TY  - JOUR
A1  - Aarts, Alexander A.
A1  - Anderson, Joanna E.
A1  - Anderson, Christopher J.
A1  - Attridge, Peter R.
A1  - Attwood, Angela
A1  - Axt, Jordan
A1  - Babel, Molly
A1  - Bahnik, Stepan
A1  - Baranski, Erica
A1  - Barnett-Cowan, Michael
A1  - Bartmess, Elizabeth
A1  - Beer, Jennifer
A1  - Bell, Raoul
A1  - Bentley, Heather
A1  - Beyan, Leah
A1  - Binion, Grace
A1  - Borsboom, Denny
A1  - Bosch, Annick
A1  - Bosco, Frank A.
A1  - Bowman, Sara D.
A1  - Brandt, Mark J.
A1  - Braswell, Erin
A1  - Brohmer, Hilmar
A1  - Brown, Benjamin T.
A1  - Brown, Kristina
A1  - Bruening, Jovita
A1  - Calhoun-Sauls, Ann
A1  - Callahan, Shannon P.
A1  - Chagnon, Elizabeth
A1  - Chandler, Jesse
A1  - Chartier, Christopher R.
A1  - Cheung, Felix
A1  - Christopherson, Cody D.
A1  - Cillessen, Linda
A1  - Clay, Russ
A1  - Cleary, Hayley
A1  - Cloud, Mark D.
A1  - Cohn, Michael
A1  - Cohoon, Johanna
A1  - Columbus, Simon
A1  - Cordes, Andreas
A1  - Costantini, Giulio
A1  - Alvarez, Leslie D. Cramblet
A1  - Cremata, Ed
A1  - Crusius, Jan
A1  - DeCoster, Jamie
A1  - DeGaetano, Michelle A.
A1  - Della Penna, Nicolas
A1  - den Bezemer, Bobby
A1  - Deserno, Marie K.
A1  - Devitt, Olivia
A1  - Dewitte, Laura
A1  - Dobolyi, David G.
A1  - Dodson, Geneva T.
A1  - Donnellan, M. Brent
A1  - Donohue, Ryan
A1  - Dore, Rebecca A.
A1  - Dorrough, Angela
A1  - Dreber, Anna
A1  - Dugas, Michelle
A1  - Dunn, Elizabeth W.
A1  - Easey, Kayleigh
A1  - Eboigbe, Sylvia
A1  - Eggleston, Casey
A1  - Embley, Jo
A1  - Epskamp, Sacha
A1  - Errington, Timothy M.
A1  - Estel, Vivien
A1  - Farach, Frank J.
A1  - Feather, Jenelle
A1  - Fedor, Anna
A1  - Fernandez-Castilla, Belen
A1  - Fiedler, Susann
A1  - Field, James G.
A1  - Fitneva, Stanka A.
A1  - Flagan, Taru
A1  - Forest, Amanda L.
A1  - Forsell, Eskil
A1  - Foster, Joshua D.
A1  - Frank, Michael C.
A1  - Frazier, Rebecca S.
A1  - Fuchs, Heather
A1  - Gable, Philip
A1  - Galak, Jeff
A1  - Galliani, Elisa Maria
A1  - Gampa, Anup
A1  - Garcia, Sara
A1  - Gazarian, Douglas
A1  - Gilbert, Elizabeth
A1  - Giner-Sorolla, Roger
A1  - Glöckner, Andreas
A1  - Göllner, Lars
A1  - Goh, Jin X.
A1  - Goldberg, Rebecca
A1  - Goodbourn, Patrick T.
A1  - Gordon-McKeon, Shauna
A1  - Gorges, Bryan
A1  - Gorges, Jessie
A1  - Goss, Justin
A1  - Graham, Jesse
A1  - Grange, James A.
A1  - Gray, Jeremy
A1  - Hartgerink, Chris
A1  - Hartshorne, Joshua
A1  - Hasselman, Fred
A1  - Hayes, Timothy
A1  - Heikensten, Emma
A1  - Henninger, Felix
A1  - Hodsoll, John
A1  - Holubar, Taylor
A1  - Hoogendoorn, Gea
A1  - Humphries, Denise J.
A1  - Hung, Cathy O. -Y.
A1  - Immelman, Nathali
A1  - Irsik, Vanessa C.
A1  - Jahn, Georg
A1  - Jaekel, Frank
A1  - Jekel, Marc
A1  - Johannesson, Magnus
A1  - Johnson, Larissa G.
A1  - Johnson, David J.
A1  - Johnson, Kate M.
A1  - Johnston, William J.
A1  - Jonas, Kai
A1  - Joy-Gaba, Jennifer A.
A1  - Kappes, Heather Barry
A1  - Kelso, Kim
A1  - Kidwell, Mallory C.
A1  - Kim, Seung Kyung
A1  - Kirkhart, Matthew
A1  - Kleinberg, Bennett
A1  - Knezevic, Goran
A1  - Kolorz, Franziska Maria
A1  - Kossakowski, Jolanda J.
A1  - Krause, Robert Wilhelm
A1  - Krijnen, Job
A1  - Kuhlmann, Tim
A1  - Kunkels, Yoram K.
A1  - Kyc, Megan M.
A1  - Lai, Calvin K.
A1  - Laique, Aamir
A1  - Lakens, Daniel
A1  - Lane, Kristin A.
A1  - Lassetter, Bethany
A1  - Lazarevic, Ljiljana B.
A1  - LeBel, Etienne P.
A1  - Lee, Key Jung
A1  - Lee, Minha
A1  - Lemm, Kristi
A1  - Levitan, Carmel A.
A1  - Lewis, Melissa
A1  - Lin, Lin
A1  - Lin, Stephanie
A1  - Lippold, Matthias
A1  - Loureiro, Darren
A1  - Luteijn, Ilse
A1  - Mackinnon, Sean
A1  - Mainard, Heather N.
A1  - Marigold, Denise C.
A1  - Martin, Daniel P.
A1  - Martinez, Tylar
A1  - Masicampo, E. J.
A1  - Matacotta, Josh
A1  - Mathur, Maya
A1  - May, Michael
A1  - Mechin, Nicole
A1  - Mehta, Pranjal
A1  - Meixner, Johannes
A1  - Melinger, Alissa
A1  - Miller, Jeremy K.
A1  - Miller, Mallorie
A1  - Moore, Katherine
A1  - Möschl, Marcus
A1  - Motyl, Matt
A1  - Müller, Stephanie M.
A1  - Munafo, Marcus
A1  - Neijenhuijs, Koen I.
A1  - Nervi, Taylor
A1  - Nicolas, Gandalf
A1  - Nilsonne, Gustav
A1  - Nosek, Brian A.
A1  - Nuijten, Michele B.
A1  - Olsson, Catherine
A1  - Osborne, Colleen
A1  - Ostkamp, Lutz
A1  - Pavel, Misha
A1  - Penton-Voak, Ian S.
A1  - Perna, Olivia
A1  - Pernet, Cyril
A1  - Perugini, Marco
A1  - Pipitone, R. Nathan
A1  - Pitts, Michael
A1  - Plessow, Franziska
A1  - Prenoveau, Jason M.
A1  - Rahal, Rima-Maria
A1  - Ratliff, Kate A.
A1  - Reinhard, David
A1  - Renkewitz, Frank
A1  - Ricker, Ashley A.
A1  - Rigney, Anastasia
A1  - Rivers, Andrew M.
A1  - Roebke, Mark
A1  - Rutchick, Abraham M.
A1  - Ryan, Robert S.
A1  - Sahin, Onur
A1  - Saide, Anondah
A1  - Sandstrom, Gillian M.
A1  - Santos, David
A1  - Saxe, Rebecca
A1  - Schlegelmilch, Rene
A1  - Schmidt, Kathleen
A1  - Scholz, Sabine
A1  - Seibel, Larissa
A1  - Selterman, Dylan Faulkner
A1  - Shaki, Samuel
A1  - Simpson, William B.
A1  - Sinclair, H. Colleen
A1  - Skorinko, Jeanine L. M.
A1  - Slowik, Agnieszka
A1  - Snyder, Joel S.
A1  - Soderberg, Courtney
A1  - Sonnleitner, Carina
A1  - Spencer, Nick
A1  - Spies, Jeffrey R.
A1  - Steegen, Sara
A1  - Stieger, Stefan
A1  - Strohminger, Nina
A1  - Sullivan, Gavin B.
A1  - Talhelm, Thomas
A1  - Tapia, Megan
A1  - te Dorsthorst, Anniek
A1  - Thomae, Manuela
A1  - Thomas, Sarah L.
A1  - Tio, Pia
A1  - Traets, Frits
A1  - Tsang, Steve
A1  - Tuerlinckx, Francis
A1  - Turchan, Paul
A1  - Valasek, Milan
A1  - Van Aert, Robbie
A1  - van Assen, Marcel
A1  - van Bork, Riet
A1  - van de Ven, Mathijs
A1  - van den Bergh, Don
A1  - van der Hulst, Marije
A1  - van Dooren, Roel
A1  - van Doorn, Johnny
A1  - van Renswoude, Daan R.
A1  - van Rijn, Hedderik
A1  - Vanpaemel, Wolf
A1  - Echeverria, Alejandro Vasquez
A1  - Vazquez, Melissa
A1  - Velez, Natalia
A1  - Vermue, Marieke
A1  - Verschoor, Mark
A1  - Vianello, Michelangelo
A1  - Voracek, Martin
A1  - Vuu, Gina
A1  - Wagenmakers, Eric-Jan
A1  - Weerdmeester, Joanneke
A1  - Welsh, Ashlee
A1  - Westgate, Erin C.
A1  - Wissink, Joeri
A1  - Wood, Michael
A1  - Woods, Andy
A1  - Wright, Emily
A1  - Wu, Sining
A1  - Zeelenberg, Marcel
A1  - Zuni, Kellylynn
T1  - Estimating the reproducibility of psychological science
JF  - Science
N2  - Reproducibility is a defining feature of science, but the extent to which it characterizes current research is unknown. We conducted replications of 100 experimental and correlational studies published in three psychology journals using high-powered designs and original materials when available. Replication effects were half the magnitude of original effects, representing a substantial decline. Ninety-seven percent of original studies had statistically significant results. Thirty-six percent of replications had statistically significant results; 47% of original effect sizes were in the 95% confidence interval of the replication effect size; 39% of effects were subjectively rated to have replicated the original result; and if no bias in original results is assumed, combining original and replication results left 68% with statistically significant effects. Correlational tests suggest that replication success was better predicted by the strength of original evidence than by characteristics of the original and replication teams.
Y1  - 2015
U6  - https://doi.org/10.1126/science.aac4716
SN  - 1095-9203
SN  - 0036-8075
VL  - 349
IS  - 6251
PB  - American Assoc. for the Advancement of Science
CY  - Washington
ER  - 
TY  - JOUR
A1  - Schubert, Mikkel
A1  - Jonsson, Hakon
A1  - Chang, Dan
A1  - Sarkissian, Clio Der
A1  - Ermini, Luca
A1  - Ginolhac, Aurelien
A1  - Albrechtsen, Anders
A1  - Dupanloup, Isabelle
A1  - Foucal, Adrien
A1  - Petersen, Bent Larsen
A1  - Fumagalli, Matteo
A1  - Raghavan, Maanasa
A1  - Seguin-Orlando, Andaine
A1  - Korneliussen, Thorfinn S.
A1  - Velazquez, Amhed M. V.
A1  - Stenderup, Jesper
A1  - Hoover, Cindi A.
A1  - Rubin, Carl-Johan
A1  - Alfarhan, Ahmed H.
A1  - Alquraishi, Saleh A.
A1  - Al-Rasheid, Khaled A. S.
A1  - MacHugh, David E.
A1  - Kalbfleisch, Ted
A1  - MacLeod, James N.
A1  - Rubin, Edward M.
A1  - Sicheritz-Ponten, Thomas
A1  - Andersson, Leif
A1  - Hofreiter, Michael
A1  - Marques-Bonet, Tomas
A1  - Gilbert, M. Thomas P.
A1  - Nielsen, Rasmus
A1  - Excoffier, Laurent
A1  - Willerslev, Eske
A1  - Shapiro, Beth
A1  - Orlando, Ludovic
T1  - Prehistoric genomes reveal the genetic foundation and cost of horse domestication
JF  - Proceedings of the National Academy of Sciences of the United States of America
Y1  - 2014
U6  - https://doi.org/10.1073/pnas.1416991111
SN  - 0027-8424
VL  - 111
IS  - 52
SP  - E5661
EP  - E5669
PB  - National Acad. of Sciences
CY  - Washington
ER  - 
TY  - JOUR
A1  - Thomas, Jessica E.
A1  - Carvalho, Gary R.
A1  - Haile, James
A1  - Rawlence, Nicolas J.
A1  - Martin, Michael D.
A1  - Ho, Simon Y. W.
A1  - Sigfusson, Arnor P.
A1  - Josefsson, Vigfus A.
A1  - Frederiksen, Morten
A1  - Linnebjerg, Jannie F.
A1  - Castruita, Jose A. Samaniego
A1  - Niemann, Jonas
A1  - Sinding, Mikkel-Holger S.
A1  - Sandoval-Velasco, Marcela
A1  - Soares, Andre E. R.
A1  - Lacy, Robert
A1  - Barilaro, Christina
A1  - Best, Juila
A1  - Brandis, Dirk
A1  - Cavallo, Chiara
A1  - Elorza, Mikelo
A1  - Garrett, Kimball L.
A1  - Groot, Maaike
A1  - Johansson, Friederike
A1  - Lifjeld, Jan T.
A1  - Nilson, Goran
A1  - Serjeanston, Dale
A1  - Sweet, Paul
A1  - Fuller, Errol
A1  - Hufthammer, Anne Karin
A1  - Meldgaard, Morten
A1  - Fjeldsa, Jon
A1  - Shapiro, Beth
A1  - Hofreiter, Michael
A1  - Stewart, John R.
A1  - Gilbert, M. Thomas P.
A1  - Knapp, Michael
T1  - Demographic reconstruction from ancient DNA supports rapid extinction of the great auk
JF  - eLife
N2  - 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.
Y1  - 2019
U6  - https://doi.org/10.7554/eLife.47509
SN  - 2050-084X
VL  - 8
PB  - eLife Sciences Publications
CY  - Cambridge
ER  - 
TY  - JOUR
A1  - Thomas, Jessica E.
A1  - Carvalho, Gary R.
A1  - Haile, James
A1  - Martin, Michael D.
A1  - Castruita, Jose A. Samaniego
A1  - Niemann, Jonas
A1  - Sinding, Mikkel-Holger S.
A1  - Sandoval-Velasco, Marcela
A1  - Rawlence, Nicolas J.
A1  - Fuller, Errol
A1  - Fjeldsa, Jon
A1  - Hofreiter, Michael
A1  - Stewart, John R.
A1  - Gilbert, M. Thomas P.
A1  - Knapp, Michael
T1  - An ‛Aukward’ tale
BT  - a genetic approach to discover the whereabouts of the  Last Great Auks
JF  - Genes
N2  - 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.
KW  - ancient DNA
KW  - extinct birds
KW  - mitochondrial genome
KW  - museum specimens
KW  - palaeogenomics
Y1  - 2017
U6  - https://doi.org/10.3390/genes8060164
SN  - 2073-4425
VL  - 8
IS  - 6
SP  - 164
PB  - MDPI
CY  - Basel
ER  - 
TY  - JOUR
A1  - Apitz, Sabine E.
A1  - Bell, Elanor M.
A1  - Damgaard, Lars
A1  - Gilbert, Franck
A1  - Glud, R
A1  - Hall, P. O. J.
A1  - Kershaw, P. J.
A1  - Nickel, L
A1  - Parker, R
A1  - Rabouille, Christophe
A1  - Shimmield, Grahamm
A1  - Solan, Martin
A1  - Soltwedel, Thomas
A1  - Spagnoli, Federico
A1  - Witte, Ursula
T1  - Coastal Ocean Benthic Observatories (COBO) : integrated tools for the in situ observation and study of benthic ecosystem biogeochemical processes
Y1  - 2005
ER  - 
TY  - JOUR
A1  - Salleh, Faezah Mohd
A1  - Ramos-Madrigal, Jazmin
A1  - Penaloza, Fernando
A1  - Liu, Shanlin
A1  - Sinding, Mikkel-Holger S.
A1  - Patel, Riddhi P.
A1  - Martins, Renata
A1  - Lenz, Dorina
A1  - Fickel, Jörns
A1  - Roos, Christian
A1  - Shamsir, Mohd Shahir
A1  - Azman, Mohammad Shahfiz
A1  - Lim, Burton K.
A1  - Rossiter, Stephen J.
A1  - Wilting, Andreas
A1  - Gilbert, M. Thomas P.
T1  - An expanded mammal mitogenome dataset from Southeast Asia
JF  - Gigascience
N2  - Background: Findings: Approximately 55 gigabases of raw sequence were generated. From this data we assembled 72 complete mitogenome sequences, with an average depth of coverage of 102.9x and 55.2x for modern samples and historical samples, respectively. This dataset represents 52 species, of which 30 species had no previous mitogenome data available. The mitogenomes were geotagged to their sampling location, where known, to display a detailed geographical distribution of the species. Conclusion:
KW  - invertebrate-derived (iDNA)
KW  - metabarcoding
KW  - GenBank
KW  - Taxonomic assignment
Y1  - 2017
SN  - 2047-217X
VL  - 6
IS  - 8
SP  - 1
EP  - 19
PB  - Oxford Univ. Press
CY  - Oxford
ER  - 
TY  - JOUR
A1  - Paijmans, Johanna L. A.
A1  - Barnett, Ross
A1  - Gilbert, M. Thomas P.
A1  - Zepeda-Mendoza, M. Lisandra
A1  - Reumer, Jelle W. F.
A1  - de Vos, John
A1  - Zazula, Grant
A1  - Nagel, Doris
A1  - Baryshnikov, Gennady F.
A1  - Leonard, Jennifer A.
A1  - Rohland, Nadin
A1  - Westbury, Michael V.
A1  - Barlow, Axel
A1  - Hofreiter, Michael
T1  - Evolutionary History of Saber-Toothed Cats Based on Ancient Mitogenomics
JF  - Current biology
N2  - Saber-toothed cats (Machairodontinae) are among the most widely recognized representatives of the now largely extinct Pleistocene megafauna. However, many aspects of their ecology, evolution, and extinction remain uncertain. Although ancient-DNA studies have led to huge advances in our knowledge of these aspects of many other megafauna species (e.g., mammoths and cave bears), relatively few ancient-DNA studies have focused on saber-toothed cats [1-3], and they have been restricted to short fragments of mitochondrial DNA. Here we investigate the evolutionary history of two lineages of saber-toothed cats (Smilodon and Homotherium) in relation to living carnivores and find that the Machairodontinae form a well-supported clade that is distinct from all living felids. We present partial mitochondrial genomes from one S. populator sample and three Homotherium sp. samples, including the only Late Pleistocene Homotherium sample from Eurasia [4]. We confirm the identification of the unique Late Pleistocene European fossil through ancient-DNA analyses, thus strengthening the evidence that Homotherium occurred in Europe over 200,000 years later than previously believed. This in turn forces a re-evaluation of its demography and extinction dynamics. Within the Machairodontinae, we find a deep divergence between Smilodon and Homotherium (similar to 18 million years) but limited diversity between the American and European Homotherium specimens. The genetic data support the hypothesis that all Late Pleistocene (or post-Villafrancian) Homotherium should be considered a single species, H. latidens, which was previously proposed based on morphological data [5, 6].
Y1  - 2017
U6  - https://doi.org/10.1016/j.cub.2017.09.033
SN  - 0960-9822
SN  - 1879-0445
VL  - 27
SP  - 3330
EP  - +
PB  - Cell Press
CY  - Cambridge
ER  - 
TY  - JOUR
A1  - Barnett, Ross
A1  - Westbury, Michael V.
A1  - Sandoval-Velasco, Marcela
A1  - Vieira, Filipe Garrett
A1  - Jeon, Sungwon
A1  - Zazula, Grant
A1  - Martin, Michael D.
A1  - Ho, Simon Y. W.
A1  - Mather, Niklas
A1  - Gopalakrishnan, Shyam
A1  - Ramos-Madrigal, Jazmin
A1  - de Manuel, Marc
A1  - Zepeda-Mendoza, M. Lisandra
A1  - Antunes, Agostinho
A1  - Baez, Aldo Carmona
A1  - De Cahsan, Binia
A1  - Larson, Greger
A1  - O'Brien, Stephen J.
A1  - Eizirik, Eduardo
A1  - Johnson, Warren E.
A1  - Koepfli, Klaus-Peter
A1  - Wilting, Andreas
A1  - Fickel, Jörns
A1  - Dalen, Love
A1  - Lorenzen, Eline D.
A1  - Marques-Bonet, Tomas
A1  - Hansen, Anders J.
A1  - Zhang, Guojie
A1  - Bhak, Jong
A1  - Yamaguchi, Nobuyuki
A1  - Gilbert, M. Thomas P.
T1  - Genomic adaptations and evolutionary history of the extinct scimitar-toothed cat
BT  - Homotherium latidens
JF  - Current biology
N2  - Homotherium was a genus of large-bodied scimitar-toothed cats, morphologically distinct from any extant felid species, that went extinct at the end of the Pleistocene [1-4]. They possessed large, saber-form serrated canine teeth, powerful forelimbs, a sloping back, and an enlarged optic bulb, all of which were key characteristics for predation on Pleistocene megafauna [5]. Previous mitochondrial DNA phylogenies suggested that it was a highly divergent sister lineage to all extant cat species [6-8]. However, mitochondrial phylogenies can be misled by hybridization [9], incomplete lineage sorting (ILS), or sex-biased dispersal patterns [10], which might be especially relevant for Homotherium since widespread mito-nuclear discrepancies have been uncovered in modern cats [10]. To examine the evolutionary history of Homotherium, we generated a -7x nuclear genome and a similar to 38x exome from H. latidens using shotgun and target-capture sequencing approaches. Phylogenetic analyses reveal Homotherium as highly divergent (similar to 22.5 Ma) from living cat species, with no detectable signs of gene flow. Comparative genomic analyses found signatures of positive selection in several genes, including those involved in vision, cognitive function, and energy consumption, putatively consistent with diurnal activity, well-developed social behavior, and cursorial hunting [5]. Finally, we uncover relatively high levels of genetic diversity, suggesting that Homotherium may have been more abundant than the limited fossil record suggests [3, 4, 11-14]. Our findings complement and extend previous inferences from both the fossil record and initial molecular studies, enhancing our understanding of the evolution and ecology of this remarkable lineage.
Y1  - 2020
U6  - https://doi.org/10.1016/j.cub.2020.09.051
SN  - 0960-9822
SN  - 1879-0445
VL  - 30
IS  - 24
PB  - Cell Press
CY  - Cambridge
ER  -