references.bib

@article{Wilkinson2016,
  doi = {10.1038/sdata.2016.18},
  url = {https://doi.org/10.1038/sdata.2016.18},
  year = {2016},
  month = mar,
  publisher = {Springer Science and Business Media {LLC}},
  volume = {3},
  number = {1},
  author = {Mark D. Wilkinson and Michel Dumontier and IJsbrand Jan Aalbersberg and Gabrielle Appleton and Myles Axton and Arie Baak and Niklas Blomberg and Jan-Willem Boiten and Luiz Bonino da Silva Santos and Philip E. Bourne and Jildau Bouwman and Anthony J. Brookes and Tim Clark and Merc{\`{e}} Crosas and Ingrid Dillo and Olivier Dumon and Scott Edmunds and Chris T. Evelo and Richard Finkers and Alejandra Gonzalez-Beltran and Alasdair J.G. Gray and Paul Groth and Carole Goble and Jeffrey S. Grethe and Jaap Heringa and Peter A.C 't Hoen and Rob Hooft and Tobias Kuhn and Ruben Kok and Joost Kok and Scott J. Lusher and Maryann E. Martone and Albert Mons and Abel L. Packer and Bengt Persson and Philippe Rocca-Serra and Marco Roos and Rene van Schaik and Susanna-Assunta Sansone and Erik Schultes and Thierry Sengstag and Ted Slater and George Strawn and Morris A. Swertz and Mark Thompson and Johan van der Lei and Erik van Mulligen and Jan Velterop and Andra Waagmeester and Peter Wittenburg and Katherine Wolstencroft and Jun Zhao and Barend Mons},
  title = {The {FAIR} Guiding Principles for scientific data management and stewardship},
  journal = {Scientific Data}
}

@article{Wickham2019,
  title = {Welcome to the {tidyverse}},
  author = {Hadley Wickham and Mara Averick and Jennifer Bryan and
    Winston Chang and Lucy D'Agostino McGowan and Romain François and
    Garrett Grolemund and Alex Hayes and Lionel Henry and Jim Hester
    and Max Kuhn and Thomas Lin Pedersen and Evan Miller and Stephan
    Milton Bache and Kirill Müller and Jeroen Ooms and David Robinson
    and Dana Paige Seidel and Vitalie Spinu and Kohske Takahashi and
    Davis Vaughan and Claus Wilke and Kara Woo and Hiroaki Yutani},
  year = {2019},
  journal = {Journal of Open Source Software},
  volume = {4},
  number = {43},
  pages = {1686},
  doi = {10.21105/joss.01686},
}

@article{FellowsYates2021,
  doi = {10.7717/peerj.10947},
  url = {https://doi.org/10.7717/peerj.10947},
  year = {2021},
  month = mar,
  publisher = {{PeerJ}},
  volume = {9},
  pages = {e10947},
  author = {James A. {Fellows Yates} and Thiseas C. Lamnidis and Maxime Borry and Aida Andrades Valtue{\~{n}}a and Zandra Fagern\"{a}s and Stephen Clayton and Maxime U. Garcia and Judith Neukamm and Alexander Peltzer},
  title = {Reproducible,  portable,  and efficient ancient genome reconstruction with nf-core/eager},
  journal = {{PeerJ}}
}

@article{Mallick2023,
  doi = {10.1101/2023.04.06.535797},
  url = {https://doi.org/10.1101/2023.04.06.535797},
  year = {2023},
  month = apr,
  publisher = {Cold Spring Harbor Laboratory},
  author = {Swapan Mallick and Adam Micco and Matthew Mah and Harald Ringbauer and Iosif Lazaridis and I{\~{n}}igo Olalde and Nick Patterson and David Reich},
  title = {The Allen Ancient {DNA} Resource ({AADR}): A curated compendium of ancient human genomes}
}

@ARTICLE{Patterson2012,
  title    = "Ancient admixture in human history",
  author   = "Patterson, Nick and Moorjani, Priya and Luo, Yontao and Mallick,
              Swapan and Rohland, Nadin and Zhan, Yiping and Genschoreck, Teri
              and Webster, Teresa and Reich, David",
  abstract = "Population mixture is an important process in biology. We present
              a suite of methods for learning about population mixtures,
              implemented in a software package called ADMIXTOOLS, that support
              formal tests for whether mixture occurred and make it possible to
              infer proportions and dates of mixture. We also describe the
              development of a new single nucleotide polymorphism (SNP) array
              consisting of 629,433 sites with clearly documented ascertainment
              that was specifically designed for population genetic analyses
              and that we genotyped in 934 individuals from 53 diverse
              populations. To illustrate the methods, we give a number of
              examples that provide new insights about the history of human
              admixture. The most striking finding is a clear signal of
              admixture into northern Europe, with one ancestral population
              related to present-day Basques and Sardinians and the other
              related to present-day populations of northeast Asia and the
              Americas. This likely reflects a history of admixture between
              Neolithic migrants and the indigenous Mesolithic population of
              Europe, consistent with recent analyses of ancient bones from
              Sweden and the sequencing of the genome of the Tyrolean
              ``Iceman.''",
  journal  = "Genetics",
  volume   =  192,
  number   =  3,
  pages    = "1065--1093",
  month    =  nov,
  year     =  2012,
  url      = "http://dx.doi.org/10.1534/genetics.112.145037",
  file     = "All Papers/P/Patterson et al. 2012 - Ancient admixture in human history.pdf",
  language = "en",
  issn     = "0016-6731, 1943-2631",
  pmid     = "22960212",
  doi      = "10.1534/genetics.112.145037",
  pmc      = "PMC3522152"
}

@ARTICLE{Peter2016,
  title     = "Admixture, Population Structure, and {F-Statistics}",
  author    = "Peter, Benjamin M",
  abstract  = "Many questions about human genetic history can be addressed by
               examining the patterns of shared genetic variation between sets
               of populations. A useful methodological framework for this
               purpose isF-statistics that measure shared genetic drift between
               sets of two, three, and four populations and can be used to test
               simple and complex hypotheses about admixture between
               populations. This article provides context from phylogenetic and
               population genetic theory. I review how F-statistics can be
               interpreted as branch lengths or paths and derive new
               interpretations, using coalescent theory. I further show that
               the admixture tests can be interpreted as testing general
               properties of phylogenies, allowing extension of some ideas
               applications to arbitrary phylogenetic trees. The new results
               are used to investigate the behavior of the statistics under
               different models of population structure and show how population
               substructure complicates inference. The results lead to
               simplified estimators in many cases, and I recommend to replace
               F3 with the average number of pairwise differences for
               estimating population divergence.",
  journal   = "Genetics",
  publisher = "Genetics",
  volume    =  202,
  number    =  4,
  pages     = "1485--1501",
  month     =  apr,
  year      =  2016,
  url       = "http://dx.doi.org/10.1534/genetics.115.183913",
  file      = "All Papers/P/Peter 2016 - Admixture, Population Structure, and F-Statistics.pdf",
  keywords  = "admixture; gene flow; phylogenetic network; phylogenetics;
               population genetics",
  language  = "en",
  issn      = "0016-6731, 1943-2631",
  pmid      = "26857625",
  doi       = "10.1534/genetics.115.183913",
  pmc       = "PMC4905545"
}


@ARTICLE{Raghavan2014,
  title    = "Upper Palaeolithic Siberian genome reveals dual ancestry of
              Native Americans",
  author   = "Raghavan, Maanasa and Skoglund, Pontus and Graf, Kelly E and
              Metspalu, Mait and Albrechtsen, Anders and Moltke, Ida and
              Rasmussen, Simon and Stafford, Jr, Thomas W and Orlando, Ludovic
              and Metspalu, Ene and Karmin, Monika and Tambets, Kristiina and
              Rootsi, Siiri and Mägi, Reedik and Campos, Paula F and
              Balanovska, Elena and Balanovsky, Oleg and Khusnutdinova, Elza
              and Litvinov, Sergey and Osipova, Ludmila P and Fedorova, Sardana
              A and Voevoda, Mikhail I and DeGiorgio, Michael and
              Sicheritz-Ponten, Thomas and Brunak, Søren and Demeshchenko,
              Svetlana and Kivisild, Toomas and Villems, Richard and Nielsen,
              Rasmus and Jakobsson, Mattias and Willerslev, Eske",
  abstract = "The origins of the First Americans remain contentious. Although
              Native Americans seem to be genetically most closely related to
              east Asians, there is no consensus with regard to which specific
              Old World populations they are closest to. Here we sequence the
              draft genome of an approximately 24,000-year-old individual
              (MA-1), from Mal'ta in south-central Siberia, to an average depth
              of 1×. To our knowledge this is the oldest anatomically modern
              human genome reported to date. The MA-1 mitochondrial genome
              belongs to haplogroup U, which has also been found at high
              frequency among Upper Palaeolithic and Mesolithic European
              hunter-gatherers, and the Y chromosome of MA-1 is basal to
              modern-day western Eurasians and near the root of most Native
              American lineages. Similarly, we find autosomal evidence that
              MA-1 is basal to modern-day western Eurasians and genetically
              closely related to modern-day Native Americans, with no close
              affinity to east Asians. This suggests that populations related
              to contemporary western Eurasians had a more north-easterly
              distribution 24,000 years ago than commonly thought. Furthermore,
              we estimate that 14 to 38\% of Native American ancestry may
              originate through gene flow from this ancient population. This is
              likely to have occurred after the divergence of Native American
              ancestors from east Asian ancestors, but before the
              diversification of Native American populations in the New World.
              Gene flow from the MA-1 lineage into Native American ancestors
              could explain why several crania from the First Americans have
              been reported as bearing morphological characteristics that do
              not resemble those of east Asians. Sequencing of another
              south-central Siberian, Afontova Gora-2 dating to approximately
              17,000 years ago, revealed similar autosomal genetic signatures
              as MA-1, suggesting that the region was continuously occupied by
              humans throughout the Last Glacial Maximum. Our findings reveal
              that western Eurasian genetic signatures in modern-day Native
              Americans derive not only from post-Columbian admixture, as
              commonly thought, but also from a mixed ancestry of the First
              Americans.",
  journal  = "Nature",
  volume   =  505,
  number   =  7481,
  pages    = "87--91",
  month    =  "2~" # jan,
  year     =  2014,
  url      = "http://dx.doi.org/10.1038/nature12736",
  file     = "All Papers/R/Raghavan et al. 2014 - Raghavan_2014.pdf;All Papers/R/Raghavan et al. 2014 - Upper Palaeolithic Siberian genome reveals dual ancestry of Native Americans.pdf",
  language = "en",
  issn     = "0028-0836, 1476-4687",
  pmid     = "24256729",
  doi      = "10.1038/nature12736",
  pmc      = "PMC4105016"
}

@ARTICLE{Lamnidis2018,
  title    = "Ancient Fennoscandian genomes reveal origin and spread of
              Siberian ancestry in Europe",
  author   = "Lamnidis, Thiseas C and Majander, Kerttu and Jeong, Choongwon and
              Salmela, Elina and Wessman, Anna and Moiseyev, Vyacheslav and
              Khartanovich, Valery and Balanovsky, Oleg and Ongyerth, Matthias
              and Weihmann, Antje and Sajantila, Antti and Kelso, Janet and
              Pääbo, Svante and Onkamo, Päivi and Haak, Wolfgang and Krause,
              Johannes and Schiffels, Stephan",
  abstract = "European population history has been shaped by migrations of
              people, and their subsequent admixture. Recently, ancient DNA has
              brought new insights into European migration events linked to the
              advent of agriculture, and possibly to the spread of
              Indo-European languages. However, little is known about the
              ancient population history of north-eastern Europe, in particular
              about populations speaking Uralic languages, such as Finns and
              Saami. Here we analyse ancient genomic data from 11 individuals
              from Finland and north-western Russia. We show that the genetic
              makeup of northern Europe was shaped by migrations from Siberia
              that began at least 3500 years ago. This Siberian ancestry was
              subsequently admixed into many modern populations in the region,
              particularly into populations speaking Uralic languages today.
              Additionally, we show that ancestors of modern Saami inhabited a
              larger territory during the Iron Age, which adds to the
              historical and linguistic information about the population
              history of Finland.",
  journal  = "Nature Communications",
  volume   =  9,
  number   =  1,
  pages    = "5018",
  month    =  "27~" # nov,
  year     =  2018,
  url      = "https://doi.org/10.1038/s41467-018-07483-5",
  annote   = "\{pdf:
              ``https://www.nature.com/articles/s41467-018-07483-5.pdf''\}",
  file     = "All Papers/L/Lamnidis et al. 2018 - Ancient Fennoscandian genomes reveal origin and spread of Siberian ancestry in Europe.pdf;All Papers/L/Lamnidis et al. 2018 - Lamnidis et al. 2018 - SI.pdf",
  keywords = "role\_lead",
  issn     = "2041-1723",
  doi      = "10.1038/s41467-018-07483-5"
}


@ARTICLE{Martin2015,
  title     = "Evaluating the use of {ABBA-BABA} statistics to locate
               introgressed loci",
  author    = "Martin, Simon H and Davey, John W and Jiggins, Chris D",
  abstract  = "Several methods have been proposed to test for introgression
               across genomes. One method tests for a genome-wide excess of
               shared derived alleles between taxa using Patterson's D
               statistic, but does not establish which loci show such an excess
               or whether the excess is due to introgression or ancestral
               population structure. Several recent studies have extended the
               use of D by applying the statistic to small genomic regions,
               rather than genome-wide. Here, we use simulations and
               whole-genome data from Heliconius butterflies to investigate the
               behavior of D in small genomic regions. We find that D is
               unreliable in this situation as it gives inflated values when
               effective population size is low, causing D outliers to cluster
               in genomic regions of reduced diversity. As an alternative, we
               propose a related statistic ƒ(d), a modified version of a
               statistic originally developed to estimate the genome-wide
               fraction of admixture. ƒ(d) is not subject to the same biases as
               D, and is better at identifying introgressed loci. Finally, we
               show that both D and ƒ(d) outliers tend to cluster in regions of
               low absolute divergence (d(XY)), which can confound a recently
               proposed test for differentiating introgression from shared
               ancestral variation at individual loci.",
  journal   = "Molecular biology and evolution",
  publisher = "Oxford University Press",
  volume    =  32,
  number    =  1,
  pages     = "244--257",
  month     =  jan,
  year      =  2015,
  url       = "http://dx.doi.org/10.1093/molbev/msu269",
  file      = "All Papers/M/Martin et al. 2015 - Evaluating the use of ABBA-BABA statistics to locate introgressed loci.pdf",
  keywords  = "ABBA–BABA; Heliconius; gene flow; introgression; population
               structure; simulation",
  language  = "en",
  issn      = "0737-4038, 1537-1719",
  pmid      = "25246699",
  doi       = "10.1093/molbev/msu269",
  pmc       = "PMC4271521"
}


@ARTICLE{Green2010,
  title     = "A draft sequence of the Neandertal genome",
  author    = "Green, Richard E and Krause, Johannes and Briggs, Adrian W and
               Maricic, Tomislav and Stenzel, Udo and Kircher, Martin and
               Patterson, Nick and Li, Heng and Zhai, Weiwei and Fritz, Markus
               Hsi-Yang and Hansen, Nancy F and Durand, Eric Y and Malaspinas,
               Anna-Sapfo and Jensen, Jeffrey D and Marques-Bonet, Tomas and
               Alkan, Can and Prüfer, Kay and Meyer, Matthias and Burbano,
               Hernán A and Good, Jeffrey M and Schultz, Rigo and Aximu-Petri,
               Ayinuer and Butthof, Anne and Höber, Barbara and Höffner,
               Barbara and Siegemund, Madlen and Weihmann, Antje and Nusbaum,
               Chad and Lander, Eric S and Russ, Carsten and Novod, Nathaniel
               and Affourtit, Jason and Egholm, Michael and Verna, Christine
               and Rudan, Pavao and Brajkovic, Dejana and Kucan, Zeljko and
               Gusic, Ivan and Doronichev, Vladimir B and Golovanova, Liubov V
               and Lalueza-Fox, Carles and de la Rasilla, Marco and Fortea,
               Javier and Rosas, Antonio and Schmitz, Ralf W and Johnson,
               Philip L F and Eichler, Evan E and Falush, Daniel and Birney,
               Ewan and Mullikin, James C and Slatkin, Montgomery and Nielsen,
               Rasmus and Kelso, Janet and Lachmann, Michael and Reich, David E
               and Pääbo, Svante",
  abstract  = "Neandertals, the closest evolutionary relatives of present-day
               humans, lived in large parts of Europe and western Asia before
               disappearing 30,000 years ago. We present a draft sequence of
               the Neandertal genome composed of more than 4 billion
               nucleotides from three individuals. Comparisons of the
               Neandertal genome to the genomes of five present-day humans from
               different parts of the world identify a number of genomic
               regions that may have been affected by positive selection in
               ancestral modern humans, including genes involved in metabolism
               and in cognitive and skeletal development. We show that
               Neandertals shared more genetic variants with present-day humans
               in Eurasia than with present-day humans in sub-Saharan Africa,
               suggesting that gene flow from Neandertals into the ancestors of
               non-Africans occurred before the divergence of Eurasian groups
               from each other.",
  journal   = "Science",
  publisher = "American Association for the Advancement of Science",
  volume    =  328,
  number    =  5979,
  pages     = "710--722",
  month     =  "7~" # may,
  year      =  2010,
  url       = "http://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pubmed&id=20448178&retmode=ref&cmd=prlinks",
  file      = "All Papers/G/Green et al. 2010 - A draft sequence of the Neandertal genome.pdf;All Papers/G/Green et al. 2010 - Green_2010_Science.pdf",
  issn      = "0036-8075"
}


@ARTICLE{Lazaridis2014,
  title    = "Ancient human genomes suggest three ancestral populations for
              present-day Europeans",
  author   = "Lazaridis, Iosif and Patterson, Nick and Mittnik, Alissa and
              Renaud, Gabriel and Mallick, Swapan and Kirsanow, Karola and
              Sudmant, Peter H and Schraiber, Joshua G and Castellano, Sergi
              and Lipson, Mark and Berger, Bonnie and Economou, Christos and
              Bollongino, Ruth and Fu, Qiaomei and Bos, Kirsten I and
              Nordenfelt, Susanne and Li, Heng and de Filippo, Cesare and
              Prüfer, Kay and Sawyer, Susanna and Posth, Cosimo and Haak,
              Wolfgang and Hallgren, Fredrik and Fornander, Elin and Rohland,
              Nadin and Delsate, Dominique and Francken, Michael and Guinet,
              Jean-Michel and Wahl, Joachim and Ayodo, George and Babiker,
              Hamza A and Bailliet, Graciela and Balanovska, Elena and
              Balanovsky, Oleg and Barrantes, Ramiro and Bedoya, Gabriel and
              Ben-Ami, Haim and Bene, Judit and Berrada, Fouad and Bravi,
              Claudio M and Brisighelli, Francesca and Busby, George B J and
              Cali, Francesco and Churnosov, Mikhail and Cole, David E C and
              Corach, Daniel and Damba, Larissa and van Driem, George and
              Dryomov, Stanislav and Dugoujon, Jean-Michel and Fedorova,
              Sardana A and Gallego Romero, Irene and Gubina, Marina and
              Hammer, Michael and Henn, Brenna M and Hervig, Tor and
              Hodoglugil, Ugur and Jha, Aashish R and Karachanak-Yankova, Sena
              and Khusainova, Rita and Khusnutdinova, Elza and Kittles, Rick
              and Kivisild, Toomas and Klitz, William and Kučinskas, Vaidutis
              and Kushniarevich, Alena and Laredj, Leila and Litvinov, Sergey
              and Loukidis, Theologos and Mahley, Robert W and Melegh, Béla and
              Metspalu, Ene and Molina, Julio and Mountain, Joanna and
              Näkkäläjärvi, Klemetti and Nesheva, Desislava and Nyambo, Thomas
              and Osipova, Ludmila and Parik, Jüri and Platonov, Fedor and
              Posukh, Olga and Romano, Valentino and Rothhammer, Francisco and
              Rudan, Igor and Ruizbakiev, Ruslan and Sahakyan, Hovhannes and
              Sajantila, Antti and Salas, Antonio and Starikovskaya, Elena B
              and Tarekegn, Ayele and Toncheva, Draga and Turdikulova, Shahlo
              and Uktveryte, Ingrida and Utevska, Olga and Vasquez, René and
              Villena, Mercedes and Voevoda, Mikhail and Winkler, Cheryl A and
              Yepiskoposyan, Levon and Zalloua, Pierre and Zemunik, Tatijana
              and Cooper, Alan and Capelli, Cristian and Thomas, Mark G and
              Ruiz-Linares, Andres and Tishkoff, Sarah A and Singh, Lalji and
              Thangaraj, Kumarasamy and Villems, Richard and Comas, David and
              Sukernik, Rem and Metspalu, Mait and Meyer, Matthias and Eichler,
              Evan E and Burger, Joachim and Slatkin, Montgomery and Pääbo,
              Svante and Kelso, Janet and Reich, David and Krause, Johannes",
  abstract = "We sequenced the genomes of a ∼7,000-year-old farmer from Germany
              and eight ∼8,000-year-old hunter-gatherers from Luxembourg and
              Sweden. We analysed these and other ancient genomes with 2,345
              contemporary humans to show that most present-day Europeans
              derive from at least three highly differentiated populations:
              west European hunter-gatherers, who contributed ancestry to all
              Europeans but not to Near Easterners; ancient north Eurasians
              related to Upper Palaeolithic Siberians, who contributed to both
              Europeans and Near Easterners; and early European farmers, who
              were mainly of Near Eastern origin but also harboured west
              European hunter-gatherer related ancestry. We model these
              populations' deep relationships and show that early European
              farmers had ∼44\% ancestry from a 'basal Eurasian' population
              that split before the diversification of other non-African
              lineages.",
  journal  = "Nature",
  volume   =  513,
  number   =  7518,
  pages    = "409--413",
  month    =  "18~" # sep,
  year     =  2014,
  url      = "http://dx.doi.org/10.1038/nature13673",
  file     = "All Papers/L/Lazaridis et al. 2014 - Ancient human genomes suggest three ancestral populations for present-day Europeans.pdf;All Papers/L/Lazaridis et al. 2014 - Lazaridis_2014.pdf",
  language = "en",
  issn     = "0028-0836, 1476-4687",
  pmid     = "25230663",
  doi      = "10.1038/nature13673",
  pmc      = "PMC4170574"
}

@article{ewels2020,
  title = {The nf-core framework for community-curated bioinformatics pipelines},
  author = {Ewels, Philip A. and Peltzer, Alexander and Fillinger, Sven and Patel, Harshil and Alneberg, Johannes and Wilm, Andreas and Garcia, Maxime Ulysse and Di Tommaso, Paolo and Nahnsen, Sven},
  year = {2020},
  month = {02},
  date = {2020-02-13},
  journal = {Nature Biotechnology},
  pages = {276--278},
  volume = {38},
  number = {3},
  doi = {10.1038/s41587-020-0439-x},
  url = {http://dx.doi.org/10.1038/s41587-020-0439-x},
  langid = {en}
}