molecular evolution from a paleo perspective
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Limited genomic signatures of population collapse in the critically endangered black abalone (Haliotis cracherodii)
Wooldridge B, Orland C, Enbody E, Escalona M, Mirchandani C, Corbett-Detig R, Kapp JD, Fletcher N, Ammann K, Raimondi P, Shapiro B
biorxiv (Pubmed Preprint)

A chromosome-level genome assembly for the dugong (Dugong dugon)
Baker N, Abueg L, Escalona M, Farquharson KA, Lanyon JM, Le Doc D, Schöneberg T, Absolon D, Sims Y, Fedrigo O, Jarvis ED, Below K, Hogg CH, Shapiro B
Journal of Hededity esae003 (Open Access)

Whole genome enrichment approach for genomic surveillance of Toxoplasma gondii
Sundararaman BJ. Shapiro K, Packham, Camp LE, Meyer RS, Shapiro B, Green RE
Food Microbiology 118: 104403


Mitogenomic analysis of a Late Pleistocene jaguar from North America
Srigyan M, Schubert BW, Bushell M, Santos SHD, Vieira Figueiró H, Sacco S, Eizirik E, Shapiro B, Shapiro B
Journal of Hededity esad082 (Open Access)

Delayed postglacial colonization of Betula in Iceland and the circum North Atlantic
Warning D, Sacco S, Thordarson T, Sepúlveda J, Shapiro B, Geirsdóttir A, Miller GH
eLife (Open Access)

Deep-time paleogenomics and the limits of DNA survival
Dalen L, Heintzman PD, Kapp JD, Shapiro B
Science 382: 48-53 pdf

A computational approach for positive genetic identification and relatedness detection from low-coverage shotgun sequencing data
Nguyen R, Kapp JD, Sacco S, Myers SP, Green RE
Journal of Heredity 114(5):504-512 (Open Access)

A hybridization target enrichment approach for pathogen genomics
Sundararaman B, Sylvester MD, Kozyreva VK, Berrada ZL, Corbett-Detig RB, Green RE
mBio 14:e0188923 (Open Access)

Whole Genome Analysis of SNV and Indel Polymorphism in Common Marmosets (Callithrix jacchus)
Harris RA, Raveendran M, Warren W, LaDeana HW, Tomlinson C, Graves-Lindsay T, Green RE, Schmidt JK, Colwell JC, Makulec AT, Cole SA, Cheeseman IH, Ross CN, Capuano S 3rd, Eichler EE, Levine JE, Rogers J
Genes 14: 2185 (Open Access)

Environmental DNA reveals invasive crayfish microbial associates and ecosystem-wide biodiversity before and after eradication
Ballare K, Worth A, Ruiz Ramos D, Beraut E, Nava H, Fairnbairn C, Wayne RK, Shapiro B, Short G, Meyer RS
Environmental DNA edn3.445 (Open Access)

A method to generate capture baits for targeted sequencing
Sundararaman BJ, Vershinina AO, Hershauer S, Kapp JD, Dunn S, Shapiro B, Green RE
Nucleic Acids Research 51: e69 (Open Access)

Ancient gene linkages support ctenophores as sister to other animals
Schultz DT, Haddock SHD, Bredeson JV, Green RE, Simakov O, Rokhsar DS
Nature 618: 110-117 (Pubmed Free Access)

Comparative genomics of Balto, a famous historic dog, captures lost diversity of 1920s sled dogs
Moon KL*, Huson HJ*, Morrill K*, Wang M-S, Li X, Srikanth K, Svenson G, Zoonomia Consortium, Karlsson EK**, Shapiro B**
Science 380 pdf

Historical processes shape contemporary extinction risk in placental mammals
Wilder AP*, Supple MA*, Subramanian A, Midude A, Swoffird R, Serres A, Steiner C, Koepfli K-P, Genereux DP, Karlsson EK, Lindblad-Toh K, Marques-Bonet T, Munoz Fuentes V, Foley K, Meyer WK, Zoonomia Consortium, Ryder OA**, Shapiro B**
Science 380 pdf

Evolutionary constraint and innovation across hundreds of placental mammals
Christmas MJ*, Kaplow IM*, Genereux DP, Dong MX, Hughes GM, Li X, Sullivan PF, Hindle AG, Andrews G, Armstrong JC, Bianchi M, Breit AM, Diekhans M, Fanter C, Foley NM, Goodman L, Keough KC, Kirilenko B, Kowalczyk A, Lawless C, Lind A, Meadows JRS, Moreira L, Ryan L, Swofford R, Valenzuela A, Wagner F, Wallerman O, Damas J, Fan K, Grimshaw J, Johnson J, Kozyrev SV, Lawner AJ, Marinescu VD, Osmanski A, Paulat NS, Phan BN, Reilly SK, Schaffer DE, Steiner C, Supple MA, Wilder AP, Wirthlin ME, Xue JR, Zoonomia Consortium, Birrem BW, Gazal S, Hubley RM, Koepfli K-P, Marques-Bonet T, Meyer W, Nweeia M, Shapiro B, Smit AFA, Springer M, Teeling E, Weng Z, Hiller M, Levesque DL, Lewin HA, Murphy WJ, Navarro A, Paten B, Pollard KS, Ray DA, Ruff I, Ryder OA, Pfenning AR, Lindblad-Ton K**, Karlson EK**
Science 380 pdf

Early dispersal of domestic horses into the Great Plains and Northern Rockies
Taylor WTT, Librado P, Isu MHT, Chief Gover CS, Arterberry J, [59 authors], Shapiro B, [19 authors], Jones EL, Running Horse Collin Y, Orlando L
Science 379:1316-1323

Whole-genome sequence and assembly of the Javan gibbon (Hylobates moloch)
Escalona M, VanCampen J, Maurer NW, Haukness M, Okhovat M, Harris RS, Watwood A, Hartley GA, O'Neill RJ, Medvedev P, Makova KD, Vollmers C, Carbone L, Green RE
Journal of Heredity esaco43 (Open Access)

Relict permafrost preserves megafauna, insects, pollen, soils and por-ice isotopes of the mammoth steppe and its collapse in central Yukon
Monteath AJ, Kuzmina S, Mahony M, Calmels F, Porter T, Mathews R, Sanborn P, Zazila G, Shapiro B, Murchie TJ, Poinar HN, Sadoway T, Hall E Hewitzon S, Froese D
Quaternary Science Reviews 299: 107878 (open access) pdf

Loss of epigenetic information as a cause of mammalian aging
Yang JH, Hayano M, Griffin PT, Amorim JA, Bonkowski MS, Apostolides JK, [48 authors], Green RE, [8 authors], Sinclair DA
Cell 186: 305-326.e27


Debating conservation: Developing critical thinking skills in introductory biology classes
Orland C, Ballare K, Garcia Vedrenne S, Palacios Mejia M, Wayne R, Shapiro B
CourseSource 9 (open access)

Seizing the moment: The opportunity and relevance of the California Conservation Genomics Project to state and federal conservation policy
Fiedler PL, Erickson B, Esgro M, Gold M, Hull JM, Norris JM, Shapiro B, Westphal M, Toffelmier E, Shaffer HB
Journal of Heredity 113: 589-596 (open access)

Modular automated microfluidic cell culture platform reduces glycolytic stress in cerebral cortex organoid
Seiler ST, Mantalas GL, Selberg J, Cordero S, Torres-Montoya S, Baudin PV, Ly VT, Amend F, Tran L, Hoffman RN, Rolandi M, Green RE, Haussler D, Salama SR, Teodorescu M
Scientific Reports 12: 20173 (open access)

Semi-automated assembly of high-quality diploid human reference genomes
Jarvis ED, Formenti G, Rhie A, Guarracino A, Yang C, Wood J, [12 authors], Escalona M, [8 authors], Green RE, [52 authors], Miga KH; Human Pangenome Reference Consortium.
Nature 611: 519-531 (open access)

Whole-genome sequence and assembly of the Javan gibbon (Hylobates moloch)
Escalona M, VanCampen J, Maurer NW, Haukness M, Okhovat M, Harris RS, Watwood A, Hartley GA, O'Neill RJ, Medvedev P, Makova KD, Vollmers C, Carbone L, Green RE
Journal of Heredity: esac043 (open access)

A draft reference genome assembly of the declining tricolored blackbird, Agelaius tricolor.
Ballare KM, Escalona M, Barr K, Seligmann W, Sacco S, Madhusudan Sahasrabudhe R, Nguyen O, Wyckoff C, Smith TB, Shapiro B
Journal of Heredity: esac053 (open access)

The genomic history and global expansion of domestic donkeys
Todd E, Tonasso-Calvière L, Chauvey L, Schiavinato S, Fages A, Seguin-Orlando A, [22 authors], Shapiro B, [19 authors], Orlando O
Science 377:1172-1180

A draft reference genome assembly of the critically endangered black Abalone, Haliotis cracherodii.
Orland C, Escalona M, Sahasrabudhe R, Marimuthu MPA, Nguyen O, Beraut E, Marshman B, Moore J, Raimondi P, Shapiro B
Journal of Heredity esac024 (open access)

Reference genomes for conservation
Paez S, Kraus RHS, Shapiro B, Gilbert MTP, Jarvis ED, the Vertebrate Genomes Project Conservation Group
Science 377: 364-366 pdf

Gray wolf genomic history reveals dual ancestry of dogs
Bergström A, Stanton DWG, Taron UH, Frantz L, Sinding M-HS, Ersmark E, Pfrengle S, Cassatt-Johnstone M, Lebrasseur O, Girdland-Flink L, [67 additional suthors] Shapiro B, Larson G, Krause J, Dalén L, Skoglund P
Nature 607: 313–320 (open access)

A polar bear paleogenome reveals extensive archaic gene flow from polar bears into brown bears
Wang M-S, Murray GGR, Mann D, Groves, P, Vershinina AO, Supple M, Kapp JD, Corbett-Detig R, Crump SE, Stirling I, Laidre KL, Kunz M, Dalén L, Green RE, Shapiro B
Nature Ecology and Evolution 6: 936–944 pdf

A discrete population of polar bears (Ursus maritimus) in Southeast Greenland
Laidre KL, Supple MA, Born EW, Regehr EV, Wiig O, Ugarte F, Aars J, Dietz R, Sonne C, Hegelund P, Isaksen C, Akse G, Cohen B, Stern H, Paetkau D, Vollmers C, Corbett-Detig R, Shapiro B
Science 376: 1333-1338 pdf

Landscape genomics to enable conservation actions: The California Conservation Genomics Project
Shaffer HB, Toffelmier E, Corbett-Detig RB, Escalona M, Erickson B, Fiedler P, Gold M, Harrigan RJ, Hodges S, Luckau TK, Miller C, Oliveira DR, Shaffer KE, Shapiro B, Sork VL, Wang IJ
Journal of Heredity: esac020 (open access)

Archaeological recovery of Late Pleistocene hair and environmental DNA from interior Alaska
Wygal BT, Krasinski KE, Metcalfe JZ, McMahan D, Holmes CE, Crass BA, Wriston TA, Shirazi S, Vershinina AO, Shapiro B
Environmental Archaeology: The Journal of Human Paleoecology pdf

Genome sequencing a gray wold from peninsular India provides new insights into the evolution and hybridization of gray wolves
Wang M-S, Thakur, M, Jhala Y, Wang S, Srinvas Y, Dai S-S, Liu Z-X, Cheng H-M, Geen RE, Koepfli, K-P, Shapiro B.
Genome Biology and Evolution 14: evac012 (open access)

Deeply conserved synteny and the evolution of metazoan chromosomes
Simakov O, Bredeson J, Berkoff K, Marletaz F, Mitros T, Schultz DT, O'Connell BL, Dear P, Martinez DE, Steele RE, Green RE, David CN, Rokhsar DS
Science Advances 8:eabi5884 (open access)

Genomic basis for skin phenotype and cold adaptation in the extinct Steller’s sea cow
Le Duc D, Akhil C, Cassatt-Johnstone M, Olsen R-A, Baleka S, Lin C-C, Lemke JR, Southon JR, Burdin A, Wang M-S, Grunewald S, Rosendahl W, Joger U, Rutschmann S, Hildebrand TA, Fritsch G, Estes JA, Kelso J, Dalen L, Hofreiter M, Shapiro B*, Schöneberg T
Science Advances: 8 (open access)

Why sequences all eukaryotes?
Blaxter M, Archibald JM, Chiders AK, Coddington JA, Crandall KA, Di Palma F, Durbin R, Edwards SV, Graves JAM, Hackett KJ, Hall N, Jarvis ED, Johnson RN, Karlsson EK. Kress WJ, Kuraki S< Lawniczak MKN, Lindblad-Toh K, Lopez JV, Moran NA, Robinson GE, Ryder OA, Shapiro B, Soltis PS, Warnow T, Zhang G, Lewin HA
Proceedings of the National Academy of Sciences USA 119: e2115636118 (open access)

Ancient DNA-based sex determination of bison hide moccasins indicates Promontory Cave occupants selected female hides for footwear
Shirazi S, Broomandkhoshbacht N, Oppenheimer J, Metcalfe JZ, Found R, Ives JW, Shapiro B
Journal of Archaeological Sciences 137: 105533 pdf


Museum Genomics
Card D, Shapiro B, Giribet G, Moritz C, Edwards S
Annual Reviews of Genetics 55: 633-659 pdf

Sedimentary DNA and molecular evidence for pre-Norse occupation of the Faroe Islands
Curtin L, D’Andrea W, Shirazi S, Shapiro B, De Wet G, Bradley R, Bakke J
Communications Earth and Environment 2: 253

Morphology, Individual Age and Sex of the Yuka Mammoth (Mammuthus primigenius) from Northern Yakutia, Russia
Maschenko EN, Potapova O, Heintzman PD, Kapp JD, Shapiro B, Protopopov AV, Boeskerov GG, Pavlov IS, Plotnikov VV, Kolesov SD, Kimovskiy AI, Kharlamova AS, van der Plicht J. Agenbroad L
Paleontological Journal (Moscow) 55: 1230-1259

A chromosome-scale genome assembly and karyotype of the ctenophore Hormiphora californensis
Schultz DT, Francis WR, McBroome JD, Christianson LM, Haddock SHD, Green RE
G3 19: jkab302 (open access)

Revisiting the effects of PCR replication and sequencing depth on biodiversity metrics in environmental DNA metabarcoding
Shirazi S, Meyer RS, Shapiro B
Ecology and Evolution 11: 15766-15779 pdf

On time and environment of Stephanorhinus kirchbergensis Jäger 1839 (Mammalia, Rhinoceratidae) in Altai and Northeastern Russia
Kirillova IV, Vershinina AO, Zazovskaya EP, Zanina OG, Cutler S, Kosintsev PA, Lapteva EG, Chernova OF, Shapiro B
Biology Bulletin 48: 1674-1687 (open access)

The origins and spread of domestic horses from the Western Eurasia steppes
Librado P, Khan N, Fages A, Kusliy MA, Suchan T, Tonasso-Calvière L, [158 additional authors including Shapiro B], Orlando L
Nature 598: 634-640

Ancient and modern genomes unravel the evolutionary history of Rhinocerotidae
Liu S, Westbury MV, Dussex N, Mitchell KV, Sinding M, Heintzman PD, Kapp JD, con Seth J, Heiniger H, Sanchez Barriero F, Margaryan A, André-Olsen R, De Cahsan B, Meng G, Yang C, Chen L, Moodle Y, Rookmaaker K, Bruford MW, Ryder O, Steiner C, van Sonsbeek L, Vartanyan S, Cooper A, Kosintsev P, Kirillova I, Lister A, Marques-Bonet T, Gopalakrishnan S, Dunn RR Lorenzen ED, Shapiro B, Zhang G, Antoine P-O, Dalén L, GIlbert MTP
Cell 184: 4874-4885

Lifetime mobility of an Arctic woolly mammoth
Wooller MJ, Bataille C, Druckenmiller P, Erickson GM, Groves P, Haubenstock N, Jose T, Irrgeher J, Mann D, Moon K, Potter B, Prohaska T, Rasic J, Reuther J, Shapiro B, Spalte KJ, Willis A
Science 373: 806-808

An ancestral recombination graph of human, Neanderthal, and Denisovan genomes
Schaefer NK, Shapiro B, Green RE
Science Advances 7: eabc0776 (Open Access)

Ancient horse genomes reveal the timing and extent of dispersals across the Bering Land Bridge
Vershinina AO, Heintzman PD, Froese DG, Zazula G, Cassatt-Johnstone M, Dalén L, Der Sarkissian C, Dunn SG, Ermini L, Gamba C, Groves P, Kapp JD, Mann DH, Seguin-Orlando A, Southon J, Stiller M, Baryshnikov G, Gimranov D, Scott E, Hall E, Hewitson S, Kirillova I, Kosintsev P, Shidlovsky F, Tong HW, Tiunov MP, Vartanyan S, Orlando L, Corbett-Detig R, MacPhee RD, Shapiro B
Molecular Ecology (Open Access)

Towards complete and error-free genome assemblies of all vertebrate species
Rhie A, McCarthy S, Fedrigo O,and the Vertebrate Genomes Project Assembly group [118 additional authors].
Nature 532: 737-746 (Open Access)

A fast and efficient single-stranded genomic library preparation method optimized for ancient DNA
Kapp JD, Green RE, Shapiro B
Journal of Heredity esab2021 (Open Access)

Metabarcoding meiofauna biodiversity assessment in four beaches of Northern Colombia: Effects of sampling protocols and primer choice
Castro LR, Meyer RS, Shapiro B, Shirazi S, Cutler S, Lagos AM, Quiroga S

An annotated draft genome for the Andean bear, Tremarctos ornatus
Saremi NF, Oppenheimer J, Vollmers C, O'Connell B, Milne SA, Byrne A, Yu K, Ryder OA, Green RE, Shapiro B
Journal of Heredity esab2021 (Open Access)

Environmental genomics of Late Pleistocene black bears and giant short-faced bears
Pedersen MW, De Sanctis B, Saremi NF, Sikora M, Puckett EE, Gu Z, Moon KL, Japp JD, Vinner L. Vardanyan Z, Ardelean CF, Arroyo-Cabreles J, Cahill JA, Heintzman PD, Zazula G, MacPhee RDE, Shapiro B, Durbin R, Willerslev E
Current Biology (Open Access)

A reference genome assembly of American bison, Bison bison bison
Oppenheimer J, Rosen BD, Heaton MP, Vander Ley BL , Shafer WR, Schuetze FT, Stroud B, Kuehn LA, McClure JC, Barfield JP, Blackburn HD, Kalbfleisch TS, Bickhart DM , Davenport KM, Kuhn KL, Green RE, Shapiro B, Smith TPL
Journal of Heredity 112: 174-183 (Open Access)

A reference genome assembly of Simmental cattle, Bos taurus taurus
Heaton MP, Smith TPL, Bickhart DM, Vander Ley BL, Kuehn LA, Oppenheimer J, Shafer WR, Schuetze FT Stroud B, McClure JC, Barfield JP, Blackburn HD, Kalbfleisch TS, Green RE, Shapiro B, Rosen BD
Journal of Heredity 112: 184-191 (Open Access)

Ancient plant DNA reveals High Arctic greening during the Last Interglacial
Crump SE, Fréchette B, Power M, Cutler S, de Wet G, Raynolds MK, Robert J, Briner JP, Thomas EK, Sepúlveda J, Shapiro B, Bunce M, Miller GH
Proceedings of the National Academy of Sciences of the USA 118 (13) e2019069118 pdf

Intended consequences statement
Phelan R, Baumgartner B, Brand S, Brister E, Burgiel SW, Charo RA, Coche I, Cofrancesco A, Delborne JA, Eswards O, Fisher JP, Gaywood M, Gordon DR, Howard G, Hunter ME, Kareiva P, Mankad A, Warvier M, Moseby K, Newhouse AW, Novak BJ, Ohrstrom G, Olsen S, Palmer MJ, Palumbi S, Patterson N Jr, Pedrono M, Pelegri F, Rohwer Y, Ryder OA, Saah JR, Scheller RM, Seddon PJ, Shaffer HB, Shapiro B, Sweeney M, Tercek MR, Thizy D, Tilt W, Weber M, Wegrzyn RD, Whitelaw B, Winkler M, Wodak J, Zimrig M, Robbins P.
Conservation Science and Practice (Open Access)

Isotopic evidence for long-distance travel by occupants of the AD Thirteenth-Century Promontory Caves Occupants
Metcalfe JZ, Ives JW, Shirazi S, Gillmore K, Hallson J, Brock F, Clark BJ, Shapiro B
American Antiquity, 1-23

The California environmental DNA "CALeDNA" Program
Meyer RS, Curd E, Schweizer T, Gold Z, Ruiz D, Shirazi S, Kandlikar G, Kwan W-Y, Lin M, Friese A, Moberg-Parker J, Munguia Ramos M, Shapiro B, Sexton JP, Pipes L, Garcia Vedrenne A, Palacios Mejia M, Aronson EL, Moore T, Nielsen R, Lewin H, Barber P, Wall J, Kraft N, Wayne RK
California Agriculture 75: 1 pdf

Conserving intraspecific variation for nature’s contributions to people
Des Roches S, Pendleton L, Shapiro B, Palkovacs EP
Nature Ecology and Evolution 5:574-582 pdf

Million-year-old DNA sheds light on the genomic history of mammoths
Van der Valk T, Pečnerová P, Díez-del-Molino D, Bergström A, Oppenheimer J, Hartmanm S, Xenikoudakis G, Thomas JA, Dehasque M, Sağlıcan E, Rabia Fidan F, Barnes I, Liu S, Somel M, Heintzman PD, Nikolskiy P, Shapiro B, Skoglund P, Hofreiter M, Lister AM, Götherström A, Dalén L
Nature 591: 265-269 pdf

Dire wolves were the last of an ancient New World canid lineage
Perri AR*, Mitchell KJ*, Moutin A*, Álvarez-Carretero S*, Hulme-Beaman A, Haile J, Jamieson A, Meachen J, Lin AT, Schubert BW, Ameen C, Antipina EE, Bover P, Brace S, Carmagnini A, Carøe C, Samaniego Castruita JA, Chatters JC, Dobney K, dos Reis M, Evin A, Gaubert P, Gopalakrishnan S, Gower G, Heiniger H, Helgen KM, Kapp JD, Kosintsev PA, Linderholm A, Ozga AT, Presslee S, Salis AT, Sarem NF, Shew C, Skerry K, Taranenko DE, Thompson M, Sablin MV, Kuzmin YV, Collins MJ, Sinding M-HS, Gilbert MTP, Stone AC, Shapiro B, Van Valkenburgh B, Wayne RK, Larson G, Cooper A, Frantz L.
Nature 591: 87-91

Reintroduction of the archaic variant of NOVA1 in cortical organdies alters neurodevelopment
Trujillo CA, Rice ES, Schaefer NK, Chaim IA, Wheeler EC, Madrigal AA, Buchanan J, Preissl S, Wang A, Negraes PD, Szeto R, Herai RH, Huseynov A, Ferraz MSA, Borges FdS, Kihara AH, Byrne A, Marin M, Vollmers V, Brooks AN, Lautz JD, Semendeferi K, Shapiro B, Yeo GW, Smith SEP, Green RE, Muotri AR
Science 371:eaax2537

Heterogenous hunter-gatherer and steppe-related ancestries in Late Neolithic and Bell Beaker genomes from present-day France
Seguin-Orlando A, Donat R, Der Sarkissian C, Southon J, Thèves C, Manen C, Tchérémissinoff Y, Crubézy E, Shapiro B, Deleuze J-F, Dalén L, Guilaine J, Orlando L
Current Biology 31: 1-12 pdf


A mummified Pleistocene gray wolf pup (Canis lupus) from Yukon Territory, Canada
Meachen J, Wooller MJ, Barst BD, Funck J, Clan C, Heath J, Cassatt-Johnstone M, Shapiro B, Hall E, Hewitson S, Zazula GRK
Current Biology 30:1467-1468

Ten strategies for a successful transition to remote learning: lessons learned with a flipped course
Garcia-Vedrenne A Orland C, Ballare K, Shapiro B, Wayne RK
Ecology and Evolution 10:12620-12634 (open access)

863 genomes reveal the origin and domestication of chicken
Wang M-S, Thakur M, Peng M-S, Jiang Y, Frantz L, [43 additional authors], Supple M, Shapiro B, Hanotte O, Zhang G, Larson G, Han J-L, Wu D-D, Zhang Y-P
Cell Research 30:693-701 pdf

The case of an arctic wild ass highlights the utility of ancient DNA for validating problematic identifications in museum collections
Vershinina A, Kapp JD, Baryshnikov G, Shapiro B
Molecular Ecology Resources 20: 1182-1190 (open access)

Nanopore sequencing and the Shasta toolkit enable efficient de novo assembly of eleven human genomes
Shafin K, Pesout T, Lorig-Roach R, Haukness M, Olsen HE, Bosworth C, Armstrong J, Tigyi K, Maurer N, Koren S, Sedlazeck FJ, Marschall T, Mayes S, Costa V, Zook JM, Liu KJ, Kilburn D, Sorensen M, Munson KM, Vollger MR, Monlong J, Garrison E, Eichler EE, Salama S, Haussler D, Green RE, Akeson M, Phillippy A, Miga KH, Carnevali P, Jain M, Paten B
Nat Biotechnology 38(9):1044-1053 (open access)

Ancient hybridization with an unknown population facilitated high altitude adaptation of canids
Wang M-S, Wang S, Thakur M, Jhala Y, Otecko NO, Si, J-F, Li Y Shapiro B, Nielsen R, Zhang Y-P, Wu D-D
Molecular Biology and Evolution 37:2616-2629 pdf

One fly-one genome: chromosome-scale genome assembly of a single outbred Drosophila melanogaster
Adams M, McBroome J, Maurer N, Pepper-Tunick E, Saremi NF, Green RE, Vollmers C, Corbett-Detig RB
Nucleic Acids Research 48(13):e75 (open access)

Rapid range shifts and megafaunal extinctions driven by late Pleistocene climate change
Seersholm FV, Werndly DJ. Grealy A, Johnson T, Keenan Early, EM, Lundelius, EL Jr, Winsborough B, Farr G, Toomey R, Hansen AJ, Shapiro B, Waters MR, McDonald G, Linderholm A, Stafford T, Bunce M
Nature Communications 11:2770 (open access)

Horseshoe-based Bayesian nonparametric estimates of effective population size trajectories
Faulkner J, Magee A, Shapiro B, Minin V.
Biometrics 76: 677-690 (open access)

Rejoinder for discussion on “Horseshoe-based Bayesian nonparametric estimates of effective population size trajectories.”
Faulkner J, Magee A, Shapiro B, Minin V.
Biometrics 76:695-699 (open access)

Deeply conserved synteny resolves early events in vertebrate evolution
Simakov O, Marlétaz F, Yue JX, O'Connell B, Jenkins J, Brandt A, Calef R, Tung CH, Huang TK, Schmutz J, Satoh N, Yu JK, Putnam NH, Green RE, Rokhsar DS
Nature Ecology and Evolution 4(6):820-830 (open access)

Continuous chromosome-scale haplotypes assembled from a single interspecies F1 hybrid of yak and cattle
Rice ES, Koren S, Rhie A, Heaton MP, Kalbfleisch TS, Hardy T, Hackett PH, Bickhart DM, Rosen BD, Ley BV, Maurer NW, Green RE, Phillippy AM, Petersen JL, Smith TPL
Gigascience 9(4):giaa029 (open access)

A High-Quality Reference Genome Assembly of the Saltwater Crocodile, Crocodylus porosus, Reveals Patterns of Selection in Crocodylidae
Ghosh A, Johnson MG, Osmanski AB, Louha S, Bayona-Vásquez NJ, Glenn TC, Gongora J, Green RE, Isberg S, Stevens RD, Ray DA
Genome Biology and Evolution 12:3635-3646 (open access)

Pre-extinction demographic stability and genomic signatures of adaptation in the woolly rhinoceros
Lord, E., Dussex N, Kierczak M, Díez-del-Molino D, Ryder O, Stanton DWG, Gilbert MTP, Sinding MHS, Fedorov S, Bocherens H, Nathan S, Goosens B, Chan YL, Prost S, Potapova O, Kirillova I, Lister AM, Heintzman PD, Kapp J, Shapiro B, Vartanyan S, Götherström A, Dalén L
Current Biology 30: 1-9 (open access)

A novel NGS library preparation method to characterize native termini of fragmented DNA
Harkins KM, Schaefer NK, Troll CJ, Rao V, Kapp JD, Naughton C, Haussler D, Shapiro B, Green RE
Nucleic Acids Research 48(8):e47 (open access)

An evolutionarily ancient sequence insertion in Mxra8 receptor confers resistance to alpha virus infection
Kim AS, Zimmerman O, Nelson CA, Basore K, Zhang R, Desai C, Bullock C, Durnell L, Deem SL, Oppenheimer J, Shapiro B, Wang T, Coyne CB, Handley SA, Landis MJ, Fremont DH, Diamond MS
27(3):428-440.e9 pdf


Puma genomes from North and South America provide insights into the genomic consequences of inbreeding
Saremi N*, Supple MA*, Byrne A, Cahill JA, Lehman Coutinho L, Dalén L, Figueiró HV, Johnson WE, Milne HJ, O’Brien SJ, O’Connell BO, Onorato DP, Riley SPD, Sikich JA, Stahler DR, Villetta PMS, Vollmers C, Wayne RK, Eizirik E, Corbett-Detig RB, Green RE, Wilmers CC, Shapiro B
Nature Communications 10:4769 (open access)

Perspective: New middle chapter in the story of human evolution
Schaefer NK, Shapiro B
Science 365:981-982 pdf

Early Pleistocene enamel proteome from Dmanisi resolves Stephanorhinus phylogeny
Cappellini E, Welker F, Pandolfi L, Ramos-Madrigal J, Samodova D, Rüther PL, [30 additional authors], Shapiro B, Rook L, Dalén L, Gilbert MTP, Olsen JV, Lordkipanidze D, Willerslev E
Nature 574: 103-107 pdf

Demographic reconstruction from ancient DNA supports rapid extinction of the Great Auk
Thomas JE, Carvalho GR, Haile J, Rawlence NJ, Martin MD, Ho SYW, [26 additional authors], Shapiro B, Hofreiter M, Stewart JR, Gilbert MTP, Knapp M
eLife 2019; 8:e47509 (open accesss)

Ancient DNA analysis of a Holocene bison from the Rauchua River, Northwestern Chukotka, and the existence of a deeply divergent mitochondrial clade
Vershinina A, Kapp JD, Soares AER, Heingzman PD, Lowson C, Cassatt-Johnstone M, Shidlovskiy FK, Kirillova IV, Shapiro BC
Zoologichesky Zhurnal. 98:1-9 (in Russian)

Tracking five millennia of horse management with extensive ancient genome time-series
Fages, A, Hanghøj K, Khan N, Gaunitz C, Seguin-Orlando A, Leonardi M et al C
Cell 177: 1419-1435.e31 (open access)

Mitogenomes illuminate the origin and migration patterns of the indigenous people of the Canary Islands
Fregel R, Ordóñez AC, Santana-Cabrera J, Cabrera VM, Velasco-Vazquez J, Alberto V, Moreno-Benítez MA, Delgado-Darias T, Rodríguez-Rodríguez AdC, Hernández JC, Pais J, González-Montelongo R, Lorenzo-Salazar JM, Flores C, Cruz de Mercadal MC, Álvarez-Rodríguez N, Shapiro B, Arnay M, Bustamante C
PLoS ONE 14(3): e0209125 (open access)

Climate‐driven ecological stability as a globally shared cause of Late Quaternary megafaunal extinctions: the Plaids and Stripes Hypothesis
Mann DH, Groves P, Gaglioti BV, Shapiro B
Biological Reviews 94: 328-352 pdf

Structural Variation Detection by Proximity Ligation from Formalin-Fixed, Paraffin-Embedded Tumor Tissue
Troll CJ, Putnam NH, Hartley PD, Rice B, Blanchette M, Siddiqui S, Ganbat JO, Powers MP, Ramakrishnan R, Kunder CA, Bustamante CD, Zehnder JL, Green RE, Costa HA
The Journal of Molecular Diagnostics (in press) pdf

New Approaches for Genome Assembly and Scaffolding
Rice ES, Green RE
Annual Review of Animal Biosciences 7: 21.1-21.4) pdf


Conservation of biodiversity in the genomics era
Supple MA, Shapiro B
Genome Biology 19: 131 pdf

Improved reference genome for the domestic horse increases assembly contiguity and composition
Kalbfleisch TS, Rice ES, DePriest MS Jr, Walenz BP, Hestand MS, Vermeesch JR, O Connell BL, Fiddes IT, Vershinina AO, Saremi NF, Petersen JL, Finno CJ, Bellone RR, McCue ME, Brooks SA, Bailey E, Orlando L, Green RE, Miller DC, Antczak DF, MacLeod JN
Communications Biology 1: 197

Improving nanopore read accuracy with the R2C2 method enables the sequencing of highly multiplexed full-length single-cell cDNA.
Volden R, Palmer T, Byrne A, Cole C, Schmitz RJ, Green RE, Vollmers C
Proceedings of the National Academy of Sciences USA 115: 9726 pdf

Improving societies' harassment policies
Anbar A, Elgin S, Jez J, O'Dowd D, Shapiro B, Zaman M
Science 361: 984-985 pdf

Evolutionary history and adaptation of a human pygmy population of Flores Island, Indonesia
Tucci S, Vohr SH, McCoy RC, Vernot B, Robinson MR, Barbieri C, Nelson BJ, Fu W, Purnomo GA, Sudoyo H, Eichler EE, Barbujani G, Visscher PM, Akey JM, Green RE M
Science 361: 511-516 pdf

Partial genomic survival of cave bears in living brown bears
Barlow A, Cahill JA, Hartmann S, Theunert C, Xenikoudakis G, Fortes GG, Paijmans JLA, Rabeder G, Frischaut C, Grandal-d’Anglade, Garcia-Vásquez A, Murtskhvaladze M, Saarma U, Anijalg P, Skrbinšek T, Bertorelle G, Gasparian B, Bar-Oz G, Pinhasi R, Slatkin M, Dalén L, Shapiro B, Hofreiter M
Nature Ecology and Evolution 2: 1563–1570 pdf

Minimizing polymerase biases in metabarcoding
Nichols RV, Vollmers C, Newsom LA, Wang Y, Heintzman PD, Leighton M, Green RE, Shapiro B
Molecular Ecology Resources 18:927-939 pdf

A probable prehistoric case of meningococcal disease from San Francisco Bay: Next generation sequencing of Neisseria meningitides from dental calculus and osteological evidence
Eerkens JW, Nichols RV, Murray GGR, Perez K, Murga E, Kaijankoski P, Rosenthal JS, Engbging L, Shapiro B
International Journal of Paleopathology 22:173-180 pdf

Ancient genomes from North Africa provide evidence for prehistoric migrations to the Maghreb from both the Levant and Europe
Fregel R, Mendez FL, Bokbot Y, Martin-Socas D, Camalich-Massieu MD, Santana J, Morales J, Ávila-Arcos MC, Underhill PA, SHapiro B, Wojcik GL, Rasmussen M, Soares AER, Kapp J, Sockell A, Rodriguez-Santos FJ, Mikdad A, Trujillo-Mederos A, Bustamante CD
Proceedings of the National Academy of Sciences USA 115:6774-6779 pdf

Genomic evidence of globally widespread admixture from polar bears into brown bears during the last ice age
Cahill JA, Heintzman PD, Harris K, Teasdale M, Kapp J, Soares AER, Stirling I, Monaghan N, Edwards CJ, Malev AV, Kisleika AA, Green RE, Shapiro B
Molecular Biology and Evolution 35:1120-1129 (2018) pdf

Epigenetic maintenance of topological domains in the highly rearranged gibbon genome
Lazar NH, Nevonen KA, O'Connell B, McCann C, O'Neill RJ, Green RE, Meyer TJ, Okhovat M, Carbone L
Genome Research 28:1-15 (2018) pdf

Experimental investigation of the dietary ecology of the extinct passenger pigeon, Ectopistes migratorius
Novak BJ, Estes J, Shaw H, Novak EV, Shapiro B
Frontiers in Ecology and Evolution (2018) [Open Access]

Natural selection and origin of a melanistic allele in North American gray wolves
Schweizer RM, Durvasula A, Smith J, Vohr SH, Stahler DR, Galaverni M, Thalmann O, Smith DW, Randi E, Ostrander EA, Green RE, Lohmueller KE, Novembre J, Wayne RK
Molecular Biology and Evolution 35: 1190-1209 (2018) pdf


A new genus of horse from Pleistocene North America
Heintzman PD, Zazula GD, MacPhee RDE, Scott E, Cahill JA, McHorse BK, Stiller M, Orlando L, Southon JR, Froese DG, Shapiro B
eLife 6:e29944(2017) pdf

Natural selection shaped the rise and fall of passenger pigeon genomic diversity
Murray GGR, Soares AER, Novak BJ, Schaefer NK, Cahill JA, Baker AJ, Demboski JR, Doll A, Da Fonseca RR, Fulton TL, Gilbert MTP, Heintzman PD, Letts B, McIntosh G, O’Connell BL, Peck M, Pipes M-L, Rice ES, Santos KM, Sohrweide AG, Vohr SH, Corbett-Detig RB, Green RE, Shapiro B
Science 358: 951-954 (2017) pdf

Survival and divergence in a small group: the extraordinary genomic history of the endangered Apennine brown bear stragglers
Benazzo A, Trucchi E, Cahill JA, Daisano Delser P, Mona S, Fumagalli M, Bunnefeld L, Cornetti L, Ghirotto S, Giradi M, Ometto L, Panziera A, Rota-Stabelli O, Zanetti E, Karamanlidis A, Groffi C, Paule L, Gentile L, Vilá C, Vicario S, Boitani L, Orlando L, Fuselli S, Cernesi C, Shapiro B, Ciucci P, Bertorelle G
Proceedings of the National Academy of Sciences USA 114:E9589-E9597 (2017) pdf

Ancient DNA resolves the history of Tetragnatha (Araneae, Tetragnathidae) spiders on Rapa Nui
Cotoras DD, Murray GGR, Kapp J, Gillespie R, Groswold C, Simison WB, Green RE, Shapiro B
Genes 8: e43 (2017) [Open Access]

A 3-way hybrid approach to generate a new high-quality chimpanzee reference genome (Pan_tro_3.0)
Kuderna LFK, Tomlinson C, Hillier LW, Tran A, Fiddes IT, Armstrong J, Laayouni H, Gordon D, Huddleston J, Garcia Perez R, Povolotskaya I, Serres Armero A, Gómez Garrido J, Ho D, Ribeca P, Alioto T, Green RE, Paten B, Navarro A, Betranpetit J, Herrero J, Eichler EE, Sharp AJ, Feuk L, Warren WC, Marques-Bonet T
GigaScience 6:1-6 (2017) pdf

Improved genome assembly of American alligator genome reveals conserved architecture of estrogen signaling
Rice ES, Kohno S, John JS, Pham S, Howard J, Lareau LF, O'Connell BL, Hickey G, Armstrong J, Deran A, Fiddes I, Platt RN 2nd, Gresham C, McCarthy F, Kern C, Haan D, Phan T, Schmidt C, Sanford JR, Ray DA, Paten B, Guillette LJ Jr, Green RE
Genome Research 27:686-696 (2017) pdf

Discovery of the skull of Stephanorhinus kirchbergensis (Jager, 1839) above the Arctic Circle
Kirillova IV, Chernova OF, Kukarsih VV, Shapiro B, van der Plischt J, Shidlovskiy FK, Heintzman PD, can Kolfschoten T, Zazina OG
Quaternary Research 88:537-550 (2017) pdf

A middle Holocene steppe bison and paleoenvironments from the Versleuce Meadows, Whitehorse, Yukon, Canada
Zazula GD, Hall E, Hare PG, Thomas C, Matthewes R, La Farge C, Martel AL, Heintzman PD, Shapiro B
Canadian Journal of Earth Sciences 54:1138-1152 (2017) pdf

The Zhenya Mammoth (Mammuthis primigenius (Blum.)): taphonomy, geology, age, morphology and ancient DNA of a 48,000 year old frozen mummy from Western Taymyr, Russia
Maschenko EN, Potapova OR, Vershinina A, Shapiro B, Streletskaya IR, Vasilev AA, Oblogov GE, Kharlamova AS, van der Plicht J. Tikhonov AN, Serdyuk NV, Tarasenko KK
Quaternary International 445: 104-134 (2017) pdf

Response to "Whole genome data do not support recent hybrid origins of red wolves and eastern wolves"
vonHoldt BM, Cahill JA, Gronau I, Shapiro B, Wall J, Wayne RK
Science Advances 3: e1701233 (2017) pdf

Paleogenomes of Eurasian straight-tusked elephants challenge the current view of elephant evolution
Meyer M, Palkopoulou E, Baleka S, Stiller M, Penkman K, Alt KW, Ishida Y, Mania D, Mallick S, Meijer T, Meller T, Nagel S, Nickel B, Ostritz S, Roca AL, Rohland N, Schauer K, Schüler T, Reich D, Shapiro B, Hofreiter M
eLife 6: e23413 (2017) pdf

The southern coastal Beringian land bridge: cryptic refugium or pseudo refugium for woody plants during the Last Glacial Maximum?
Wang Y, Heintzman P, Newsom L, Bigelow N, Wooller M, Shapiro B, Williams J
Journal of Biogeography 44:1559-1571 (2017) pdf

AD-LIBS: Inferring ancestry across hybrid genomes using low-coverage sequence data
Schaefer NK, Shapiro B, Green RE
BMC Bioinformatics. 18:203 (2017) pdf

Stable C and N isotope analysis of hair suggest undernourishment as a factor in the death of a mummified girl from late 19th century San Francisco, CA
Eerkens JW, Hull B, Goodman J, Evoy A, Kapp JD, Hussain S, Green RE
PloS One 12:e0184921 (2017)

Fossil and genomic evidence constrains the timing of bison arrival in North America
Froese D, Stiller M, Heintzman PD, Reyes AV, Zazula GD, Soares AE, Meyer M, Hall E, Jensen BJ, Arnold LJ, MacPhee RD, Shapiro B
PNAS early edition (2017) pdf

Improved genome assembly of American alligator genome reveals conserved architecture of estrogen signaling
Rice ES, Kohno S, John JS, Pham S, Howard J, Lareau LF, O'Connell BL, Hickey G, Armstrong J, Deran A, Fiddes I, Platt RN 2nd, Gresham C, McCarthy F, Kern C, Haan D, Phan T, Schmidt C, Sanford JR, Ray DA, Paten B, Guillette LJ Jr, Green RE.
Genome Research (advanced access) (2017) pdf

The evolutionary and phylogeographic history of woolly mammoths: a comprehensive mitogenomic analysis
Chang D*, Knapp M*, Enk J*, Lippold S, Kircher M, Lister A, MacPhee RDE, Widga C, Czechowski P, Sommer R, Hodges E, Stümpel N, Barnes I, Dalén L, Derevianko A, Germonpré M, Hillebrand-Voiculescu A, Constantin S, Kuznetsova T, Mol D, Rathgeber R, Rosendahl W, Tikhonov AN, WIllerslev E, Hannon G, Lalueza-Fox C, Joger U, Poinar H, Hofreiter M, Shapiro B
Scientific Reports 7:44585 (2017) pdf

Complex admixture preceded and followed the extinction of wisent in the wild
Węcek K, Hartmann S, Paijmans JLA, Taron U, Xenikoudakis G, Cahill JA, Heintzman PD, Shapiro B, Baryshnikov G, Bunevich AN, Crees JJ, Dobosz R, Manaserian N, Okarma H, Tokarska M, Turvey ST, Wójcik JM, Żyła W, Szymura JM, Hofreiter M, Barlow A
Molecular Biology and Evolution 34: 598-612 (2016) pdf


Complete mitochondrial genomes of living and extinct pigeons revise the timing of the columbiform radiation
Soares AER, Novak B, Haile J, Fjeldså J, GIlbert MTP, Poinar H, Church G, Shapiro B
BMC Evolutionary Biology 16: 1-9 (2016) pdf

Whole-genome sequence analysis shows that two endemic species of North American wolf are admixtures of the coyote and gray wolf
vonHoldt BM, Cahill JA, Fan Z, Gronau I, Robinson J, Pollinger JP, Shapiro B, Wall J, Wayne RK
Science Advances 2: e150175 (2016) pdf

Bermuda 2.0: reflections from Santa Cruz
Reardon J, Ankeny RA, Bangham J, Darling KW, Hilgartner S, MaxsonJones K, Shapiro B, Stevens H, and the Genomic Open Workshop Group
Gigascience 5:1-4 (2016) pdf

Declining freshwater availability caused the extinction of the last North American mammoth
Graham RW, Belmecheri S, Choy K, Cullerton B, Davies LH, Froese D, Heintzman PD, Hritz C, Kapp JD, Newsom L, Rawcliffe R, Saulnier-Talbot E, Shapiro B, Wang Y, Williams JW, Wooller MJ
PNAS 113:9310-9314 (2016) pdf

Early cave art and ancient DNA record the origin of European bison
Soubrier J, Gower G, Chen K, Richards SM, Llamas B, Mitchell KJ, Ho SY, Kosintsev P, Lee MS, Baryshnikov G, Bollongino R, Bover P, Burger J, Chivall D, Crégut-Bonnoure E, Decker JE, Doronichev VB, Douka K, Fordham DA, Fontana F, Fritz C, Glimmerveen J, Golovanova LV, Groves C, Guerreschi A, Haak W, Higham T, Hofman-Kamińska E, Immel A, Julien MA, Krause J, Krotova O, Langbein F, Larson G, Rohrlach A, Scheu A, Schnabel RD, Taylor JF, Tokarska M, Tosello G, van der Plicht J, van Loenen A, Vigne JD, Wooley O, Orlando L, Kowalczyk R, Shapiro B, Cooper A.
Nature Communications 7: 13158 (2016) pdf

Genomic analysis of 6,000-year-old cultivated grain illuminates the domestication history of barley
Mascher M, Schuenemann VJ, Davidovich U, Marom N, Himmelbach A, Hübner S, Korol A, David M, Reiter E, Riehl S, Schreiber M, Vohr SH, Green RE, Dawson IK, Russell J, Kilian B, Muehlbauer GJ, Waugh R, Fahima T, Krause J, Weiss E, Stein N
Nature Genetics 48: 1089-1093(2016) pdf

Pathways to de-extinction: How close can we get to resurrection of an extinct species?
Shapiro B
Functional Ecology doi:10.1111/1365-2435.12705 (2016) pdf

The complete mitochondrial genome of the black surfperch, Embiotoca jacksoni: Selection and substitution rates among surfperches (Embiotocidae).?
Longo GC, O'Connell B, Green RE, Bernardi G.
Marine Genomics 18: 107-112 (2016) pdf

Bison phylogeography constrains dispersal and viability of the ‘Ice Free Corridor’ in western Canada
Heintzman PD, Froese DG, Ives JW, Soares AER, Zazula GD, Letts B, Andrews TD, Driver JC, Hall E, Hare PG, Jass CN, MacKay G, Southon JR, Stiller M, Woywitka R, Suchard MA, Shapiro B
PNAS 113: 8057-8063 (2016) pdf

Chromosome-scale shotgun assembly using an in vitro method for long-range linkage.
Putnam NH, O'Connell BL, Stites JC, Rice BJ, Blanchette M, Calef R, Troll CJ, Fields A, Hartley PD, Sugnet CW, Haussler D, Rokhsar DS, Green RE
Genome Research 26: 342-350 (2016)

Detecting hybridization using ancient DNA
Schaefer NK, Shapiro B, Green RE
Molecular Ecology 25: 2398-2412 (2016) pdf

Inferring species divergence times using Pairwise Sequential Markovian Coalescent (PSMC) modeling and low coverage genomic data
Cahill JA, Soares AER, Green RE, Shapiro B
Phil Trans Roy Soc, B 371: 20150138 (2016) pdf

Mammuthus population dynamics in Late Pleistocene North America: Divergence, phylogeography and introgression<
Enk J, Devault A, Widga C, Saunders J, Szpak P, Southon JR, Rouillard J-M, Shapiro B, Golding B, Zazula GD, Froese DG, Fisher D. MacPhee RD, Poinar H
Frontiers in Ecology and Evolutionary Biology 4:00042 (2016) pdf

Morphological and genetic identification and isotopic determinations of the hair of a cave lion from the Malyi Anyui River (Chukotka, Russia)
Chernova O, Kirillova I, Shapiro B, Shidlovskiy F, Soares, AER, Levchenko V, Bertuch F
Quaternary Science Reviews 142: 61-73 (2016) pdf

The effects of demineralisation and sampling point variability on the measurement of glutamine diminution in type I collagen extracted from bone
Simpson JP, Penkman KEH, Demarchi D, Koon H, Collins MJ, Thomas-Oates J, Shapiro B, Stark M, Wilson J
J Arch Sci 69: 29-38 (2016) pdf

Using ancient DNA and coalescent-based methods to infer extinction
Chang D, Shapiro B
Proc. Natl. Acad. Sci. USA 112: 14301-14306 (2016) pdf

Targeted capture and resequencing of 1040 genes reveal environmentally driven functional variation in grey wolves
Schweizer RM, Robinson J, Harrigan R, Silva P, Galverni M, Musiani M, Green RE, Novembre J, Wayne RK
Molecular Ecology 25: 357-379 (2016) pdf


Life and extinction of megafauna in the ice-age Arctic
Mann DH, Groves P, Reanier RE, Gaglioti BV, Kunz ML, Shapiro B
Proc. Natl. Acad. Sci. USA 112: 14301-14306 (2015) pdf

Genetic relatedness in two-tiered plains zebra societies suggests that females choose to associate with kin
Tong W, Shapiro B, Rubenstein DI
Behavior 152: 2059-2078 (2015) pdf

Mammoth 2.0: will genome engineering resurrect extinct species?
Shapiro B
Genome Biology 16:228; DOI 10.1186/s13059-015-0800-4 (2015) pdf

An ancient bison from the mouth of the Rauchua River, Chukotka, Russia
Kirillova IV, Zamina OG, Chernova OF, Lapteva EG, Trofimova SS, Lebedev VS, Tiunov AV, Soares AER, Shidlovskiy FK, Shapiro B
Quaternary Research 84: 232-245 (2015) pdf

A method for positive forensic identification of samples from extremely low-coverage sequence dat
Vohr SH, Buen Abad Najar CF, Shapiro B, Green RE
BMC Genomics 16:1034 DOI: 10.1186/s12864-015-2241-6(2015) pdf

Time-dependent estimates of molecular evolutionary rates: evidence and causes
Ho SYW, Duchene S, Molak M, Shapiro B
Molecular Ecology 24: 6007-6012 (2015) pdf

Genomic data from extinct North American Camelops revise camel evolutionary history
Heintzman PD, Zazula GD, Cahill JA, Reyes AV, MacPhee RDE, Shapiro B
Molecular Biology and Evolution 32: 2433-2440(2015) pdf

Heintzman PD, Soares AER, Chang D, Shapiro B
Reviews in Cell Biology and Molecular Medicine1: 243-267(2015) pdf

Genome-wide evidence reveals that African and Eurasian Golden Jackals are distinct species
Koepfli K-P, Pollinger J, Godinho R, Robinson J, Lea A, Hendricks S, Schweitzer RM, Thalmann O, Silva P, Fan Z, Yurchenko AA, Dobrynin P, Makunin A, Cahill JA, Shapiro B, Álvares F, Brito JC, Geffen E, Leonard JA, Helgen KM, Johnson WE, O’Brien SJ, Van Valkenburgh B, Wayne RK
Current Biology 17: 2158-2165 (2015) pdf

Pros and cons of methylation-based enrichment methods for ancient DNA
Seguin-Orlando A, Gamba C, DerSarkissian C, Ermini L, Louvel G, Boulygina E, Sokolov A, Nedoluzhko A, Lorenzen E, Lopez P, McDonald HG, Scott E, Tikhonov A, Stafford TW Jr, Shapiro B, WIllerslev E, Prokhortchouk E, Orlando L
Scientific Reports 5: 11826 (2015) pdf

Development: Aneuploidy and mother's genes
Vohr SH, Green RE
Science 348: 180-181 (2015) pdf

Genomic evidence of geographically widespread effect of gene flow from polar bears into brown bears
Cahill JA, Green RE, Kistler L, Salamzade R, Ersmark E, Fulton TL, Stiller M, Shapiro B
Molecular Ecology 24: 1205-1217 (2015) pdf

Post-glacial dispersal of northern pike (Esox cf. lucius) in Eastern Beringia inferred using radiocarbon and ancient DNA results from an 8,800 year old fish skull preserved in Quartz Lake, interior Alaska
Wooller M, Gaglioti B, Fulton TL, Shapiro B
Quaternary Science Reviews 120: 118-125. (2015) pdf

Amplification bias in TruSeq DNA libraries uncovers ancient methylation signatures
Seguin-Orlando A, Hoover C, Vasiliev S, Ovodov ND, Shapiro B, Cooper A, Rubin E, Willerslev E, Orlando L
Science and Technology of Archaeological Research (STAR) 1: 112054892315Y.0000000005 (2015)

Climate impacts on trans-ocean dispersal and habitat in gray whales from the Pleistocene to the year 2100
Alter SE, Meyer M, Post K, Czechowski P, Gravlund P, Gaines C, Rosenbaum HC, Turvey ST van der Plicht H, Shapiro B, Hofreiter M
Molecular Ecology 24: 1510-1522 (2015) pdf

A revised evolutionary history of armadillos (Dasypus) in North America based on ancient DNA
Shapiro B, Graham RD, Letts B
Boreas 44:14-23 (2015) pdf

Empirical calibrated radiocarbon sampler: a tool for incorporating radiocarbon-date and calibration error into Bayesian phylogenetic analyses of ancient DNA
Molak M, Suchard MA, Ho SYW, Beilman D, Shapiro B
Molecular Ecology Resources 15: 81-86 (2015) pdf

The Genome 10K Project: A way forward
Koepfli KP- Paten B, The Genome 10K Community of Scientists*, O’Brien SJ
Annual Review of Animal Biosciences 3: 57-111 (2015) pdf


Prehistoric horse genomes reveal the genetic foundation and cost of domestication
Schubert M*, Jónsson H*, Chang D*, Der Sarkissian C, Emini Km Ginolhac A, Albrechtsen A, Dupanloup Im Foucal A, Petersen B, Raghavan M, Seguin-Orlando A, Korneliussen TF, Velasquez AMV, Stenderup J, Hoover CA, Rubin CJ, Alfarhan AM, Alquaraishi SA, Al-Rasheid KAS, MacHugh DE, Kalbfleish T, MacLeod JN, Rubin EM, Sicheritz-Ponten T, Andersson L, Hofreiter M, Marques-Bonet T, Gilbert MTP, Nielsen R, Excoffier L, Willerslev E, Shapiro B, Orlando L
Proc Natl Acad Sci USA 111: E5661-E5669 (2014) pdf

Three Crocodilian Genomes Reveal Ancestral Patterns of Evolution among Archosaurs
Green RE, Braun EL, Armstrong J, Earl D, Nguyen N, Hickey G, Vandewege MW, St John JA, Capella-Gutiérrez S, Castoe TA, Kern C, Fujita MF, Opazo JC, Jurka J, Kojima KK, Caballero J, Hubley RM, Smit AF, Platt RN, Lavoie CA, Ramakodi MP, Finger JW Jr, Suh A, Isberg SR, Miles L, Chong AY, Jaratlerdsiri W, Gongora J, Moran C, Iriarte A, McCormack J, Burgess SC, Edwards SV, Lyons E, Williams C, Breen M, Howard JT, Gresham CR, Peterson DG, Schmitz J, Pollock DD, Haussler D, Triplett EW, Zhang G, Irie N, Jarvis ED, Brochu CA, Schmidt CJ, McCarthy FM, Faircloth BC, Hoffmann FG, Glenn TC, Gabaldón T, Paten B, Ray DA
Science 346: 1254449 (2014) pdf

Whole Genome Analyses Resolve the Early Branches to the Tree of Life of Modern Birds
Jarvis E, Mirarab S, [31 others], Green RE, [29 others], Shapiro B, [38 others], Jun W, Gilbert MTP, Zhang G
Science 346: 1320-1331 (2014) pdf

Comparative Genomics Reveal Insights into Avian Genome Evolution and Adaptation
Zhang G, Li C, Li Q, Li B, Larkin DM, Lee C, [77 others], Green RE [21 others] and the Avian enome Consortium
Science 346: 1311-1320 (2014) pdf

Multiple Lineages of Ancient Cr1 Retroposons Shaped the Early Genome Evolution of Amniotes
Suh A, Churakov G, Ramakodi MP, Platt RN II, Jurka J, Kojima KK, Caballero J, Smit A, Vliet KA, Hoffmann FG, Brosius J, Green RE, Braun EL, Ray DA, Schmitz J
Genome Biology and Evolution (2014) pdf

Early Mesozoic Coexistence of Amniotes and Hepadnaviridae
Suh A, Weber CC, Kehlmaier C, Braun EL, Green RE, Fritz U, Ray DA, Ellegren H
PLoS Genetics 1004559 (2014) pdf

Preservation of viral genomes in 700-year-old caribou feces from a subarctic ice patch
Ng TFF, Zhou Y, Chen L-F, Shapiro B, Stiller M, Heintzman PD, Varsani A, Kondov NO, Wong W, Deng X, Andrews TD, Moorman BJ, Meulendyk R, MacJay G, Gilbertson RL, Delwart E
Proc Natl Aacd Sci USA 111: 16842-16847 (2014) pdf

Empirical calibrated radiocarbon sampler: a tool for incorporating radiocarbon-date and calibration error into Bayesian phylogenetic analyses of ancient DNA
Molak M, Suchard MA, Ho SYW, Beilman DW, Shapiro B
Molecular Ecology Resources (early view) (2014) pdf

Ancient mitochondrial DNA and the genetic history of Eurasian beavers Castor fiber
Horn S, Prost S, Stiller M, Makowiecki D, Kusnetsova T, Benecke N, Pucher E, Hufthammer AK, Schouwenburg C, Shapiro B, Hofreiter M
Molecular Ecology 23: 1717-1729 (2014) pdf

Shotgun profiling of fossil remains
Der Sarkissian C, Emini L, Jónsson H, Alekseev A, Crubézy E, Shapiro B, Orlando L
Molecular Ecology 23: 1780-1798 (2014) pdf

Revealing the maternal demographic history of Panthera leo using ancient DNA and a spatially explicit genealogical analysis
Barnett R, Yamaguchi N, Shapiro B, Ho, SYW, Barnes I, Burger J, Sabin R, Werdelin L, Cuisin J, Larson G
BMC Evolutionary Biology 14: 80 (2014) pdf

Transoceanic drift and the domestication of African bottle gourds in the Americas
Kistler L, Montenegro A, Smith BD, Gifford JD, Green RE, Newsom LA, Shapiro B
Proc Natl Acad Sci USA 111:2937-2941 (2014) pdf

Brown bear (Ursus arctos) (9880±35 BP) from Lateglacial Champlain Sea deposits of Saint-Nicolas, Québec, Canada, and the dispersal history of bears
Harington CR, Cournoyer M, Chartier M, Fulton TL, Shapiro B
Canadian Journal of Zoology 51: 527-535 (2014) pdf

A paleogenomic perspective on evolution and gene function: New insights from ancient DNA
Shapiro B, Hofreiter M
Science 343: 1236573 (2014) pdf

The complete genome sequence of a Neanderthal from the Altai Mountains
Prüfer K, Racimo F, Patterson N, Jay F, Sankararaman S, Sawyer SK, [19 others] Vohr SH, Green RE, [17 others], Pääbo S
Nature 505: 489-501 (2014) pdf

Ancient hyaenas highlight the old problem of estimating evolutionary rates
Shapiro B, Ho SYW
Molecular Ecology 23: 43-49 (2014) pdf


Complete mitochondrial genomes of ancient canids suggests a European origin of domestic dogs
Thalmann O, Shapiro B, Schuenemann VJ, Sawyer SK, Greenfield DL, Germonpre MB, [22 others], Green RE, Wayne RK
Science 342: 871-874 (2013) pdf

Recalibrating Equus evolution using the genome sequence of an early Middle Pleistocene horse
Orlando L, Ginolhac A, Zhang G, Froese D, Albrechtsen A, Stiller M, [17 others], Cahill J, [29 others], Shapiro B, Wang J, Willerslev E
Nature 499: 74-78 (2013) pdf

Human evolution: turning back the clock
Green RE, Shapiro B
Current Biology 23(7):R268-8 (2013) pdf

Ancient DNA supports southern survival of Richardson's collared lemming (Dicrostonyx richardsoni) during the Last Glacial Maximum
Fulton TL, Norris RW, Graham RE, Semken HA Jr, Shapiro B
Molecular Ecology 22:2540-2548 (2013) pdf

Genomic evidence for island population conversion resolves conflicting theories of polar bear evolution
Cahill JA, Green RE, Fulton TL, Stiller M, Jay F, Ovsyanikov N, Salamzade R, St John J, Stirling I, Slatkin M, Shapiro B
PloS Genetics 9(3):e1003345 (2013) pdf

Mitochondrial phylogenomics of modern and ancient equids
Vilstrup JT, Senguin-Orlando Am Stiller M, Ginolhac A, Raghavan M, Nielsen SCA, Weinstock J Friese D, Vasiliev SK, Ovodov ND, Clary J, Helgen KM, Fleischer RC, Cooper A, Shapiro B, Orlando L
PLoS ONE 8: e55950 (2013)

Improving Bayesian population dynamics inference: a coalescent-based model for multiple loci
Gill MS, Lemey P, Faria NR, Rambuat A, Shapiro B, Suchard M
Molecular Biology and Evolution 30: 253-262 (2013) pdf

Phylogenetic estimation of timescales using ancient DNA: the effects of temporal sampling scheme and uncertainty in sample ages
Molak M, Lorenzen ED, Shapiro B, Ho SYW
Molecular Biology and Evolution 30: 253-262 (2013) pdf

The western painted turtle genome, a model for the evolution of extreme physiological adaptations in a slowly evolving lineage
Abramyan J, Badenhorst D, Biggar KK, Borchert GM, Botka CW, Bowden RM, Braun EL, Bronikowski AM, Bruneau BG, Buck LT, Capel B, Castoe TA, Czerwinski M, Delehaunty KD, Edwards SV, Fronick CC, Fujita MK, Fulton L, Graves TA, Green RE, Haerty W, Hariharan R, Hillier LH, Holloway AK, Janes D, Janzen FJ, Kandoth C, Kong L, de Koning J, Li Y, Literman R, Mardis ER, McGaugh SE, Minx P, Mork L, O 8217 Laughlin M, Paitz RT, Pollock DD, Ponting CP, Radhakrishnan S, Raney BJ, Richman JM, St John J, Schwartz T, Sethuraman A, Shaffer B, Shedlock AM, Spinks PQ, Storey KB, Thane N, Thomson RC, Valenzuela N, Vinar T, Warren DE, Warren WC, Wilson RK, Zimmerman LM, Hernandez O, Amemiya CT.
Genome Biology 14(3):R28 (2013)

A mouse following in the footsteps of human prehistory
Vohr SH, Green RE
Cell 152(4):667-8 (2013) pdf

Comparative population genomics of the ejaculate in humans and the great apes
Good JM, Wiebe V, Albert FW, Burbano HA, Kircher M, Green RE, Halbwax M, André C, Atencia R, Fischer A, Pääbo S
Molecular Biology and Evolution 30(4):964-76 (2013 pdf


A High-Coverage Genome Sequence from an Archaic Denisovan Individual
Meyer M, Kircher M, Gansauge MT, Li H, Racimo F, Mallick S, Schraiber JG, Jay F, Prüfer K, de Filippo C, Sudmant PH, Alkan C, Fu Q, Do R, Rohland N, Tandon A, Siebauer M, Green RE, Bryc K, Briggs AW, Stenzel U, Dabney J, Shendure J, Kitzman J, Hammer MF, Shunkov MV, Derevianko AP, Patterson N, Andrés AM, Eichler EE, Slatkin M, Reich D, Kelso J, Pääbo S
Science 338: 222-226 (2012) pdf

Homotherium and Cervalces from the Great Lakes region, USA: geochronology, morphology and ancient DNA
Widga C, Fulton TL, Martin LD, Shapiro B
Boreas 41: 546-556 (2012) pdf

Partial genetic turnover in Neandertal: continuity in the east and population replacement in the west
Dalén L, Orlando L, Shapiro B, Durling MB, Quam R, Gilbert MTP, Fernández-Lomana JCD, Willerslev E, Arsuaga JL, Götherström A
Molecular Biology and Evolution 29: 1893-1897 (2012) pdf

Pattern of extinction of the woolly mammoth in Beringia
MacDonald GM, Beilman DW. Kuzmin YV, Orlova LA, Kremenetski KV, Shapiro B, Wayne RK, Van Valkenburgh B
Nature Communications 3: 893 (2012)

Analysis of human accelerated DNA regions using archaic hominin genomes
Burbano HA, Green RE, Maricic T, Lalueza-Fox C, de la Rasilla M, Rosas A, Kelso J, Pollard KS, Lachmann M, Pääbo S
PLoS One 7: e32877 (2012)

Sequencing three crocodilian genomes to illuminate the evolution of archosaurs and amniotes
St John JA, Braun EL, Isberg SR, Miles LG, Chong AY, Gongora J, Dalzell P, Moran C, Bed'hom B, Abzhanov A, Burgess SC, Cooksey AM, Castoe TA, Crawford NG, Densmore LD, Drew JC, Edwards SV, Faircloth BC, Fujita MK, Greenwold MJ, Hoffmann FG, Howard JM, Iguchi T, Janes DE, Khan SY, Kohno S, de Koning AJ, Lance SL, McCarthy FM, McCormack JE, Merchant ME, Peterson DG, Pollock DD, Pourmand N, Raney BJ, Roessler KA, Sanford JR, Sawyer RH, Schmidt CJ, Triplett EW, Tuberville TD, Venegas-Anaya M, Howard JT, Jarvis ED, Guillette LJ Jr, Glenn TC, Green RE, Ray DA
Genome Biology 13: 415 (2012)

Nuclear DNA from the extinct passenger pigeon (Ectopistes migratorius) confirms its phylogenetic placement within the Columbinae
Fulton TL, Wagner SM, Fisher C, Shapiro B
Annals of Anatomy 194: 52-57 (2012) pdf

Nuclear Ancient DNA reveals genetic continuity in woodland caribou of the Central Mackenzie Mountains, Northwest Territories, Canada
Letts B, Fulton TL, Stiller M, Andrews T, MacKay G, Popkp R, Shapiro B
Arctic 65 suppl 1: 85-94 (2012) pdf

Improving the performance of true single-molecule sequencing for ancient DNA
Ginolhac A, Vilstrup J, Stenderup J, Rasmussen M, Stiller M, Shapiro B, Zazula G, Froese D, Steinmann KE, Thompson JD, AL-Rasheid KAS, Gilbert MTP, Willerslev E, Orlando L
BMC Genomics 13: 177 (2012)

The origin of the 'Mycoplasma mycoides cluster' coincides with domestication of ruminants
Fischer A, Shapiro B, Muriuki C, Heller M, Schnee C, Bongcam-Rudloff E, Frey J, Jores J
PLoS ONE e36150 (2012)

Multiple losses of flight and recent speciation in steamer ducks
Fulton TL, Letts B, Shapiro B
Proceedings of the Royal Society B 279: 2339-2346 (2012) pdf

Case study: Recovery of ancient nuclear DNA from toe pads of the extinct passenger pigeon
Fulton TL, Wagmer SM, Shapiro B
Methods on Molecular Biology 840: 29-35 (2012) (website)

Case Study: Ancient DNA recovered from Pleistocene-age remains of a Florida armadillo
Letts B, Shapiro B
Methods in Molecular Biology 840: 87-92 (2012) (website)


The earliest evidence for anatomically modern humans in northwestern Europe
Higham T, Compton T, Stringer C, Jacobi R, Shapiro B, Trinkaus E, Chandler B, Gröning F, Collins C, Hillson S, O'Higgins P, Fagan M
Nature 479: 521-524 (2011) pdf

Species-specific responses of Late Quaternary megafauna to climate and humans
Lorenzen ED, Nogues-Bravo D, Orlando L, Weinstock J, Binladen J, Marske KA, 52 additional authors, Shapiro B, Rahbek C, Willerslev E
Nature 479: 359-364 (2011) pdf supplementary materials

True single-molecule ancient DNA sequencing of a Pleistocene horse bone
Orlando L, Ginolhac A, Raghavan M, Vilstrup J, Rasmussen M, Magnussen K, Steinmann K, Kapranov P, Thompson JF, Shapiro B, Zazula G, Froese D, Hofreiter M, Al-Rasheid KAS, Mundy J, Gilbert MTP, Willerslev E
Genome Research 21: 1705-1019 (2011)

Assemblathon 1: a competitive assessment of de novo short read assembly methods
Earl D, Bradnam K, St John J, Darling A, Lin D, Fass J, Yu HO, Buffalo V, Zerbino DR, Diekhans M, Nguyen N, Ariyaratne PN, Sung WK, Ning Z, Haimel M, Simpson JT, Fonseca NA, Birol İ, Docking TR, Ho IY, Rokhsar DS, Chikhi R, Lavenier D, Chapuis G, Naquin D, Maillet N, Schatz MC, Kelley DR, Phillippy AM, Koren S, Yang SP, Wu W, Chou WC, Srivastava A, Shaw TI, Ruby JG, Skewes-Cox P, Betegon M, Dimon MT, Solovyev V, Seledtsov I, Kosarev P, Vorobyev D, Ramirez-Gonzalez R, Leggett R, MacLean D, Xia F, Luo R, Li Z, Xie Y, Liu B, Gnerre S, MacCallum I, Przybylski D, Ribeiro FJ, Yin S, Sharpe T, Hall G, Kersey PJ, Durbin R, Jackman SD, Chapman JA, Huang X, DeRisi JL, Caccamo M, Li Y, Jaffe DB, Green RE, Haussler D, Korf I, Paten B
Genome Research 21: 2224-41 (2011)

Ancient hybridization and a recent Irish origin for the modern polar bear matriline
Edwards CJE, Suchard MA, Lemey P, Welch JJ, Barnes I, Fulton TL, Barnett R, O'Connell TC, Coxon P, Monaghan N, Valdiosera C, Lorenzen ED, Willerslev E, Baryshnikov GF, Rambaut A, Thomas MG, Bradley DG, Shapiro B
Current Biology 21: 1-8 (2011) pdf

The shaping of modern human immune systems by multiregional admixture with archaic humans
Rached L, Jobin MJ, Kulkarni S, McWhinnie A, Dalva K, Gragert L, Babrzadeh F, Gharizadeh B, Luo M, Plummer FA, Kimani J, Carrington M, Middleton D, Rajalingam R, Beksac M, Marsh SG, Maiers M, Guethlein LA, Tavoularis S, Little AM, Green RE, Norman PJ, Parham P
Science 334: 89-94 (2011) pdf

Evolution of a tissue-specific splicing network
Taliaferro JM, Alvarez N, Green RE, Blanchette M, Rio DC
Genes and Development 25: 608-620 (2011)

Targeted resequencing of a genomic region influencing tameness and aggression reveals multiple signals of positive selection
Albert FW, Hodges E, Jensen JD, Bensier F, Xuan Z, Rooks M, Bhattacharjee A, Brizuela L, Good JM, Green RE, Burbano HA, Plyusnina IZ, Trut L, Andersson L, Schöneberg T, Carlborg O, Hannon GJ, Pääbo S
Heredity 107:205 (2011)

The developmental transcriptome of Drosophila melanogaster
Graveley BR, [25 others], Green RE, [19 others], Celniker SE
Nature 471: 473-9 (2011)

Ancient DNA confirms a local origin of domesticated chenopod in Eastern North America
Kistler L, Shapiro B
Journal of Archaeological Science 38: 3459-3554 (2011) pdf

Discovery of lost diversity of paternal horse lineages using ancient DNA
Lippold S, Knapp M, Kuznetsova T, Leonard JA, Benecke N, Ludwig A, Rasmussen M, Weinstock J, Willerslev E, Shapiro B, Hofreiter M
Nature Communications 2:450 (2011)

Population-level genotyping of coat colour polymorphism in woolly mammoth ( Mammuthus primigenius).
Workman C, Dalen L, Vartanyan S, Shapiro B, Kosintev P, Sher A, Gotherstrom A, Barnes I
Quaternary Science Reviews 30: 2304-2308 (2011) pdf

Bayesian estimation of substitution rates from ancient DNA sequences with low information content
Ho SYW, Lanfear R, Phillips MJ, Barnes I, Thomas JA, Kolokotronis S-O, Shapiro B
Systematic Biology 60: 366-375 (2011)

Skyline-plot methods for estimating demographic history from nucleotide sequences
Ho SYW, Shapiro B
Molecular Ecology Resources 11: 423-434 (2011) pdf

Genomic analysis of Hepatitis B Virus reveals antigen state and genotype as source of evolutionary rate variation
Harrison GL, Lemey P, Hurles M, Moyes C, Horn S, Pryor J, Malani J, Supuri M, Masta A, Teriboriki B, Toatu T, Penny D, Rambaut A, Shapiro B
Viruses 3: 83-101 (2011) pdf

A Bayesian phylogenetic method to estimate unknown sequence ages
Shapiro B, Ho SYW, Drummond AJ, Suchard MA, Pybus O, Rambaut A
Molecular Biology and Evolution 28: 879-887 (2011)


Genetic history of an archaic hominin group from Denisova cave in Siberia
Reich D, Green RE*, [25 others], Pääbo S (* co-first author)
Nature 468: 1053-60 (2010)

Genomic DNA sequences from mastodon and woolly mammoth reveal deep speciation of forest and savanna elephants
Rohland N, Reich D, Mallick S, Meyer M, Green RE, Georgiadis NJ, Roca AL, Hofreiter M
PLoS Biology 8: e1000564 (2010)

A draft sequence of the Neandertal genome
Green RE, [55 others], Pääbo S
Science 328: 710-22 (2010) pdf

Computational challenges in the analysis of ancient DNA
Prüfer K, Stenzel U, Hofreiter, Pääbo S, Kelso J, Green RE
Genome Biology 11: R47 (2010)

Targeted investigation of the Neandertal genome by array-based capture
Burbano HA, Hodges E, Green RE, Briggs AW, Krause J, Meyer M, Good JM, Maricic T, Johnson PLF, Xuan Z, Rooks M, Bhattacharjee A, Brizuela L, Albert FW, de la Rasilla M, Fortea J, Rosas A, Lachmann M, Hannon GJ, and Pääbo S
Science 328: 723-5 (2010)

Using time-structured data to estimate evolutionary rates of double-stranded DNA viruses
Firth C, Kitchen A, Shapiro B, Suchard MA, Holmes EC, Rambaut A
Molecular Biology and Evolution 27: 2038-2051 (2010)

The analysis of ancient human genomes: using next generation sequencing, 20-fold coverage of the genome of a 4,000-year-old human from Greenland has been obtained
Shapiro B, Hofreiter M
Bioessays 32: 388-391 (2010) pdf

Modern and ancient DNA reveal recent partial replacement of caribou in the southwest Yukon
Kuhn TS, McFarlane K, Groves P, Moers AO, Shapiro B
Molecular Ecology 9: 1312-1318 (2010) pdf

Ancient DNA analysis excludes humans as the driving force behind late Pleistocene musk ox (Ovibos moschatus) population dynamics
Campos P, Willerslev E, Sher A, Axelsson E, Tikhonov A, Aaris-Sørensen K, Greenwood A, Kahlke R-D, Kosintsev P, Krakhmalnaya T, Kuznetsova T, Lemey P, MacPhee RD, Norris CA, Shepherd K, Suchard MA, Zazula GD, Shapiro B, Gilbert MTP
Proceedings of the National Academy of Sciences USA 107: 5675-5680 (2010) pdf

A complete mitochondrial genome sequence from a mesolithic wild aurochs (Bos primigenius)
Edwards CJ, Magee DA, Park SD, McGettigan PA, Lohan AJ, Murphy A, Finlay EK, Shapiro B, Chamberlain AT, Richards MB, Bradley DG, Loftus BJ, Machugh DE
PLoS ONE (5:e9255 (2010) pdf

Ancient DNA typing of archaeological pig remains corroborates historical records
Haile J, Larson G, Owens K, Dobney K, Shapiro B
Journal of Archaeological Sciences 37:174-177 (2010) pdf

Protocols for sampling viral sequences to study epidemic dynamics
Stack JC, Welch D, Ferrari MJ, Shapiro B, Grenfell BT
Journal of the Royal Society Interface 7: 1119-1127 (2010) pdf


The evolutionary history of the extinct ratite moa and New Zealand Neogene paleogeography
Bunce M, Worthy T, Phillips M, Holdaway R, Willerslev E, Haile J, Shapiro B, Scofield P, Drummond A, Kamp P, Cooper A
Proceedings of the National Academy of Sciences U S A 106: 20646-20651 (2009) pdf

A Late Pleistocene steppe bison (Bison priscus) partial carcass from Tsiigehtchic, Northwest Territories, Canada
Zazula GD, MacKay G, Andrews TD, Shapiro B, Letts B, Brock F
Quaternary Science Reviews 28: 2734-2742 (2009) pdf

Phylogeography of lions (Panthera leo) reveals a Late Pleistocene reduction in genetic diversity
Barnett R, Shapiro B, Ho SYW, Barnes I, Burger J, Yamaguchi N, Higham T, Wheeler HT, Rosendhal W, Sher AV, Baryshnikov G, Cooper A
Molecular Ecology 18: 1668-1677 (2009) pdf

The global spread of Hepatitis C Virus 1a and 1b: a phylodynamic and phylogeographic analysis
Magiorkinis G, Magiorkinis E, Paraskevis D, Ho SYW, Shapiro B, Pybus O, Allain JP, Hatzakis A
PLoS Medicine 6: e1000198 (2009) pdf

The Neandertal genome and ancient DNA authenticity
Green RE, Briggs AW, Krause J, Prüfer K, Burbano HA, Siebauer M, Lachmann M, Pääbo S
EMBO Journal 28: 2494-502 (2009)

Targeted retrieval and analysis of five Neandertal mtDNA genomes
Briggs AW, Good JM, Green RE, Krause J, Maricic T, Stenzel U, Lalueza-Fox C, Rudan P, Brajkovic D, Kucan Z, Gusic I, Schmitz R, Doronichev VB, Golovanova LV, de la Rasilla M, Fortea J, Rosas A, Pääbo S
Science 325: 318-21 (2009)

Genome-wide identification of alternative splice forms down-regulated by nonsense-mediated mRNA decay in Drosophila
Hansen KD, Lareau LF, Blanchette M, Green RE, Meng Q, Rehwinkel J, Gallusser FL, Izaurralde E, Rio DC, Dudoit S, Brenner SE
PLoS Genetics 5: e1000525 (2009)

Genome-wide analysis of alternative pre-mRNA splicing and RNA-binding specificities of the Drosophila hnRNA A/B family members
Blanchette M, Green RE, MacArthur S, Brooks AN, Brenner SE, Eisen MB, Rio DC
Molecular Cell 33: 438-49 (2009)

Is amino acid racemization a useful tool for screening for ancient DNA in bone?
Collins MJ, Penkman KEH, Rohalnd N, Shapiro B, Dobberstein RC, Rotz-Timme A, Hofretier M
Proceedings of the Royal Society of London - Series B 276: 2971-2977 (2009) pdf

The Late Pleistocene distribution of vicuñas (Vicugna vicugna) and the “extinction” of the gracile llama (Lama gracilis): New molecular data
Weinstock J. Shapiro B, Prieto A, Martin JC, Gonzáles BA, Gilbert MPT, Willerslev E
Quaternary Science Reviews 28: 15-16 (2009) pdf

Accommodating the effect of ancient DNA damage on inferences of demographic histories
Rambaut A, Ho SYW, Drummond AJ, Shapiro B
Molecular Biology and Evolution 26: 245-248 (2009) pdf

Mid-Holocene vertebrate bone Concentration-Lagerstätte on oceanic island Mauritius provides a window into the ecosystem of the dodo (Raphus cucullatus)
Rijsdijk KF, Hume JP, Bunnik F, Florens V, Baider C, Shapiro B, van der Plicht J, Janoo A, Griffiths O, van den Hoek Ostende LW, Cremer H, Vernimmen T, De Louw P, Bholah A, Saumtally S, Porch N, Haile J, Buckley M, Collins MC, Gittenberger E
Quaternary Science Reviews 28: 14-24 (2009) pdf

Insights into the evolutionary history of an emerging livestock pathogen: Porcine Circovirus 2
Firth C, Charleston MA, Duffy S, Shapiro B, Holmes EC
Journal of Virology 83: 12813-12821 (2009) pdf

Grevy's zebra conservation: overcoming threats of isolation, genetic hybridization and demographic instability
Cordingly JE, Sundaresan SR, Larison BJ, Shapiro B, Rubenstein DI
Animal Conservation 12: 520-521 (2009) pdf

Is the endangered Grevy's zebra threatened by hybridization?
Cordingly JE, Sundarisan SR, Fischhoff IR, Shapiro B, Ruskey J, Rubenstein DI
Animal Conservation 12: 505-513 (2009) abstract pdf


A complete Neandertal mitochondrial genome sequence determined by high-throughput sequencing
Green RE, Malaspinas AS, Krause J, Briggs AW, Johnson PL, Uhler C, Meyer M, Good JM, Maricic T, Stenzel U, Prüfer K, Siebauer M, Burbano HA, Ronan M, Rothberg JM, Egholm M, Rudan P, Brajković D, Kućan Z, Gusić I, Wikström M, Laakkonen L, Kelso J, Slatkin M, Pääbo S
Cell 134: 416-26 (2008) pdf

PatMaN: rapid alignment of short sequences to large databases
Prüfer K, Stenzel U, Dannemann M, Green RE, Lachmann M, Kelso J
Bioinformatics 24: 1530-1 (2008)

Identification and analysis of genomic regions with large between-population differentiation in humans
Myles S, Tang K, Somel M, Green RE, Kelso J, Stoneking M
Annals of Human Genetics 72(Pt 1): 99-110 (2008)

Engineered polymerases amplify the potential of ancient DNA
Shapiro B
Trends in Biotechnology 26: 285-287 (2008) pdf

Late Pleistocene Northward-dispersing Bison antiquus from the Bighill Creek Formation, Gallelli Gravel Pit, Alberta, Canada, and the Fate of Bison occidentalis
Wilson M, Shapiro B, Hills LV
Canadian Journal of Earth Sciences 45: 827-859 (2008) abstract pdf

Correlating Bayesian date estimates with climatic events and domestication using a bovine case study
Ho SYW, Larson G, Edwards CJ, Heupink TH, Lakin KE, Holland PWH, Shapiro B
Biology Letters 274: 1377-1385 (2008) pdf

The effect of inappropriate calibration in molecular ecological studies: evidence from three case studies
Ho SYW, Saarma U, Barnett R, Haile J, Shapiro B
PLoS ONE 3: e1615 (2008) link pdf

Recovery of DNA from footprints in the snow
Dalén L, Götherström A, Shapiro B
Canadian Field Naturalist 12: 321-324 (2008) pdf

Ancient DNA analysis indicates the first English lions originated from North Africa
Barnett R, Yamaguchi N, Shapiro B, Sabin R
Contributions to Zoology 77: 7-16 (2008) pdf

Comment on "Protein sequences from mastodon and Tyrannosaurus rex revealed by mass spectrometry"
Buckley M, Walker A, Ho SYW, Yang Y, Smith C, Ashton P, Oates JT, Cappellini E, Koon H, Penkman K, Elsworth B, Ashford D, Solazzo C, Andrews P, Strahler J, Shapiro B, Ostrom P, Gandhi H, Miller W, Raney B, Zylber MI, Gilbert MT, Prigodich RV, Ryan M, Rijsdijk KF, Janoo A, Collins MJ
Science 319:33 (2008) abstract pdf supporting material

Multiple independent origins of a protease inhibitor resistance mutation in salvage therapy patients
Kapoor A, Shapiro B, Shafer RW, Rhee S-Y, Delwart EL

Retrovirology 5: 7 (2008) full text


The derived FOXP2 variant of modern humans was shared with Neandertals
Krause J, Lalueza-Fox C, Orlando L, Enard W, Green RE, Burbano HA, Hublin JJ, Hänni C, Fortea J, de la Rasilla M, Bertranpetit J, Rosas A, Pääbo S
Current Biology 17: 1908-12 (2007) pdf

Patterns of damage in genomic DNA sequences from a Neandertal
Briggs AW, Stenzel U, Johnson PL, Green RE, Kelso J, Prüfer K, Meyer M, Krause J, Ronan MT, Lachmann M, Pääbo S
Proceedings of the National Academy of Science U S A. 104: 14616-21 (2007)

The joint allele-frequency spectrum in closely related species
Chen H, Green RE, Pääbo S, Slatkin M
Genetics 177: 387-98 (2007)

Unproductive splicing of SR genes associated with highly conserved and ultraconserved DNA elements
Lareau LF, Inada M, Green RE, Wengrod JC, Brenner SE
Nature 2007 446: 926-9 (2007)

Using ancient DNA techniques to identify the origin of an unprovenanced museum specimen, as illustrated by the identification of a 19th century lion from Amsterdam
Barnett R, Yamaguchi N, Shapiro B, Nijman VB
Contributions to Zoology 76: 87-94 (2007) abstract pdf

Genetic structure and extinction of the woolly mammoth Mammuthus primigenius (Blum.)
Barnes I, Shapiro B, Kuznetsova T, Sher A, Guthrie D, Lister A, Thomas MG
Current Biology 17: 1072-1075 (2007) abstract pdf

Bayesian estimation of sequence damage in ancient DNA
Ho SYW, Heupink, TH, Rambaut, A, Shapiro B
Molecular Biology and Evolution 24:1416-1422 (2007) abstract pdf

Mitochondrial DNA analysis shows a Near Eastern Neolithic origin for domestic cattle and no indication of domestication of European aurochs
Edwards CJ, Bollongino R, Scheu A, Chamberlain A, Tresset A, Vigne J-D, Baird JF, Larson G, Ho SYW, Heupink TH, Shapiro B, Freeman AR, Thomas MG, Arbogast R-M, Arndt B, Bartosiewicz L, Benecke N, Budja M, Chaix L, Choyke AM, Coqueugniot E, Dohle H-J, Goldner H, Hartz S, Helmer D, Herzig B, Hongo H, Mashkour M, Ozdogan M, Pucher E, Roth G, Schade-Lindig S, Schmolcke U, Schulting RJ, Stephan E, Uerpmann H-P, Voros I, Voytek B, Bradley DG, Burger J
Proceedings of the Royal Society B 274: 1377-1385 (2007) abstract pdf

Ancient DNA chronology within sediment deposits: are paleobiological reconstructions possible and is DNA leaching a factor?
Haile J, Holdaway R, Oliver K, Bunce M, Gilbert MTP, Nielsen R, Munch K, Ho, SYW, Shapiro B, Willerslev E
Molecular Biology and Evolution 24: 982-989 (2007) abstract pdf

Estimating the relative contribution of dNTP pool imbalance and APOBEC3G/3F editing to HIV evolution in vivo
Deforche K, Camacho R, Laethem KV, Shapiro B, Moreau Y, Rambaut A, Vandamme A-M, Lemey P
Journal of Computational Biology 14:1105-14 (2007) pdf

Recombination is confounding the early evolutionary history of HIV-1: subtype G is a circulating recombinant form
Abecasis AB, Lemey P, Vidal N, de Oliveira T, Peeters M, Camacho R, Shapiro B, Rambaut A, Vandamme A-M
Journal of Virology 81: 8543-51 (2007) abstract

Ancient papillomavirus-host co-speciation in Felidae
Rector A, Lemey P, Tachezy R, Mostmans S, Ghim S-G, Van Doorslaer K, Roelke M, Bush M, Montali RJ, Joslin J, Burk RD, Jenson AB, Sundberg JP, Shapiro B, Van Ranst M
Genome Biology 8:R57 (2007) full text

Synonymous substitution rates predict HIV disease progression as a result of underlying replication dynamics
Lemey P. Kosakovsky-Pond SL, Drummond AJ, Pybus OG, Shapiro B, Barroso H, Taveira N, Rambaut A
PLoS Computational Biology 3:e29 (2007) full text

Evidence for time dependency of molecular rate estimates
Ho SYW, Shapiro B, Phillips MJ, Cooper A, Drummond AJ
Systematic Biology 56: 515-522 (2007) pdf


Analysis of one million base pairs of Neanderthal DNA
Green RE, Krause J, Ptak SE, Briggs AW, Ronan MT, Simons JF, Du L, Egholm M, Rothberg JM, Paunovic M, Pääbo S
Nature 444: 330-6 (2006)

Functionality of intergenic transcription: an evolutionary comparison
Khaitovich P, Kelso J, Franz H, Visagie J, Giger T, Joerchel S, Petzold E, Green RE, Lachmann M, Pääbo S
PLoS Genetics 2: e171 (2006)

Patterns of nucleotide misincorporations during enzymatic amplification and direct large-scale sequencing of ancient DNA
Stiller M, Green RE, Ronan M, Simons JF, Du L, He W, Egholm M, Rothberg JM, Keates SG, Ovodov ND, Antipina EE, Baryshnikov GF, Kuzmin YV, Vasilevski AA, Wuenschell GE, Termini J, Hofreiter M, Jaenicke-Despres V, Pääbo S
Proceedings of the National Academy of Science U S A. 103:14977 (2006)

No proof that typhoid caused the Plague of Athens
Shapiro B, Rambaut A, Gilbert MTP
International Journal of Infectious Disease 10:334-335 (2006) pdf

Metagenomics to paleogenomics: large scale sequencing of mammoth DNA
Poinar HN, Schwartz C, Qi J, Shapiro B, MacPhee RD, Biogues B, Tikhonov A, Huson D, Tonsho LP, Auch A, Rampp M, Miller W, Schuster SC
Science 311: 392-394 (2006) abstract pdf

A phylogenetic method to detect positive epistasis and its application to RNA virus evolution
Shapiro B, Drummond AJ, Rambaut A, Pybus OJ, Holmes EC
Molecular Biology and Evolution 23: 1724-1730 (2006) full text

Choosing appropriate substitution models for the phylogenetic analysis of protein-coding sequences
Shapiro B, Rambaut A, Drummond AJ
Molecular Biology and Evolution 23: 7-9 (2006) full text


Bayesian coalescent inference of past population dynamics from molecular sequences
Drummond AJ, Pybus OG, Shapiro B, Rambaut A
Molecular Biology and Evolution 22: 1185-1192 (2005) full text

Post-mortem DNA damage hotspots in Bison (Bison bison and B. bonasus) provide supporting evidence for mutational hotspots in human mitochondria
Gilbert MTP, Shapiro B, Drummond A, Cooper A
Journal of Archaeological Sciences 32:1053-1060 (2005) pdf

Ancient DNA provides new insights into the evolutionary history of New Zealand’s extinct giant eagle
Bunce M, Szulkin M, Lerner HRL, Barnes I, Shapiro B, Cooper A, Holdaway RN
PLoS Biology 3(1) e20 (2005) abstract pdf

The transcriptional landscape of the mammalian genome
Carninci P, [53 others], Green RE, [139 others], Hayashizaki Y
Science 309: 1559-63 (2005)

Pairwise alignment incorporating dipeptide covariation
Crooks GE*, Green RE*, Brenner SE (* co-first author)
Bioinformatics 21: 3704-10 (2005)

Statistical evaluation of pairwise protein sequence comparison with the Bayesian bootstrap
Price GA, Crooks GE, Green RE, Brenner SE
Bioinformatics 21: 4318 (2005)

Global analysis of positive and negative pre-mRNA splicing regulators in Drosophila
Blanchette M*, Green RE*, Brenner SE, Rio DC. (* co-first author)
Genes and Development 19: 1306-14 (2005)


Rise and fall of the Beringian steppe bison
Shapiro B, Drummond AJ, Rambaut A, Wilson MC, Matheus P, Sher AV, Pybus OG, Gilbert MTP, Barnes I, Binladen J, Willerslev E, Hansen A, Baryshnikov GF, Burns JA, Davydov S, Driver JC, Froese D, Harington CR, Keddie G, Kosintsev P, Kunz ML, Martin LD, Stephenson RO, Storer J, Tedford R, Zimov S, Cooper A
Science 306: 1561-1565 (2004) abstract pdf

Ancient mitochondrial DNA from hair
Gilbert MTP, Wilson AS, Bunce M, Hansen AJ, Willerslev E, Shapiro B, Higham TFG, Richards MP, O’Connell TC, Tobin DJ, Janaway RC, Cooper A
Current Biology 14: R463-464 (2004) pdf

Genome-wide analysis reveals an unexpected function for the Drosophila splicing factor U2AF50 in the nuclear export of intronless mRNAs
Blanchette M, Labourier E, Green RE, Brenner SE, Rio DC
Molecular Cell 14:775-86 (2004)

The evolving roles of alternative splicing
Lareau LF, Green RE, Bhatnagar RS, Brenner SE
Current Opinion in Structural Biology 14: 273-82. Review. (2004)

An unappreciated role for RNA surveillance
Hillman RT*, Green RE*, Brenner SE. (* co-first author)
Genome Biology 5: R8 (2004)


Beringia as an Ice Age genetic museum
Shapiro B, Cooper A
Quaternary Research 60 (1): 94-100 (2003) pdf

Diverse plant and animal genetic records from Holocene and Pleistocene sediments
Willerslev E, Hansen AJ, Binladen J, Brand TB, Gilbert MTP, Shapiro B, Bunce M, Wiuf C, Gilichinsky DA, Cooper A
Science 300: 791-795 (2003) abstract pdf

Widespread predicted nonsense-mediated mRNA decay of alternatively-spliced transcripts of human normal and disease genes
Green RE, Lewis BP, Hillman RT, Blanchette M, Lareau LF, Garnett AT, Rio DC, Brenner SE
Bioinformatics 19 Suppl 1:i 118-21 (2003)

Evidence for the widespread coupling of alternative splicing and nonsense-mediated mRNA decay in humans
Lewis BP*, Green RE*, Brenner SE. (* co-first author)
Proceedings of the National Academy of Science U S A. 100:189-92 (2003)


Exceptional preservation in bison bones older than 55 ka demonstrated by protein and DNA sequences
Nielsen-Marsh, CM, Ostrom PH, Gandhi H, Shapiro B, Cooper A, Collins MJ

Geology 30: 1099-1102 (2002) pdf

Molecular phylogeny and evolution of the extinct bovid Myotragus balearicus
Lalueza-Fox, C, Shapiro B, Bover P, Alcover JA, Bertranpetit J
Molecular Phylogenetics and Evolution 25 (3): 501-510 (2002) pdf

Flight of the Dodo
Shapiro B, Sibthorpe D, Austin J, Wragg G, Lee PLM, Bininda-Emonds ORP, and Cooper A
Science 295: 1683 (2002) abstract pdf

Dynamics of mammal population extinctions in eastern Beringia during the last glaciation
Barnes I, Matheus P, Shapiro B, Jensen D, Cooper A
Science 295: 2267-2270 (2002) abstract pdf

Sulfotransferases and sulfatases in mycobacteria
Mougous JD, Green RE, Williams SJ, Brenner SE, Bertozzi CR
Chemistry and Biology 9:767-76. Review. (2002)

A genetic algorithm approach to study the evolution of female preference based on male age
Beck CW, Shapiro B, Choksi S, Promislow DEL
Evolutionary Ecology Research 4: 275-292 (2004) pdf


Methylation of the protein phosphatase 2A catalytic subunit is essential for association of Balpha regulatory subunit but not SG2NA, striatin, or polyomavirus middle tumor antigen
Yu XX, Du X, Moreno CS, Green RE, Ogris E, Feng Q, Chou L, McQuoid MJ, Pallas DC
Molecular Biology of the Cell 12:185-99 (2001)


Rainfall and parasitic wasp (Hymenoptera: Ichneumonoidea) activity in successional forest stages at Barro Colorado Nature Monument, Panama and La Selva Biological Station, Costa Rica
Shapiro BA, Pickering J
Agricultural and Forest Entomology 2: 39-47 (2000) pdf


Ancient DNA
Shapiro B
In Losos J, Ed., Princeton Guide to Evolution. Princeton University Press (2013) (pdf)

Natural selection and adaptation of molecular sequences
Pybus OG, Shapiro B
In Lemey P, Salemi M, Vandamme A-M, Eds., The Phylogenetic Handbook: A Practical Approach to Phylogenetic Analysis and Hypothesis Testing (2nd Edition). Cambridge University Press (2009).

Using DNA to investigate human evolution
Shapiro B, Gilbert MTP, Barnes I
In Schutkowski H, Ed., Between Biology and Culture. Cambridge University Press (2008)

Ancient DNA from vertebrate fossils
Barnett R, Shapiro B, Barnes I
In Elias SA, Ed., Encyclopedia of Quaternary Science. Elsevier (2006)


How To Clone A Mammoth: The Science of De-extinction
Shapiro B
Princeton University Press (2015) (website)

Methods in Molecular Biology: Ancient DNA
Shapiro B
Shapiro B, Hofreiter M J, Eds., Springer (2012) (website)





Extracting and characterizing DNA from fossil remains.

Using genome-wide and environmentally-derived data to infer population history and inform management decisions

Investigating patterns and processes in genome evolution.