Detecting Local Adaptation with Climate-Informed Spatial Genetic Models

Publications

A western route of prehistoric human migration from Africa into the Iberian Peninsula

Auteurs: González-Fortes, G.; Tassi, F.; Trucchi, E.; Henneberger, K.; Paijmans, J. L. A.; Díez-del-Molino, D.; Schroeder, H.; Susca, R. R.; Barroso-Ruíz, C.; Bermudez, F. J.; Barroso-Medina, C.; Bettencourt, A. M. S.; Sampaio, H. A.; Grandal-d'Anglade, A.; Salas, A.; de Lombera-Hermida, A.; Fabregas Valcarce, R.; Vaquero, M.; Alonso, S.; Lozano, M.; Rodríguez-Alvarez, X. P.; Fernández-Rodríguez, C.;
Publié dans: Proceedings of the Royal Society, Numéro 5, 2019, ISSN 0962-8452
Éditeur: Royal Society of London
DOI: 10.1098/rspb.2018.2288

Simulation-based reconstruction of global bird migration over the past 50,000 years.

Auteurs: Somveille, M., Wikelski, M., Beyer, R. M., Rodrigues, A. S., Manica, A., & Jetz, W.
Publié dans: Nature Communications, 2020, ISSN 2041-1723
Éditeur: Nature Publishing Group
DOI: 10.1038/s41467-020-14589-2

An empirical evaluation of bias correction methods for palaeoclimate simulations

Auteurs: Robert Beyer, Mario Krapp, Andrea Manica
Publié dans: Climate of the Past, Numéro 16/4, 2020, Page(s) 1493-1508, ISSN 1814-9332
Éditeur: Copernicus Publishing
DOI: 10.5194/cp-16-1493-2020

Ancient DNA suggests modern wolves trace their origin to a Late Pleistocene expansion from Beringia.

Auteurs: Loog, Liisa; Thalmann, Olaf; Sinding, Mikkel‐Holger S.; Schuenemann, Verena J.; Perri, Angela; Germonpré, Mietje; Bocherens, Herve; Witt, Kelsey E.; Samaniego Castruita, Jose A.; Velasco, Marcela S.; Lundstrøm, Inge K. C.; Wales, Nathan; Sonet, Gontran; Frantz, Laurent; Schroeder, Hannes; Budd, Jane; Jimenez, Elodie‐Laure; Fedorov, Sergey; Gasparyan, Boris; Kandel, Andrew W.; Lázničková
Publié dans: Molecular Ecology, Numéro 9, 2019, ISSN 0962-1083
Éditeur: Blackwell Publishing Inc.
DOI: 10.17863/cam.47308

Environmental conditions do not predict diversification rates in the Bantu languages

Auteurs: Robert Beyer, Joy S. Singarayer, Jay T. Stock, Andrea Manica
Publié dans: Heliyon, Numéro 5/10, 2019, Page(s) e02630, ISSN 2405-8440
Éditeur: Elsevier
DOI: 10.1016/j.heliyon.2019.e02630

A spatiotemporally explicit paleoenvironmental framework for the Middle Stone Age of eastern Africa

Auteurs: Timbrell L, Grove M, Manica A, Rucina S, Blinkhorn J. A
Publié dans: Scientific Reports, 2022, ISSN 2045-2322
Éditeur: Nature Publishing Group
DOI: 10.1038/s41598-022-07742-y

Removing reference bias and improving indel calling in ancient DNA data analysis by mapping to a sequence variation graph

Auteurs: Rui Martiniano, Erik Garrison, Eppie R. Jones, Andrea Manica, Richard Durbin
Publié dans: Genome Biology, Numéro 21/1, 2020, ISSN 1474-760X
Éditeur: Nature Springer
DOI: 10.1186/s13059-020-02160-7

Climatic windows for human migration out of Africa in the past 300,000 years.

Auteurs: Beyer, R. M., Krapp, M., Eriksson, A., & Manica, A.
Publié dans: Nature Communications, 2021, ISSN 2041-1723
Éditeur: Nature Publishing Group
DOI: 10.1038/s41467-021-24779-1

Parallel adaptation of rabbit populations to myxoma virus

Auteurs: Alves JM, Carneiro M, Cheng JY, Lemos de Matos A, Rahman MM, Loog L, Campos PF, Wales N, Eriksson A, Manica A, Strive T, Graham SC, Afonso S, Bell DJ, Belmont L, Day JP, Fuller SJ, Marchandeau S, Palmer WJ, Queney G, Surridge AK, Vieira FG, McFadden G, Nielsen R, Gilbert MTP, Esteves PJ, Ferrand N, Jiggins FM.
Publié dans: Science, 2019, ISSN 0036-8075
Éditeur: American Association for the Advancement of Science
DOI: 10.1126/science.aau7285

Bayesian Skyline Plots disagree with range size changes based on Species Distribution Models for Holarctic birds

Auteurs: Eleanor F. Miller, Rhys E. Green, Andrew Balmford, Pierpaolo Maisano Delser, Robert Beyer, Marius Somveille, Michela Leonardi, William Amos, Andrea Manica
Publié dans: Molecular Ecology, Numéro 30/16, 2021, Page(s) 3993-4004, ISSN 0962-1083
Éditeur: Blackwell Publishing Inc.
DOI: 10.1111/mec.16032

High-resolution terrestrial climate, bioclimate and vegetation for the last 120,000 years

Auteurs: Robert M. Beyer, Mario Krapp, Andrea Manica
Publié dans: Scientific Data, Numéro 7/1, 2020, ISSN 2052-4463
Éditeur: Nature Springer
DOI: 10.1038/s41597-020-0552-1

Global and country-level data of the biodiversity footprints of 175 crops and pasture

Auteurs: Robert Beyer, Andrea Manica
Publié dans: Data in Brief, Numéro 36, 2021, Page(s) 106982, ISSN 2352-3409
Éditeur: Elsevier BV
DOI: 10.1016/j.dib.2021.106982

Different environmental variables predict body and brain size evolution in Homo

Auteurs: Manuel Will, Mario Krapp, Jay T. Stock, Andrea Manica
Publié dans: Nature Communications, Numéro 12/1, 2021, ISSN 2041-1723
Éditeur: Nature Publishing Group
DOI: 10.1038/s41467-021-24290-7

The configuration of Northern Hemisphere ice sheets through the Quaternary.

Auteurs: Batchelor, Christine; Margold, Martin; Krapp, Mario; Murton, Della K; Dalton, April S; Gibbard, Philip; Stokes, Chris R; Murton, Julian B; Manica, Andrea
Publié dans: Nature Communications, Numéro 1, 2019, ISSN 2041-1723
Éditeur: Nature Publishing Group
DOI: 10.1038/s41467-019-11601-2

Relocating croplands could drastically reduce the environmental impacts of global food production.

Auteurs: Beyer, R., Hua, F., Martin, P., Manica, A., & Rademacher, T.
Publié dans: Communications Earth and Environment, Numéro 1, 2022, ISSN 2662-4435
Éditeur: Nature Publishing
DOI: 10.1038/s43247-022-00360-6

An earlier revolution: genetic and genomic analyses reveal pre-existing cultural differences leading to Neolithization

Auteurs: Michela Leonardi, Guido Barbujani, Andrea Manica
Publié dans: Scientific Reports, Numéro 7/1, 2017, ISSN 2045-2322
Éditeur: Nature Publishing Group
DOI: 10.1038/s41598-017-03717-6

Estimating mobility using sparse data: Application to human genetic variation

Auteurs: Liisa Loog, Marta Mirazón Lahr, Mirna Kovacevic, Andrea Manica, Anders Eriksson, Mark G. Thomas
Publié dans: Proceedings of the National Academy of Sciences, Numéro 114/46, 2017, Page(s) 12213-12218, ISSN 0027-8424
Éditeur: National Academy of Sciences
DOI: 10.1073/pnas.1703642114

Inferring Allele Frequency Trajectories from Ancient DNA Indicates That Selection on a Chicken Gene Coincided with Changes in Medieval Husbandry Practices

Auteurs: Liisa Loog, Mark G. Thomas, Ross Barnett, Richard Allen, Naomi Sykes, Ptolemaios D. Paxinos, Ophélie Lebrasseur, Keith Dobney, Joris Peters, Andrea Manica, Greger Larson, Anders Eriksson
Publié dans: Molecular Biology and Evolution, Numéro 34/8, 2017, Page(s) 1981-1990, ISSN 0737-4038
Éditeur: Oxford University Press
DOI: 10.1093/molbev/msx142

Ancient genomes show social and reproductive behavior of early Upper Paleolithic foragers

Auteurs: Martin Sikora, Andaine Seguin-Orlando, Vitor C. Sousa, Anders Albrechtsen, Thorfinn Korneliussen, Amy Ko, Simon Rasmussen, Isabelle Dupanloup, Philip R. Nigst, Marjolein D. Bosch, Gabriel Renaud, Morten E. Allentoft, Ashot Margaryan, Sergey V. Vasilyev, Elizaveta V. Veselovskaya, Svetlana B. Borutskaya, Thibaut Deviese, Dan Comeskey, Tom Higham, Andrea Manica, Robert Foley, David J. Meltzer, Rasmu
Publié dans: Science, Numéro 358/6363, 2017, Page(s) 659-662, ISSN 0036-8075
Éditeur: American Association for the Advancement of Science
DOI: 10.1126/science.aao1807

Paleogenomic Evidence for Multi-generational Mixing between Neolithic Farmers and Mesolithic Hunter-Gatherers in the Lower Danube Basin

Auteurs: Gloria González-Fortes, Eppie R. Jones, Emma Lightfoot, Clive Bonsall, Catalin Lazar, Aurora Grandal-d’Anglade, María Dolores Garralda, Labib Drak, Veronika Siska, Angela Simalcsik, Adina Boroneanţ, Juan Ramón Vidal Romaní, Marcos Vaqueiro Rodríguez, Pablo Arias, Ron Pinhasi, Andrea Manica, Michael Hofreiter
Publié dans: Current Biology, Numéro 27/12, 2017, Page(s) 1801-1810.e10, ISSN 0960-9822
Éditeur: Cell Press
DOI: 10.1016/j.cub.2017.05.023

Ancient human parallel lineages within North America contributed to a coastal expansion

Auteurs: C. L. Scheib, Hongjie Li, Tariq Desai, Vivian Link, Christopher Kendall, Genevieve Dewar, Peter William Griffith, Alexander Mörseburg, John R. Johnson, Amiee Potter, Susan L. Kerr, Phillip Endicott, John Lindo, Marc Haber, Yali Xue, Chris Tyler-Smith, Manjinder S. Sandhu, Joseph G. Lorenz, Tori D. Randall, Zuzana Faltyskova, Luca Pagani, Petr Danecek, Tamsin C. O’Connell, Patricia Martz, Alan S
Publié dans: Science, Numéro 360/6392, 2018, Page(s) 1024-1027, ISSN 0036-8075
Éditeur: American Association for the Advancement of Science
DOI: 10.1126/science.aar6851

Did Our Species Evolve in Subdivided Populations across Africa, and Why Does It Matter?

Auteurs: Eleanor M.L. Scerri, Mark G. Thomas, Andrea Manica, Philipp Gunz, Jay T. Stock, Chris Stringer, Matt Grove, Huw S. Groucutt, Axel Timmermann, G. Philip Rightmire, Francesco d’Errico, Christian A. Tryon, Nick A. Drake, Alison S. Brooks, Robin W. Dennell, Richard Durbin, Brenna M. Henn, Julia Lee-Thorp, Peter deMenocal, Michael D. Petraglia, Jessica C. Thompson, Aylwyn Scally, Lounès Chikhi
Publié dans: Trends in Ecology & Evolution, Numéro 33/8, 2018, Page(s) 582-594, ISSN 0169-5347
Éditeur: Elsevier BV
DOI: 10.1016/j.tree.2018.05.005

Late Quaternary horses in Eurasia in the face of climate and vegetation change

Auteurs: Michela Leonardi, Francesco Boschin, Konstantinos Giampoudakis, Robert M. Beyer, Mario Krapp, Robin Bendrey, Robert Sommer, Paolo Boscato, Andrea Manica, David Nogues-Bravo, Ludovic Orlando
Publié dans: Science Advances, Numéro 4/7, 2018, Page(s) eaar5589, ISSN 2375-2548
Éditeur: AAAS
DOI: 10.1126/sciadv.aar5589

Ancient goat genomes reveal mosaic domestication in the Fertile Crescent

Auteurs: Kevin G. Daly, Pierpaolo Maisano Delser, Victoria E. Mullin, Amelie Scheu, Valeria Mattiangeli, Matthew D. Teasdale, Andrew J. Hare, Joachim Burger, Marta Pereira Verdugo, Matthew J. Collins, Ron Kehati, Cevdet Merih Erek, Guy Bar-Oz, François Pompanon, Tristan Cumer, Canan Çakırlar, Azadeh Fatemeh Mohaseb, Delphine Decruyenaere, Hossein Davoudi, Özlem Çevik, Gary Rollefson, Jean-Denis Vigne,
Publié dans: Science, Numéro 361/6397, 2018, Page(s) 85-88, ISSN 0036-8075
Éditeur: American Association for the Advancement of Science
DOI: 10.1126/science.aas9411

A genomic history of Aboriginal Australia

Auteurs: Anna-Sapfo Malaspinas, Michael C. Westaway, Craig Muller, Vitor C. Sousa, Oscar Lao, Isabel Alves, Anders Bergström, Georgios Athanasiadis, Jade Y. Cheng, Jacob E. Crawford, Tim H. Heupink, Enrico Macholdt, Stephan Peischl, Simon Rasmussen, Stephan Schiffels, Sankar Subramanian, Joanne L. Wright, Anders Albrechtsen, Chiara Barbieri, Isabelle Dupanloup, Anders Eriksson, Ashot Margaryan, Ida Moltke
Publié dans: Nature, Numéro 538/7624, 2016, Page(s) 207-214, ISSN 0028-0836
Éditeur: Nature Publishing Group
DOI: 10.1038/nature18299

The Neolithic Transition in the Baltic Was Not Driven by Admixture with Early European Farmers

Auteurs: Eppie R. Jones, Gunita Zarina, Vyacheslav Moiseyev, Emma Lightfoot, Philip R. Nigst, Andrea Manica, Ron Pinhasi, Daniel G. Bradley
Publié dans: Current Biology, Numéro 27/4, 2017, Page(s) 576-582, ISSN 0960-9822
Éditeur: Cell Press
DOI: 10.1016/j.cub.2016.12.060

Genome-wide data from two early Neolithic East Asian individuals dating to 7700 years ago

Auteurs: Veronika Siska, Eppie Ruth Jones, Sungwon Jeon, Youngjune Bhak, Hak-Min Kim, Yun Sung Cho, Hyunho Kim, Kyusang Lee, Elizaveta Veselovskaya, Tatiana Balueva, Marcos Gallego-Llorente, Michael Hofreiter, Daniel G. Bradley, Anders Eriksson, Ron Pinhasi, Jong Bhak, Andrea Manica
Publié dans: Science Advances, Numéro 3/2, 2017, Page(s) e1601877, ISSN 2375-2548
Éditeur: American Association for the Advancement of Science
DOI: 10.1126/sciadv.1601877

Upper Palaeolithic genomes reveal deep roots of modern Eurasians

Auteurs: Eppie R. Jones, Gloria Gonzalez-Fortes, Sarah Connell, Veronika Siska, Anders Eriksson, Rui Martiniano, Russell L. McLaughlin, Marcos Gallego Llorente, Lara M. Cassidy, Cristina Gamba, Tengiz Meshveliani, Ofer Bar-Yosef, Werner Müller, Anna Belfer-Cohen, Zinovi Matskevich, Nino Jakeli, Thomas F. G. Higham, Mathias Currat, David Lordkipanidze, Michael Hofreiter, Andrea Manica, Ron Pinhasi, Daniel
Publié dans: Nature Communications, Numéro 6, 2015, Page(s) 8912, ISSN 2041-1723
Éditeur: Nature Publishing Group
DOI: 10.1038/ncomms9912

The genetics of an early Neolithic pastoralist from the Zagros, Iran

Auteurs: M. Gallego-Llorente, S. Connell, E. R. Jones, D. C. Merrett, Y. Jeon, A. Eriksson, V. Siska, C. Gamba, C. Meiklejohn, R. Beyer, S. Jeon, Y. S. Cho, M. Hofreiter, J. Bhak, A. Manica, R. Pinhasi
Publié dans: Scientific Reports, Numéro 6/1, 2016, ISSN 2045-2322
Éditeur: Nature Publishing Group
DOI: 10.1038/srep31326

Ancient Ethiopian genome reveals extensive Eurasian admixture in Eastern Africa

Auteurs: M. G. Llorente, E. R. Jones, A. Eriksson, V. Siska, K. W. Arthur, J. W. Arthur, M. C. Curtis, J. T. Stock, M. Coltorti, P. Pieruccini, S. Stretton, F. Brock, T. Higham, Y. Park, M. Hofreiter, D. G. Bradley, J. Bhak, R. Pinhasi, A. Manica
Publié dans: Science, Numéro 350/6262, 2015, Page(s) 820-822, ISSN 0036-8075
Éditeur: American Association for the Advancement of Science
DOI: 10.1126/science.aad2879

Genomic analyses inform on migration events during the peopling of Eurasia

Auteurs: Luca Pagani, Daniel John Lawson, Evelyn Jagoda, Alexander Mörseburg, Anders Eriksson, Mario Mitt, Florian Clemente, Georgi Hudjashov, Michael DeGiorgio, Lauri Saag, Jeffrey D. Wall, Alexia Cardona, Reedik Mägi, Melissa A. Wilson Sayres, Sarah Kaewert, Charlotte Inchley, Christiana L. Scheib, Mari Järve, Monika Karmin, Guy S. Jacobs, Tiago Antao, Florin Mircea Iliescu, Alena Kushniarevich, Qasim
Publié dans: Nature, Numéro 538/7624, 2016, Page(s) 238-242, ISSN 0028-0836
Éditeur: Nature Publishing Group
DOI: 10.1038/nature19792

Climate shaped how Neolithic farmers and European hunter-gatherers interacted after a major slowdown from 6,100 bce to 4,500 bce

Auteurs: Lia Betti, Robert M. Beyer, Eppie R. Jones, Anders Eriksson, Francesca Tassi, Veronika Siska, Michela Leonardi, Pierpaolo Maisano Delser, Lily K. Bentley, Philip R. Nigst, Jay T. Stock, Ron Pinhasi, Andrea Manica
Publié dans: Nature Human Behaviour, Numéro 4/10, 2020, Page(s) 1004-1010, ISSN 2397-3374
Éditeur: Springer Nature
DOI: 10.1038/s41562-020-0897-7

A statistics-based reconstruction of high-resolution global terrestrial climate for the last 800,000 years.

Auteurs: Krapp, M., Beyer, R.M, Edmundson, S., Valdes, P.J., Manica. A.
Publié dans: Scientific Data, 2021, ISSN 2052-4463
Éditeur: Nature Publishing
DOI: 10.1038/s41597-021-01009-3

Did Going North Give Us Migraine? An Evolutionary Approach on Understanding Latitudinal Differences in Migraine Epidemiology

Auteurs: Viganò, Alessandro; Manica, Andrea; Di Piero, Vittorio; Leonardi, Michela
Publié dans: Headache, Numéro 1, 2019, ISSN 0017-8748
Éditeur: Blackwell Publishing Inc.
DOI: 10.1111/head.13520

Historical and projected future range sizes of the world’s mammals, birds, and amphibians

Auteurs: Robert M. Beyer, Andrea Manica
Publié dans: Nature Communications, Numéro 11/1, 2020, ISSN 2041-1723
Éditeur: Nature Publishing Group
DOI: 10.1038/s41467-020-19455-9

A curated dataset of modern and ancient high-coverage shotgun human genomes

Auteurs: Pierpaolo Maisano Delser, Eppie R. Jones, Anahit Hovhannisyan, Lara Cassidy, Ron Pinhasi, Andrea Manica
Publié dans: Scientific Data, Numéro 8/1, 2021, ISSN 2052-4463
Éditeur: Springer Nature
DOI: 10.1038/s41597-021-00980-1

Range Sizes of the World's Mammals, Birds, and Amphibians from the Mid-Holocene to the Industrial Period.

Auteurs: Beyer R, Manica A.
Publié dans: Animals, 2021, ISSN 2076-2615
Éditeur: MDPI
DOI: 10.3390/ani11123561

Shifts in global bat diversity suggest a possible role of climate change in the emergence of SARS-CoV-1 and SARS-CoV-2.

Auteurs: Beyer, R. M., Manica, A., & Mora, C.
Publié dans: Science of The Total Environment, 2021, ISSN 0048-9697
Éditeur: Elsevier BV
DOI: 10.1016/j.scitotenv.2021.145413

Climate and mountains shaped human ancestral genetic lineages

Auteurs: Pierpaolo Maisano Delser, Mario Krapp, Robert Beyer, Eppie R Jones, Eleanor F Miller, Anahit Hovhannisyan, Michelle Parker, Veronika Siska, Maria Teresa Vizzari, Elizabeth J. Pearmain, Ivan Imaz-Rosshandler, Michela Leonardi, Gian Luigi Somma, Jason Hodgson, Eirlys Tysall, Zhe Xue, Lara Cassidy, Daniel G Bradley, Anders Eriksson, Andrea Manica
Publié dans: bioRxiv, 2021, ISSN 2692-8205
Éditeur: Cold Spring Harbour Laoratory
DOI: 10.1101/2021.07.13.452067

Post-glacial expansion dynamics, not refugial isolation, shaped the genetic structure of a migratory bird, the Yellow Warbler (Setophaga petechia)

Auteurs: Eleanor F. Miller, Michela Leonardi, Robert Beyer, Mario Krapp, Marius Somveille, Gian Luigi Somma, Pierpaolo Maisano Delser, Andrea Manica
Publié dans: bioRxiv, 2021, ISSN 2692-8205
Éditeur: Cold Spring Harbour Laboratory
DOI: 10.1101/2021.05.10.443405

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