguinus impennis, ever reliably seen were killed. Their internal organs can be found in the collections of the Natural History Museum of Denmark, but the location of their skins has remained a mystery. In 1999, Great Auk expert Errol Fuller proposed a list of five potential candidate skins in museums around the world. Here we take a palaeogenomic approach to test which—if any—of Fuller's candidate skins likely belong to either of the two birds. Using mitochondrial genomes from the five candidate birds (housed in museums in Bremen, Brussels, Kiel, Los Angeles, and Oldenburg) and the organs of the last two known individuals, we partially solve the mystery that has been on Great Auk scholars' minds for generations and make new suggestions as to the whereabouts of the still-missing skin from these two birds.}, language = {en} } @article{MohandesanSpellerPetersetal.2017, author = {Mohandesan, Elmira and Speller, Camilla F. and Peters, Joris and Uerpmann, Hans-Peter and Uerpmann, Margarethe and De Cupere, Bea and Hofreiter, Michael and Burger, Pamela A.}, title = {Combined hybridization capture and shotgun sequencing for ancient DNA analysis of extinct wild and domestic dromedary camel}, series = {Molecular ecology resources}, volume = {17}, journal = {Molecular ecology resources}, number = {2}, publisher = {Wiley}, address = {Hoboken}, issn = {1755-098X}, doi = {10.1111/1755-0998.12551}, pages = {300 -- 313}, year = {2017}, abstract = {The performance of hybridization capture combined with next-generation sequencing (NGS) has seen limited investigation with samples from hot and arid regions until now. We applied hybridization capture and shotgun sequencing to recover DNA sequences from bone specimens of ancient-domestic dromedary (Camelus dromedarius) and its extinct ancestor, the wild dromedary from Jordan, Syria, Turkey and the Arabian Peninsula, respectively. Our results show that hybridization capture increased the percentage of mitochondrial DNA (mtDNA) recovery by an average 187-fold and in some cases yielded virtually complete mitochondrial (mt) genomes at multifold coverage in a single capture experiment. Furthermore, we tested the effect of hybridization temperature and time by using a touchdown approach on a limited number of samples. We observed no significant difference in the number of unique dromedary mtDNA reads retrieved with the standard capture compared to the touchdown method. In total, we obtained 14 partial mitochondrial genomes from ancient-domestic dromedaries with 17-95\% length coverage and 1.27-47.1-fold read depths for the covered regions. Using whole-genome shotgun sequencing, we successfully recovered endogenous dromedary nuclear DNA (nuDNA) from domestic and wild dromedary specimens with 1-1.06-fold read depths for covered regions. Our results highlight that despite recent methodological advances, obtaining ancient DNA (aDNA) from specimens recovered from hot, arid environments is still problematic. Hybridization protocols require specific optimization, and samples at the limit of DNA preservation need multiple replications of DNA extraction and hybridization capture as has been shown previously for Middle Pleistocene specimens.}, language = {en} } @article{FagesHanghojKhanetal.2019, author = {Fages, Antoine and Hanghoj, Kristian and Khan, Naveed and Gaunitz, Charleen and Seguin-Orlando, Andaine and Leonardi, Michela and Constantz, Christian McCrory and Gamba, Cristina and Al-Rasheid, Khaled A. S. and Albizuri, Silvia and Alfarhan, Ahmed H. and Allentoft, Morten and Alquraishi, Saleh and Anthony, David and Baimukhanov, Nurbol and Barrett, James H. and Bayarsaikhan, Jamsranjav and Benecke, Norbert and Bernaldez-Sanchez, Eloisa and Berrocal-Rangel, Luis and Biglari, Fereidoun and Boessenkool, Sanne and Boldgiv, Bazartseren and Brem, Gottfried and Brown, Dorcas and Burger, Joachim and Crubezy, Eric and Daugnora, Linas and Davoudi, Hossein and Damgaard, Peter de Barros and de Chorro y de Villa-Ceballos, Maria de los Angeles and Deschler-Erb, Sabine and Detry, Cleia and Dill, Nadine and Oom, Maria do Mar and Dohr, Anna and Ellingvag, Sturla and Erdenebaatar, Diimaajav and Fathi, Homa and Felkel, Sabine and Fernandez-Rodriguez, Carlos and Garcia-Vinas, Esteban and Germonpre, Mietje and Granado, Jose D. and Hallsson, Jon H. and Hemmer, Helmut and Hofreiter, Michael and Kasparov, Aleksei and Khasanov, Mutalib and Khazaeli, Roya and Kosintsev, Pavel and Kristiansen, Kristian and Kubatbek, Tabaldiev and Kuderna, Lukas and Kuznetsov, Pavel and Laleh, Haeedeh and Leonard, Jennifer A. and Lhuillier, Johanna and von Lettow-Vorbeck, Corina Liesau and Logvin, Andrey and Lougas, Lembi and Ludwig, Arne and Luis, Cristina and Arruda, Ana Margarida and Marques-Bonet, Tomas and Silva, Raquel Matoso and Merz, Victor and Mijiddorj, Enkhbayar and Miller, Bryan K. and Monchalov, Oleg and Mohaseb, Fatemeh A. and Morales, Arturo and Nieto-Espinet, Ariadna and Nistelberger, Heidi and Onar, Vedat and Palsdottir, Albina H. and Pitulko, Vladimir and Pitskhelauri, Konstantin and Pruvost, Melanie and Sikanjic, Petra Rajic and Papesa, Anita Rapan and Roslyakova, Natalia and Sardari, Alireza and Sauer, Eberhard and Schafberg, Renate and Scheu, Amelie and Schibler, Jorg and Schlumbaum, Angela and Serrand, Nathalie and Serres-Armero, Aitor and Shapiro, Beth and Seno, Shiva Sheikhi and Shevnina, Irina and Shidrang, Sonia and Southon, John and Star, Bastiaan and Sykes, Naomi and Taheri, Kamal and Taylor, William and Teegen, Wolf-Rudiger and Vukicevic, Tajana Trbojevic and Trixl, Simon and Tumen, Dashzeveg and Undrakhbold, Sainbileg and Usmanova, Emma and Vahdati, Ali and Valenzuela-Lamas, Silvia and Viegas, Catarina and Wallner, Barbara and Weinstock, Jaco and Zaibert, Victor and Clavel, Benoit and Lepetz, Sebastien and Mashkour, Marjan and Helgason, Agnar and Stefansson, Kari and Barrey, Eric and Willerslev, Eske and Outram, Alan K. and Librado, Pablo and Orlando, Ludovic}, title = {Tracking five millennia of horse management with extensive ancient genome time series}, series = {Cell}, volume = {177}, journal = {Cell}, number = {6}, publisher = {Cell Press}, address = {Cambridge}, issn = {0092-8674}, doi = {10.1016/j.cell.2019.03.049}, pages = {1419 -- 1435}, year = {2019}, abstract = {Horse domestication revolutionized warfare and accelerated travel, trade, and the geographic expansion of languages. Here, we present the largest DNA time series for a non-human organism to date, including genome-scale data from 149 ancient animals and 129 ancient genomes (>= 1-fold coverage), 87 of which are new. This extensive dataset allows us to assess the modem legacy of past equestrian civilisations. We find that two extinct horse lineages existed during early domestication, one at the far western (Iberia) and the other at the far eastern range (Siberia) of Eurasia. None of these contributed significantly to modern diversity. We show that the influence of Persian-related horse lineages increased following the Islamic conquests in Europe and Asia. Multiple alleles associated with elite-racing, including at the MSTN "speed gene," only rose in popularity within the last millennium. Finally, the development of modem breeding impacted genetic diversity more dramatically than the previous millennia of human management.}, language = {en} } @article{ChangKnappEnketal.2017, author = {Chang, Dan and Knapp, Michael and Enk, Jacob and Lippold, Sebastian and Kircher, Martin and Lister, Adrian M. and MacPhee, Ross D. E. and Widga, Christopher and Czechowski, Paul and Sommer, Robert and Hodges, Emily and St{\"u}mpel, Nikolaus and Barnes, Ian and Dal{\´e}n, Love and Derevianko, Anatoly and Germonpr{\´e}, Mietje and Hillebrand-Voiculescu, Alexandra and Constantin, Silviu and Kuznetsova, Tatyana and Mol, Dick and Rathgeber, Thomas and Rosendahl, Wilfried and Tikhonov, Alexey N. and Willerslev, Eske and Hannon, Greg and Lalueza i Fox, Carles and Joger, Ulrich and Poinar, Hendrik N. and Hofreiter, Michael and Shapiro, Beth}, title = {The evolutionary and phylogeographic history of woolly mammoths}, series = {Scientific reports}, volume = {7}, journal = {Scientific reports}, publisher = {Nature Publishing Group}, address = {London}, issn = {2045-2322}, doi = {10.1038/srep44585}, pages = {10}, year = {2017}, abstract = {Near the end of the Pleistocene epoch, populations of the woolly mammoth (Mammuthus primigenius) were distributed across parts of three continents, from western Europe and northern Asia through Beringia to the Atlantic seaboard of North America. Nonetheless, questions about the connectivity and temporal continuity of mammoth populations and species remain unanswered. We use a combination of targeted enrichment and high-throughput sequencing to assemble and interpret a data set of 143 mammoth mitochondrial genomes, sampled from fossils recovered from across their Holarctic range. Our dataset includes 54 previously unpublished mitochondrial genomes and significantly increases the coverage of the Eurasian range of the species. The resulting global phylogeny confirms that the Late Pleistocene mammoth population comprised three distinct mitochondrial lineages that began to diverge ~1.0-2.0 million years ago (Ma). We also find that mammoth mitochondrial lineages were strongly geographically partitioned throughout the Pleistocene. In combination, our genetic results and the pattern of morphological variation in time and space suggest that male-mediated gene flow, rather than large-scale dispersals, was important in the Pleistocene evolutionary history of mammoths.}, language = {en} } @article{DolotovskayaBordalloHausetal.2017, author = {Dolotovskaya, Sofya and Bordallo, Juan Torroba and Haus, Tanja and Noll, Angela and Hofreiter, Michael and Zinner, Dietmar and Roos, Christian}, title = {Comparing mitogenomic timetrees for two African savannah primate genera (Chlorocebus and Papio)}, series = {Zoological Journal of the Linnean Society}, volume = {181}, journal = {Zoological Journal of the Linnean Society}, number = {2}, publisher = {Oxford Univ. Press}, address = {Oxford}, issn = {0024-4082}, doi = {10.1093/zoolinnean/zlx001}, pages = {471 -- 483}, year = {2017}, abstract = {Complete mitochondrial (mtDNA) genomes have proved to be useful in reconstructing primate phylogenies with higher resolution and confidence compared to reconstructions based on partial mtDNA sequences. Here, we analyse complete mtDNA genomes of African green monkeys (genus Chlorocebus), a widely distributed primate genus in Africa representing an interesting phylogeographical model for the evolution of savannah species. Previous studies on partial mtDNA sequences revealed nine major clades, suggesting several cases of para- and polyphyly among Chlorocebus species. However, in these studies, phylogenetic relationships among several clades were not resolved, and divergence times were not estimated. We analysed complete mtDNA genomes for ten Chlorocebus samples representing major mtDNA clades to find stronger statistical support in the phylogenetic reconstruction than in the previous studies and to estimate divergence times. Our results confirmed para- and polyphyletic relationships of most Chlorocebus species, while the support for the phylogenetic relationships between the mtDNA clades increased compared to the previous studies. Our results indicate an initial west-east division in the northern part of the Chlorocebus range with subsequent divergence into north-eastern and southern clades. This phylogeographic scenario contrasts with that for another widespread African savannah primate genus, the baboons (Papio), for which a dispersal from southern Africa into East and West Africa was suggested.}, language = {en} } @article{BeermannWestburyHofreiteretal.2018, author = {Beermann, Jan and Westbury, Michael V. and Hofreiter, Michael and Hilgers, Leon and Deister, Fabian and Neumann, Hermann and Raupach, Michael J.}, title = {Cryptic species in a well-known habitat}, series = {Scientific reports}, volume = {8}, journal = {Scientific reports}, publisher = {Nature Publ. Group}, address = {London}, issn = {2045-2322}, doi = {10.1038/s41598-018-25225-x}, pages = {26}, year = {2018}, abstract = {Taxonomy plays a central role in biological sciences. It provides a communication system for scientists as it aims to enable correct identification of the studied organisms. As a consequence, species descriptions should seek to include as much available information as possible at species level to follow an integrative concept of 'taxonomics'. Here, we describe the cryptic species Epimeria frankei sp. nov. from the North Sea, and also redescribe its sister species, Epimeria cornigera. The morphological information obtained is substantiated by DNA barcodes and complete nuclear 18S rRNA gene sequences. In addition, we provide, for the first time, full mitochondrial genome data as part of a metazoan species description for a holotype, as well as the neotype. This study represents the first successful implementation of the recently proposed concept of taxonomics, using data from high-throughput technologies for integrative taxonomic studies, allowing the highest level of confidence for both biodiversity and ecological research.}, language = {en} } @article{WestburyDalerumbNorenetal.2017, author = {Westbury, Michael V. and Dalerumb, Fredrik and Noren, Karin and Hofreiter, Michael}, title = {Complete mitochondrial genome of a bat-eared fox (Otocyon megalotis), along with phylogenetic considerations}, series = {Mitochondrial DNA. Part B}, volume = {2}, journal = {Mitochondrial DNA. Part B}, number = {1}, publisher = {Routledge, Taylor \& Francis Group}, address = {London}, issn = {2380-2359}, doi = {10.1080/23802359.2017.1331325}, pages = {298 -- 299}, year = {2017}, abstract = {The bat-eared fox, Otocyon megalotis, is the only member of its genus and is thought to occupy a basal position within the dog family. These factors can lead to challenges in complete mitochondrial reconstructions and accurate phylogenetic positioning. Here, we present the first complete mitochondrial genome of the bat-eared fox recovered using shotgun sequencing and iterative mapping to three distantly related species. Phylogenetic analyses placed the bat-eared fox basal in the Canidae family within the clade including true foxes (Vulpes) and the raccoon dog (Nyctereutes) with high support values. This position is in good agreement with previously published results based on short fragments of mitochondrial and nuclear genes, therefore adding more support to the basal positioning of the bat-eared fox within Canidae.}, language = {en} } @article{AgnePreickStraubeetal.2022, author = {Agne, Stefanie and Preick, Michaela and Straube, Nicolas and Hofreiter, Michael}, title = {Simultaneous Barcode Sequencing of Diverse Museum Collection Specimens Using a Mixed RNA Bait Set}, series = {Frontiers in Ecology and Evolution}, volume = {10}, journal = {Frontiers in Ecology and Evolution}, publisher = {Frontiers Media S.A.}, address = {Lausanne, Schweiz}, issn = {2296-701X}, doi = {10.3389/fevo.2022.909846}, pages = {5}, year = {2022}, abstract = {A growing number of publications presenting results from sequencing natural history collection specimens reflect the importance of DNA sequence information from such samples. Ancient DNA extraction and library preparation methods in combination with target gene capture are a way of unlocking archival DNA, including from formalin-fixed wet-collection material. Here we report on an experiment, in which we used an RNA bait set containing baits from a wide taxonomic range of species for DNA hybridisation capture of nuclear and mitochondrial targets for analysing natural history collection specimens. The bait set used consists of 2,492 mitochondrial and 530 nuclear RNA baits and comprises specific barcode loci of diverse animal groups including both invertebrates and vertebrates. The baits allowed to capture DNA sequence information of target barcode loci from 84\% of the 37 samples tested, with nuclear markers being captured more frequently and consensus sequences of these being more complete compared to mitochondrial markers. Samples from dry material had a higher rate of success than wet-collection specimens, although target sequence information could be captured from 50\% of formalin-fixed samples. Our study illustrates how efforts to obtain barcode sequence information from natural history collection specimens may be combined and are a way of implementing barcoding inventories of scientific collection material.}, language = {en} } @article{HilgersHartmannHofreiteretal.2018, author = {Hilgers, Leon and Hartmann, Stefanie and Hofreiter, Michael and von Rintelen, Thomas}, title = {Novel Genes, Ancient Genes, and Gene Co-Option Contributed o the Genetic Basis of the Radula, a Molluscan Innovation}, series = {Molecular biology and evolution}, volume = {35}, journal = {Molecular biology and evolution}, number = {7}, publisher = {Oxford Univ. Press}, address = {Oxford}, issn = {0737-4038}, doi = {10.1093/molbev/msy052}, pages = {1638 -- 1652}, year = {2018}, abstract = {The radula is the central foraging organ and apomorphy of the Mollusca. However, in contrast to other innovations, including the mollusk shell, genetic underpinnings of radula formation remain virtually unknown. Here, we present the first radula formative tissue transcriptome using the viviparous freshwater snail Tylomelania sarasinorum and compare it to foot tissue and the shell-building mantle of the same species. We combine differential expression, functional enrichment, and phylostratigraphic analyses to identify both specific and shared genetic underpinnings of the three tissues as well as their dominant functions and evolutionary origins. Gene expression of radula formative tissue is very distinct, but nevertheless more similar to mantle than to foot. Generally, the genetic bases of both radula and shell formation were shaped by novel orchestration of preexisting genes and continuous evolution of novel genes. A significantly increased proportion of radula-specific genes originated since the origin of stem-mollusks, indicating that novel genes were especially important for radula evolution. Genes with radula-specific expression in our study are frequently also expressed during the formation of other lophotrochozoan hard structures, like chaetae (hes1, arx), spicules (gbx), and shells of mollusks (gbx, heph) and brachiopods (heph), suggesting gene co-option for hard structure formation. Finally, a Lophotrochozoa-specific chitin synthase with a myosin motor domain (CS-MD), which is expressed during mollusk and brachiopod shell formation, had radula-specific expression in our study. CS-MD potentially facilitated the construction of complex chitinous structures and points at the potential of molecular novelties to promote the evolution of different morphological innovations.}, language = {en} } @article{HofreiterHartmann2020, author = {Hofreiter, Michael and Hartmann, Stefanie}, title = {Reconstructing protein-coding sequences from ancient DNA}, series = {Odorant binding and chemosensory proteins}, volume = {642}, journal = {Odorant binding and chemosensory proteins}, publisher = {Academic Press, an imprint of Elsevier}, address = {Cambridge, MA.}, isbn = {978-0-12-821157-1}, issn = {0076-6879}, doi = {10.1016/bs.mie.2020.05.008}, pages = {21 -- 33}, year = {2020}, abstract = {Obtaining information about functional details of proteins of extinct species is of critical importance for a better understanding of the real-life appearance, behavior and ecology of these lost entries in the book of life. In this chapter, we discuss the possibilities to retrieve the necessary DNA sequence information from paleogenomic data obtained from fossil specimens, which can then be used to express and subsequently analyze the protein of interest. We discuss the problems specific to ancient DNA, including mis-coding lesions, short read length and incomplete paleogenome assemblies. Finally, we discuss an alternative, but currently rarely used approach, direct PCR amplification, which is especially useful for comparatively short proteins.}, language = {en} } @article{PaijmansBarlowFoersteretal.2018, author = {Paijmans, Johanna L. A. and Barlow, Axel and F{\"o}rster, Daniel W. and Henneberger, Kirstin and Meyer, Matthias and Nickel, Birgit and Nagel, Doris and Wors{\o}e Havm{\o}ller, Rasmus and Baryshnikov, Gennady F. and Joger, Ulrich and Rosendahl, Wilfried and Hofreiter, Michael}, title = {Historical biogeography of the leopard (Panthera pardus) and its extinct Eurasian populations}, series = {BMC Evolutionary Biology}, volume = {18}, journal = {BMC Evolutionary Biology}, number = {156}, publisher = {BioMed Central und Springer}, address = {London, Berlin und Heidelberg}, issn = {1471-2148}, doi = {10.1186/s12862-018-1268-0}, pages = {12}, year = {2018}, abstract = {Background Resolving the historical biogeography of the leopard (Panthera pardus) is a complex issue, because patterns inferred from fossils and from molecular data lack congruence. Fossil evidence supports an African origin, and suggests that leopards were already present in Eurasia during the Early Pleistocene. Analysis of DNA sequences however, suggests a more recent, Middle Pleistocene shared ancestry of Asian and African leopards. These contrasting patterns led researchers to propose a two-stage hypothesis of leopard dispersal out of Africa: an initial Early Pleistocene colonisation of Asia and a subsequent replacement by a second colonisation wave during the Middle Pleistocene. The status of Late Pleistocene European leopards within this scenario is unclear: were these populations remnants of the first dispersal, or do the last surviving European leopards share more recent ancestry with their African counterparts? Results In this study, we generate and analyse mitogenome sequences from historical samples that span the entire modern leopard distribution, as well as from Late Pleistocene remains. We find a deep bifurcation between African and Eurasian mitochondrial lineages (~ 710 Ka), with the European ancient samples as sister to all Asian lineages (~ 483 Ka). The modern and historical mainland Asian lineages share a relatively recent common ancestor (~ 122 Ka), and we find one Javan sample nested within these. Conclusions The phylogenetic placement of the ancient European leopard as sister group to Asian leopards suggests that these populations originate from the same out-of-Africa dispersal which founded the Asian lineages. The coalescence time found for the mitochondrial lineages aligns well with the earliest undisputed fossils in Eurasia, and thus encourages a re-evaluation of the identification of the much older putative leopard fossils from the region. The relatively recent ancestry of all mainland Asian leopard lineages suggests that these populations underwent a severe population bottleneck during the Pleistocene. Finally, although only based on a single sample, the unexpected phylogenetic placement of the Javan leopard could be interpreted as evidence for exchange of mitochondrial lineages between Java and mainland Asia, calling for further investigation into the evolutionary history of this subspecies.}, language = {en} } @article{KehlmaierBarlowHastingsetal.2017, author = {Kehlmaier, Christian and Barlow, Axel and Hastings, Alexander K. and Vamberger, Melita and Paijmans, Johanna L. A. and Steadman, David W. and Albury, Nancy A. and Franz, Richard and Hofreiter, Michael and Fritz, Uwe}, title = {Tropical ancient DNA reveals relationships of the extinct bahamian giant tortoise Chelonoidis alburyorum}, series = {Proceedings of the Royal Society of London : Series B, Biological sciences}, volume = {284}, journal = {Proceedings of the Royal Society of London : Series B, Biological sciences}, publisher = {The Royal Society}, address = {London}, issn = {0962-8452}, doi = {10.1098/rspb.2016.2235}, pages = {8}, year = {2017}, abstract = {Ancient DNA of extinct species from the Pleistocene and Holocene has provided valuable evolutionary insights. However, these are largely restricted to mammals and high latitudes because DNA preservation in warm climates is typically poor. In the tropics and subtropics, non-avian reptiles constitute a significant part of the fauna and little is known about the genetics of the many extinct reptiles from tropical islands. We have reconstructed the near-complete mitochondrial genome of an extinct giant tortoise from the Bahamas (Chelonoidis alburyorum) using an approximately 1000-year-old humerus from a water-filled sinkhole (blue hole) on Great Abaco Island. Phylogenetic and molecular clock analyses place this extinct species as closely related to Galapagos (C. niger complex) and Chaco tortoises (C. chilensis), and provide evidence for repeated overseas dispersal in this tortoise group. The ancestors of extant Chelonoidis species arrived in South America from Africa only after the opening of the Atlantic Ocean and dispersed from there to the Caribbean and the Galapagos Islands. Our results also suggest that the anoxic, thermally buffered environment of blue holes may enhance DNA preservation, and thus are opening a window for better understanding evolution and population history of extinct tropical species, which would likely still exist without human impact.}, language = {en} } @article{HartmannPreickAbeltetal.2020, author = {Hartmann, Stefanie and Preick, Michaela and Abelt, Silke and Scheffel, Andr{\´e} and Hofreiter, Michael}, title = {Annotated genome sequences of the carnivorous plant Roridula gorgonias and a non-carnivorous relative, Clethra arborea}, series = {BMC Research Notes}, volume = {13}, journal = {BMC Research Notes}, publisher = {Biomed Central}, address = {London}, issn = {1756-0500}, doi = {10.1186/s13104-020-05254-4}, pages = {6}, year = {2020}, abstract = {Objective Plant carnivory is distributed across the tree of life and has evolved at least six times independently, but sequenced and annotated nuclear genomes of carnivorous plants are currently lacking. We have sequenced and structurally annotated the nuclear genome of the carnivorous Roridula gorgonias and that of a non-carnivorous relative, Madeira's lily-of-the-valley-tree, Clethra arborea, both within the Ericales. This data adds an important resource to study the evolutionary genetics of plant carnivory across angiosperm lineages and also for functional and systematic aspects of plants within the Ericales. Results Our assemblies have total lengths of 284 Mbp (R. gorgonias) and 511 Mbp (C. arborea) and show high BUSCO scores of 84.2\% and 89.5\%, respectively. We used their predicted genes together with publicly available data from other Ericales' genomes and transcriptomes to assemble a phylogenomic data set for the inference of a species tree. However, groups of orthologs showed a marked absence of species represented by a transcriptome. We discuss possible reasons and caution against combining predicted genes from genome- and transriptome-based assemblies.}, language = {en} } @article{BarlowHartmannGonzalezetal.2020, author = {Barlow, Axel and Hartmann, Stefanie and Gonzalez, Javier and Hofreiter, Michael and Paijmans, Johanna L. A.}, title = {Consensify}, series = {Genes / Molecular Diversity Preservation International}, volume = {11}, journal = {Genes / Molecular Diversity Preservation International}, number = {1}, publisher = {MDPI}, address = {Basel}, issn = {2073-4425}, doi = {10.3390/genes11010050}, pages = {22}, year = {2020}, abstract = {A standard practise in palaeogenome analysis is the conversion of mapped short read data into pseudohaploid sequences, frequently by selecting a single high-quality nucleotide at random from the stack of mapped reads. This controls for biases due to differential sequencing coverage, but it does not control for differential rates and types of sequencing error, which are frequently large and variable in datasets obtained from ancient samples. These errors have the potential to distort phylogenetic and population clustering analyses, and to mislead tests of admixture using D statistics. We introduce Consensify, a method for generating pseudohaploid sequences, which controls for biases resulting from differential sequencing coverage while greatly reducing error rates. The error correction is derived directly from the data itself, without the requirement for additional genomic resources or simplifying assumptions such as contemporaneous sampling. For phylogenetic and population clustering analysis, we find that Consensify is less affected by artefacts than methods based on single read sampling. For D statistics, Consensify is more resistant to false positives and appears to be less affected by biases resulting from different laboratory protocols than other frequently used methods. Although Consensify is developed with palaeogenomic data in mind, it is applicable for any low to medium coverage short read datasets. We predict that Consensify will be a useful tool for future studies of palaeogenomes.}, language = {en} } @article{SignorePaijmansHofreiteretal.2019, author = {Signore, Anthony V. and Paijmans, Johanna L. A. and Hofreiter, Michael and Fago, Angela and Weber, Roy E. and Springer, Mark S. and Campbell, Kevin L.}, title = {Emergence of a chimeric globin pseudogene and increased Hemoglobin Oxygen Affinity Underlie the evolution of aquatic specializations in Sirenia}, series = {Molecular biology and evolution}, volume = {36}, journal = {Molecular biology and evolution}, number = {6}, publisher = {Oxford Univ. Press}, address = {Oxford}, issn = {0737-4038}, doi = {10.1093/molbev/msz044}, pages = {1134 -- 1147}, year = {2019}, abstract = {As limits on O2 availability during submergence impose severe constraints on aerobic respiration, the oxygen binding globin proteins of marine mammals are expected to have evolved under strong evolutionary pressures during their land-to-sea transition. Here, we address this question for the order Sirenia by retrieving, annotating, and performing detailed selection analyses on the globin repertoire of the extinct Steller's sea cow (Hydrodamalis gigas), dugong (Dugong dugon), and Florida manatee (Trichechus manatus latirostris) in relation to their closest living terrestrial relatives (elephants and hyraxes). These analyses indicate most loci experienced elevated nucleotide substitution rates during their transition to a fully aquatic lifestyle. While most of these genes evolved under neutrality or strong purifying selection, the rate of nonsynonymous/synonymous replacements increased in two genes (Hbz-T1 and Hba-T1) that encode the α-type chains of hemoglobin (Hb) during each stage of life. Notably, the relaxed evolution of Hba-T1 is temporally coupled with the emergence of a chimeric pseudogene (Hba-T2/Hbq-ps) that contributed to the tandemly linked Hba-T1 of stem sirenians via interparalog gene conversion. Functional tests on recombinant Hb proteins from extant and ancestral sirenians further revealed that the molecular remodeling of Hba-T1 coincided with increased Hb-O2 affinity in early sirenians. Available evidence suggests that this trait evolved to maximize O2 extraction from finite lung stores and suppress tissue O2 offloading, thereby facilitating the low metabolic intensities of extant sirenians. In contrast, the derived reduction in Hb-O2 affinity in (sub)Arctic Steller's sea cows is consistent with fueling increased thermogenesis by these once colossal marine herbivores.}, language = {en} }