Rosenberg lab at Stanford University

Online supplements

[1999-2005] [2006-2010] [2011-2015] [2016-2020] [2021] [2022] [2023] [2024]


L Agranat-Tamir, JA Mooney, NA Rosenberg (2024). Counting the genetic ancestors from source populations in members of an admixed population. Genetics 226: iyae011. [Supplement]

DJ Cotter, AL Severson, JTL Kang, HN Godrej, S Carmi, NA Rosenberg (2024) Modeling the effects of consanguinity on autosomal and X-chromosomal runs of homozygosity and identity-by-descent sharing. G3: Genes, Genomes, Genetics 14: jkad264. [Supplement]

E Lappo, NA Rosenberg (2024). Solving the Arizona search problem by imputation. iScience 27: 108831. [Supplement]

X Liu, NM Kopelman, NA Rosenberg (2023) Clumppling: cluster matching and permutation program with integer linear programming. Bioinformatics 40: btad751. [Supplement]


E Lappo, NA Rosenberg, MW Feldman (2023) Cultural transmission of move choice in chess. Proceedings of the Royal Society B: Biological Sciences 290: 37964528. [Supplement]

J Kim, NA Rosenberg (2023) Record-matching of STR profiles with fragmentary genomic SNP data. European Journal of Human Genetics 31: 1283-1290. [Supplement]

ML Morrison, NA Rosenberg (2023) Mathematical bounds on Shannon entropy given the abundance of the ith most abundant taxon. Journal of Mathematical Biology 87: 76. [Supplement]

X Liu, NM Kopelman, NA Rosenberg (2023) A Dirichlet model of alignment cost in mixed-membership unsupervised clustering. Journal of Computational and Graphical Statistics 32: 1145-1159. [Supplement]

JA Mooney, L Agranat-Tamir, JK Pritchard, NA Rosenberg (2023) On the number of genealogical ancestors tracing to the source groups of an admixed population (2023) Genetics 224: iyad079. [Supplement]

DJ Cotter, EF Hofgard, J Novembre, ZA Szpiech, NA Rosenberg (2023) A rarefaction approach for measuring population differences in rare and common variation. Genetics 224: iyad070. [Supplement]


ML Morrison, N Alcala, NA Rosenberg (2022) FSTruct: an FST-based tool for measuring ancestry variation in inference of population structure. Molecular Ecology Resources 22: 2614-2626. [Supplement]

X Liu, NA Rosenberg, G Greenbaum (2022) Extracting hierarchical features of cultural variation using network-based clustering. Evolutionary Human Sciences 4: e18. [Supplement] [Supplementary code] [Supplementary data]

N Alcala, NA Rosenberg (2022) Mathematical constraints on FST: multiallelic markers in arbitrarily many populations. Philosophical Transactions of the Royal Society B: Biological Sciences 377: 20200414. [Supplement]

AL Severson, BF Byrd, EK Mallott, AC Owings, M DeGiorgio, A de Flamingh, C, Nijmeh, MV Arellano, A Leventhal, NA Rosenberg, RS Malhi (2022) Ancient and modern genomics of the Ohlone Indigenous population of California. Proceedings of the National Academy of Sciences USA 119: e2111533119. [Supplement]


J Kim, MD Edge, A Goldberg, NA Rosenberg (2021) Skin deep: the decoupling of genetic admixture levels from phenotypes that differed between source populations. American Journal of Physical Anthropology 175: 406-421 (2021). [Supplement]

G Greenbaum, MW Feldman, NA Rosenberg, J Kim (2021) Designing gene drives to limit spillover to non-target populations. PLoS Genetics 17: e1009278. [Text S1] [Figure S1] [Figure S2] [Figure S3] [Figure S4] [Figure S5] [Figure S6] [Figure S7] [Figure S8] [Figure S9] [Figure S10] [Figure S11] [Figure S12] [Figure S13] [Figure S14]

A Harpak, N Garud, NA Rosenberg, DA Petrov, M Combs, PS Pennings, J Munshi-South (2021) Genetic adaptation in New York City rats. Genome Biology and Evolution 13: evaa247. [Supplement]


J Kim, NA Rosenberg, JA Palacios (2020) Distance metrics for ranked evolutionary trees. Proceedings of the National Academy of Sciences 117: 28876-28886. [Supplement]

AL Fortier, J Kim, NA Rosenberg (2020) Human-genetic ancestry inference and false positives in forensic familial searching. G3: Genes, Genomes, Genetics 18: 2893-2902. [Supplement]

RS Mehta, NA Rosenberg (2020) Modelling anti-vaccine sentiment as a cultural pathogen. Evolutionary Human Sciences 2: e21. [Supplement]

NM Kopelman, L Stone, DG Hernandez, D Gefel, AB Singleton, E Heyer, MW Feldman, J Hillel, NA Rosenberg (2020) High-resolution inference of genetic relationships among Jewish populations. European Journal of Human Genetics 28: 804-814. [Supplement]

NA Rosenberg (2020) Fifty years of Theoretical Population Biology. Theoretical Population Biology 133: 1-12. [Supplement]


G Greenbaum, A Rubin, AR Templeton, NA Rosenberg (2019) Network-based hierarchical population structure analysis for large genomic datasets. Genome Research 29: 2020-2033. [Supplement] [Supplementary Code]

G Greenbaum, WM Getz, NA Rosenberg, MW Feldman, E Hovers, O Kolodny (2019) Disease transmission and introgression can explain the long-lasting contact zone of modern humans and Neanderthals. Nature Communications 10: 5003. [Supplement]

N Alcala, A Goldberg, U Ramakrishnan, NA Rosenberg (2019) Coalescent theory of migration network motifs. Molecular Biology and Evolution 36: 2358-2374. [Supplement]

RS Mehta, AF Feder, SM Boca, NA Rosenberg (2019) The relationship between haplotype-based FST and haplotype length. Genetics 213: 281-295. [Supplementary Figure 1] [Supplementary Figure 2] [Supplementary Figure 3] [Supplementary Figure 4]

AL Severson*, LH Uricchio*, IM Arbisser*, EC Glassberg, NA Rosenberg (2019) Analysis of author gender in TPB, 1991-2018. Theoretical Population Biology 127: 1-6. [Supplement]

N Alcala, AE Launer, MF Westphal, R Seymour, EM Cole*, NA Rosenberg* (2019) Use of stochastic patch occupancy models in the California red-legged frog for Bayesian inference regarding past events and future persistence. Conservation Biology 33: 685-696. [Supplement]

N Alcala, NA Rosenberg (2019) G'ST, Jost's D, and FST are similarly constrained by allele frequencies: a mathematical, simulation, and empirical study. Molecular Ecology 28: 1624-1636. [Supplement]

J Kim, F Disanto, NM Kopelman, NA Rosenberg (2019) Mathematical and simulation-based analysis of the behavior of admixed taxa in the neighbor-joining algorithm. Bulletin of Mathematical Biology 81: 452-493. [Supplement]


J Kim, MD Edge, BFB Algee-Hewitt, JZ Li, NA Rosenberg (2018) Statistical detection of relatives typed with disjoint forensic and biomedical loci. Cell 175: 848-858. [Supplement]

TJ Pemberton*, P Verdu*, NS Becker, CJ Willer, BS Hewlett, S Le Bomin, A Froment, NA Rosenberg, E Heyer (2018) A genome scan for genes underlying adult body size differences between Central African hunter-gatherers and farmers. Human Genetics 137: 487-509. [Supplement]


P Verdu*, EM Jewett*, TJ Pemberton, NA Rosenberg, M Baptista (2017) Parallel trajectories of genetic and linguistic admixture in a genetically admixed creole population. Current Biology 27: 2529-2535. [Supplement]

OK Kamneva, J Syring, A Liston, NA Rosenberg (2017) Evaluating allopolyploid origins in strawberries (Fragaria) using haplotypes generated from target capture sequencing. BMC Evolutionary Biology 17: 180. [File S1 Table S1] [File S2 Sequences] [File S3 Table S2] [File S4 Figures S1-S11] [File S5 Table S3] [File S6 R code]

N Alcala, NA Rosenberg (2017) Mathematical constraints on FST: biallelic markers in arbitrarily many populations. Genetics 206: 1581-1600. [File S1] [File S2]

MD Edge, BFB Algee-Hewitt, TJ Pemberton, JZ Li, NA Rosenberg (2017) Linkage disequilibrium matches forensic genetic records to disjoint genomic marker sets. Proceedings of the National Academy of Sciences USA 114: 5671-5676. [Supplement]

A Goldberg, T Günther, NA Rosenberg, M Jakobsson (2017) Ancient X chromosomes reveal contrasting sex bias in Neolithic and Bronze Age migrations. Proceedings of the National Academy of Sciences USA 114: 2657-2662. [Supplement]

OK Kamneva, NA Rosenberg (2017) Simulation-based evaluation of hybridization network reconstruction methods in the presence of incomplete lineage sorting. Evolutionary Bioinformatics 13: 1176934317691935. [Supplement]


RS Mehta, D Bryant, NA Rosenberg (2016) The probability of monophyly of a sample of gene lineages on a species tree. Proceedings of the National Academy of Sciences USA 113: 8002-8009. [Supplement]

T Stadler, JH Degnan, NA Rosenberg (2016) Does gene tree discordance explain the mismatch between macroevolutionary models and empirical patterns of tree shape and branching times? Systematic Biology 65: 628-639. [Supplement]

BFB Algee-Hewitt*, MD Edge*, J Kim, JZ Li, NA Rosenberg (2016) Individual identifiability predicts population identifiability in forensic microsatellite markers. Current Biology 26: 935-942. [Supplement]


R Ronen*, G Tesler*, A Akbari*, S Zakov, NA Rosenberg, V Bafna (2015) Predicting carriers of ongoing selective sweeps without knowledge of the favored allele. PLoS Genetics 11: e1005527. [Fig S1] [Fig S2] [Fig S3] [Fig S4] [Fig S5] [Fig S6] [Fig S7] [Fig S8] [Fig S9] [Fig S10] [Fig S11] [Fig S12] [Fig S13] [Fig S14] [Fig S15] [Table S1] [Text S1] [Source code]

NA Rosenberg, JTL Kang (2015) Genetic diversity and societally important disparities. Genetics 201: 1-12. [Supplement]

NM Kopelman, J Mayzel, M Jakobsson, NA Rosenberg, I Mayrose (2015) CLUMPAK: a program for identifying clustering modes and packaging population structure inferences across K. Molecular Ecology Resources 15: 1179-1191. [Supplement]

N Creanza, M Ruhlen, T Pemberton, NA Rosenberg, MW Feldman, S Ramachandran (2015) Comparison of worldwide phonemic and genetic variation in human populations. Proceedings of the National Academy of Sciences USA 112: 1265-1272. [Supplementary Appendix] [Supplementary Data S1] [Supplementary Data S2] [Supplementary Data S3]


P Verdu, TJ Pemberton, R Laurent, BM Kemp, A Gonzalez-Oliver, C Gorodezky, CE Hughes, MR Shattuck, B Petzelt, J Mitchell, H Harry, T William, R Worl, JS Cybulski, NA Rosenberg, RS Malhi (2014) Patterns of admixture and population structure in native populations of northwest North America. PLoS Genetics 10: e1004530. [Supplementary Figure 1 (.tif)] [Supplementary Figure 2 (.tif)] [Supplementary Figure 3 (.tif)] [Supplementary Figure 4 (.tif)] [Supplementary Figure 5 (.tif)] [Supplementary Figure 6 (.tif)] [Supplementary Figure 7 (.tif)] [Supplementary Figure 8 (.tif)] [Supplementary Figure 9 (.tif)] [Supplementary Figure 10 (.tif)] [Supplementary Table 1 (.docx)] [Supplementary Table 2 (.txt)]

TJ Pemberton, NA Rosenberg (2014) Population-genetic influences on genomic estimates of the inbreeding coefficient: a global perspective. Human Heredity 77: 37-48. [Supplementary Figure 1] [Supplementary Figure 2] [Supplementary Table 1] [Supplementary Table 2] [Supplementary Table 3]

M DeGiorgio, J Syring, AJ Eckert, AI Liston, R Cronn, DB Neale, NA Rosenberg (2014) An empirical evaluation of two-stage species tree inference strategies using a multilocus dataset from North American pines. BMC Evolutionary Biology 14: 67. [Supplementary File 1 (.xlsx, accession numbers)] [Supplementary File 2 (.pdf, supplementary analyses)] [Supplementary File 3 (.zip, data)]


ZA Szpiech, J Xu, TJ Pemberton, W Peng, S Zöllner, NA Rosenberg, JZ Li (2013) Long runs of homozygosity are enriched for deleterious variation. American Journal of Human Genetics 93: 90-102. [Supplement]

TJ Pemberton, M DeGiorgio, NA Rosenberg (2013) Population structure in a comprehensive data set on human microsatellite variation. G3: Genes, Genomes, Genetics 3: 891-907. [Supplement] [Data (.zip) - File S1]


C Wang, KB Schroeder, NA Rosenberg (2012) A maximum-likelihood method to correct for allelic dropout in microsatellite data with no replicate genotypes. Genetics 192: 651-669. [Supplement]

C Wang, S Zöllner, NA Rosenberg (2012) A quantitative comparison of the similarity between genes and geography in worldwide human populations. PLoS Genetics 8: e1002886. [Supplement]

TJ Pemberton, F-Y Li, EK Hanson, NU Mehta, S Choi, J Ballantyne, JW Belmont, NA Rosenberg, C Tyler-Smith, PI Patel (2012) Impact of restricted marital practices on genetic variation in an endogamous Gujarati group. American Journal of Physical Anthropology 149: 92-103. [Supplement (.docx)]

TJ Pemberton, D Absher, MW Feldman, RM Myers, NA Rosenberg, JZ Li (2012) Genomic patterns of homozygosity in worldwide human populations. American Journal of Human Genetics 91: 275-292. [Main Supplement] [Supplementary Table 2 (.zip)] [Supplementary Table 3 (.zip)] [Supplementary Table 4 (.zip)] [Supplementary Table 5 (.zip)]

D Bryant, R Bouckaert, J Felsenstein, NA Rosenberg, A RoyChoudhury (2012) Inferring species trees directly from biallelic genetic markers: bypassing gene trees in a full coalescent analysis. Molecular Biology and Evolution 29: 1917-1932. [Supplement]


L Huang*, M Jakobsson*, TJ Pemberton, M Ibrahim, T Nyambo, S Omar, JK Pritchard, SA Tishkoff, NA Rosenberg (2011) Haplotype variation and genotype imputation in African populations. Genetic Epidemiology 35: 766-780. [Supplement]

P Verdu, NA Rosenberg (2011) A general mechanistic model for admixture histories of hybrid populations. Genetics 189: 1413-1426. [Supplementary Text] [Supplementary Figure 1] [Supplementary Table 1]

S Ramachandran, NA Rosenberg (2011) A test of the influence of continental axes of orientation on patterns of human gene flow. American Journal of Physical Anthropology 146: 515-529. [Supplementary Figure 1] [Supplementary Figure 2] [Supplementary Tables]


TJ Pemberton, C Wang, JZ Li, NA Rosenberg (2010) Inference of unexpected genetic relatedness among individuals in HapMap Phase III. American Journal of Human Genetics 87: 457-464. [Supplement]

E Borràs*, M Pineda*, I Blanco, EM Jewett, F Wang, A Teulé, T Caldés, M Urioste, C Martínez-Bouzas, J Brunet, J Balmaña, A Torres, T Ramón y Cajal, J Sanz, L Pérez-Cabornero, S Castellví-Bel, A Alonso, A Lanas, S González, V Moreno, SB Gruber, NA Rosenberg, B Mukherjee, C Lázaro, G Capellá (2010) MLH1 founder mutations with moderate penetrance in Spanish Lynch syndrome families. Cancer Research 70: 7379-7391. [Supplementary Figure 1] [Supplementary Table 1] [Supplementary Table 2] [Supplementary Methods]

JT Mosher, TJ Pemberton, K Harter, C Wang, EO Buzbas, P Dvorak, C Simon, SJ Morrison, NA Rosenberg (2010) Lack of population diversity in commonly used human embryonic stem-cell lines. New England Journal of Medicine 362: 183-185. [Supplement]


TJ Pemberton, CI Sandefur, M Jakobsson, NA Rosenberg (2009) Sequence determinants of human microsatellite variability. BMC Genomics 10: 612. [Supplementary table 1 (XLS)] [Supplementary table 1 (TXT)] [Supplementary table 2 (XLS)] [Supplementary table 2 (TXT)] [Supplementary tables 3-6 (PDF)]

L Huang, C Wang, NA Rosenberg (2009) The relationship between imputation error and statistical power in genetic association studies in diverse populations. American Journal of Human Genetics 85: 692-698. [Supplement]

M DeGiorgio, M Jakobsson, NA Rosenberg (2009) Explaining worldwide patterns of human genetic variation using a coalescent-based serial founder model of migration outward from Africa. Proceedings of the National Academy of Sciences USA 106: 16057-16062. [Supplement]

JH Degnan, NA Rosenberg (2009) Gene tree discordance, phylogenetic inference, and the multispecies coalescent. Trends in Ecology and Evolution 24: 332-340. [Supplement]

KB Schroeder, M Jakobsson, MH Crawford, TG Schurr, SM Boca, DF Conrad, RY Tito, LP Osipova, LA Tarskaia, SI Zhadanov, JD Wall, JK Pritchard, RS Malhi, DG Smith, NA Rosenberg (2009) Haplotypic background of a private allele at high frequency in the Americas. Molecular Biology and Evolution 26: 995-1016. [Supplement]

L Huang, Y Li, AB Singleton, JA Hardy, G Abecasis, NA Rosenberg, P Scheet (2009) Genotype-imputation accuracy across worldwide human populations. American Journal of Human Genetics 84: 235-250. [Supplement]


O François, MGB Blum, M Jakobsson, NA Rosenberg (2008) Demographic history of European populations of Arabidopsis thaliana. PLoS Genetics 4: e1000075. [Supplement]

NA Rosenberg, R Tao (2008) Discordance of species trees with their most likely gene trees: the case of five taxa. Systematic Biology 57: 131-140. [Supplement]

M Jakobsson*, SW Scholz*, P Scheet*, JR Gibbs, JM VanLiere, H-C Fung, ZA Szpiech, JH Degnan, K Wang, R Guerreiro, JM Bras, JC Schymick, DG Hernandez, BJ Traynor, J Simon-Sanchez, M Matarin, A Britton, J van de Leemput, I Rafferty, M Bucan, HM Cann, JA Hardy, NA Rosenberg, AB Singleton (2008) Genotype, haplotype and copy-number variation in worldwide human populations. Nature 451: 998-1003. [Supplement]


S Wang*, CM Lewis Jr*, M Jakobsson*, S Ramachandran, N Ray, G Bedoya, W Rojas, MV Parra, JA Molina, C Gallo, G Mazzotti, G Poletti, K Hill, AM Hurtado, D Labuda, W Klitz, R Barrantes, MC Bortolini, FM Salzano, ML Petzl-Erler, LT Tsuneto, E Llop, F Rothhammer, L Excoffier, MW Feldman, NA Rosenberg, A Ruiz-Linares (2007) Genetic variation and population structure in Native Americans. PLoS Genetics 3: 2049-2067. [Supplement]

KB Schroeder, TG Schurr, JC Long, NA Rosenberg, MH Crawford, LA Tarskaia, LP Osipova, SI Zhadanov, DG Smith (2007). A private allele ubiquitous in the Americas. Biology Letters 3: 218-223. [Supplement]


NA Rosenberg, S Mahajan, C Gonzalez-Quevedo, MGB Blum, L Nino-Rosales, V Ninis, P Das, M Hegde, L Molinari, G Zapata, JL Weber, JW Belmont, PI Patel (2006) Low levels of genetic divergence across geographically and linguistically diverse populations from India. PLoS Genetics 2: 2052-2061. [Supplement (DOC)] [Supplement (PDF)]

DF Conrad*, M Jakobsson*, G Coop*, X Wen, JD Wall, NA Rosenberg, JK Pritchard (2006) A worldwide survey of haplotype variation and linkage disequilibrium in the human genome. Nature Genetics 38: 1251-1260. [Supplement (methods, note, and figures)] [Supplementary Table 1]

NA Rosenberg (2006) Standardized subsets of the HGDP-CEPH Human Genome Diversity Cell Line Panel, accounting for atypical and duplicated samples and pairs of close relatives. Annals of Human Genetics 70: 841-847. [Supplement]


S Ramachandran, O Deshpande, CC Roseman, NA Rosenberg, MW Feldman, LL Cavalli-Sforza (2005) Support from the relationship of genetic and geographic distance in human populations for a serial founder effect originating in Africa. Proceedings of the National Academy of Sciences USA 102: 15942-15947. [Supplementary Figure 6] [Supplementary Table 2] [Supplementary text]


NA Rosenberg, LM Li, R Ward, JK Pritchard (2003) Informativeness of genetic markers for inference of ancestry. American Journal of Human Genetics 73: 1402-1422. [Supplement]


NA Rosenberg, JK Pritchard, JL Weber, HM Cann, KK Kidd, LA Zhivotovsky, MW Feldman (2002) Genetic structure of human populations. Science 298: 2381-2385. [Supplement]