Rosenberg lab - research

Research

Our research is in the general fields of evolutionary biology, human genetics, and population genetics. We utilize mathematical theory, computer simulation, and statistical methods to address problems in these fields. We also engage in the development and implementation of new algorithms and statistical approaches.

Read about some of the specific areas of theory under active research in the lab...

Examine a classification of our published articles by subtopic...

Some research themes of particular current interest

Within the collection of major research interests of the group, these topics list a set of more specific themes that have considerable current emphasis (June 2023). The theory research page describes a number of these topics in more detail. Trainees interested in joining the lab are encouraged to focus their interest on one or more of these areas.

Consanguinity, inbreeding, and runs of homozygosity
[Rosenberg et al. (2013)] [Szpiech et al. (2013)] [Pemberton & Rosenberg (2014)] [Kang et al. (2016)] [Severson et al. (2019)] [Severson et al. (2021)] [Cotter et al. (2021)] [Cotter et al. (2022)] [Cotter et al. (2024)]
Cultural evolution and genes & languages
[Creanza et al. (2015)] [Verdu et al. (2017)] [Mehta & Rosenberg (2020)] [Liu et al. (2022)] [Laurent et al. (2023)] [Lappo et al. (2023)]
Design of imputation and sequencing studies
[Huang et al. (2013)] [Zhang et al. (2013)] [Kang et al. (2015)] [Edge et al. (2017)] [Kim et al. (2018)] [Cotter et al. (2023)] [Lappo & Rosenberg (2024b)]
Discrete combinatorial structures in mathematical phylogenetics
[Rosenberg (2013)] [Disanto & Rosenberg (2014)] [Disanto & Rosenberg (2015)] [Mehta et al. (2016)] [Disanto & Rosenberg (2016)] [Disanto & Rosenberg (2017)] [Rosenberg (2019)] [Disanto & Rosenberg (2019a)] [Disanto & Rosenberg (2019b)] [Mehta & Rosenberg (2019)] [Himwich & Rosenberg (2020)] [Kim, Rosenberg & Palacios (2020)] [Rosenberg (2021)] [Alimpiev & Rosenberg (2021)] [King & Rosenberg (2021)] [Palacios et al. (2022)] [Mehta et al. (2022)] [Disanto et al. (2022)] [Mathur & Rosenberg (2023)] [King & Rosenberg (2023) [Disanto et al. (2024)] [Maranca & Rosenberg (2024)] [Lappo & Rosenberg (2024)] [Agranat-Tamir et al. (2024a)] [Doboli et al. (2024)] [Agranat-Tamir et al. (2024c)]
Gene tree evolution on species trees
[Rosenberg (2013)] [DeGiorgio & Rosenberg (2016)] [Stadler et al. (2016)] [Mehta et al. (2016)] [Mehta & Rosenberg (2019)] [Kim, Rosenberg & Degnan (2020)] [Mehta et al. (2022)]
Genetics of Native American populations
[Verdu et al. (2014)] [Severson et al. (2022)]
Human genetic variation problems closely connected to topics of social significance
[Rosenberg et al. (2013)] [Edge & Rosenberg (2015)] [Rosenberg & Kang (2015)] [Algee-Hewitt et al. (2016)] [Edge et al. (2017)] [Kim et al. (2018)] [Rosenberg et al. (2019)] [Mehta & Rosenberg (2020)] [Fortier et al. (2020)] [Edge et al. (2022)] [Cotter et al. (2023)] [Mooney et al. (2023)] [Kim & Rosenberg (2023)] [Lappo & Rosenberg (2024b)] [Agranat-Tamir et al. (2024b)]
Mathematical bounds on population-genetic statistics
[Jakobsson et al. (2013)] [Edge & Rosenberg (2014)] [Garud & Rosenberg (2015)] [Alcala & Rosenberg (2017)] [Aw & Rosenberg (2018)] [Alcala & Rosenberg (2019)] [Mehta et al. (2019)] [Kang & Rosenberg (2019)] [Rosenberg & Zulman (2020)] [Arbisser & Rosenberg (2020)] [Boca et al. (2020)] [Alcala & Rosenberg (2022)] [Morrison et al. (2022)] [Morrison & Rosenberg (2023)] [Liu et al. (2023b)] [Gress & Rosenberg (2024)]
Models for unsupervised clustering
[Morrison et al. (2022)] [Liu et al. (2023)] [Liu et al. (2024)]
Population-genetic models of admixture
[Kopelman et al. (2013)] [Goldberg et al. (2014)] [Goldberg & Rosenberg (2015)] [Rosenberg (2016)] [Goldberg et al. (2017)] [Goldberg et al. (2020)] [Boca et al. (2020)] [Kim et al. (2021)] [Laurent et al. (2023)] [Mooney et al. (2023)] [Agranat-Tamir et al. (2024b)]
Population genetics in the forensic DNA testing context
[Algee-Hewitt et al. (2016)] [Edge et al. (2017)] [Kim et al. (2018)] [Fortier et al. (2020)] [Kim & Rosenberg (2023)] [Lappo & Rosenberg (2024b)]
Population structure and genotype-phenotype relationships
[Edge & Rosenberg (2015a)] [Edge & Rosenberg (2015b)] [Rosenberg (2018)] [Rosenberg et al. (2019)]
Species tree and network inference from gene trees
[DeGiorgio et al. (2014)] [DeGiorgio & Rosenberg (2016)] [Uricchio et al. (2016)] [Kamneva & Rosenberg (2017)] [Kamneva et al. (2017)] [Kim, Rosenberg & Degnan (2020)]

Major research directions

Mathematical models in population genetics [articles] [entry point: theory research site]
We are interested in mathematical population genetics and in understanding how the various forces of evolution influence patterns of genetic variation. A particular focus is on population-genetic theory for species that have diverged recently enough to generate discordant gene trees. We are interested in how mathematical theory enables predictions about population-genetic data and how it can therefore aid in the development of statistical methods for analyzing these data.

Gene trees and species trees [articles] [entry point: Degnan & Rosenberg (2009) review]
For closely related species, the evolutionary history of an individual gene need not reflect the history of species divergences. Partly because of this phenomenon of gene tree discordance, phylogenies reconstructed from different parts of a genome can suggest different relationships among the various species examined. We are developing theory that makes predictions about gene tree discordance, and we are also devising statistical methods for phylogenetic inference in closely related species.

Human variation and inference of human evolutionary history from genetic markers [articles] [entry point: Rosenberg (2011) review, republished in 2020 with a new foreword]
The genomes of individuals in a species record features of the history of the species. We are interested in understanding the geographic distribution of human genetic variation and in devising and applying statistical methods that use this variation to make inferences about human evolutionary history. We are broadly interested in the properties of statistical methods for analyzing genetic variation and in inferring genetic history, both from human data and from various other organisms.

The relationship of human population genetics to the search for disease-susceptibility genes [articles] [entry point: Rosenberg et al. (2010) review; Edge et al. (2013) review]
The pattern of variation of a genetic marker in diseased and non-diseased individuals can potentially be used to identify a disease association with the marker. However, the history of the human population can affect the strength of the signal of association between markers and disease, as well as the replicability of observed associations across studies. We are designing statistical methods for genetic mapping that take population-genetic factors into account in order to advance the prospects for locating disease-susceptibility genes.

Mathematical models in population genetics

L Agranat-Tamir, JA Mooney, NA Rosenberg (2024) Counting the genetic ancestors from source populations in members of an admixed population. Genetics 226: iyae011. [Abstract] [PDF] [Supplement]
L Agranat-Tamir, S Mathur, NA Rosenberg (2024) Enumeration of rooted binary unlabeled galled trees. Bulletin of Mathematical Biology 86: 45. [Abstract] [PDF]
TD Gress, NA Rosenberg (2024) Mathematical constraints on a family of biodiversity measures via connections with Rényi entropy. BioSystems 237: 105153. [Abstract]
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. [Abstract] [PDF] [Supplement]
X Liu, NM Kopelman, NA Rosenberg (2024) Clumppling: cluster matching and permutation program with integer linear programming. Bioinformatics 40: btad751. [Abstract] [PDF] [Supplement]
MC King, NA Rosenberg (2023) A mathematical connection between single-elimination sports tournaments and evolutionary trees. Mathematics Magazine 96: 484-497. [Abstract] [PDF]
X Liu, Z Ahsan, TK Martheswaran, NA Rosenberg (2023) When is the allele-sharing dissimilarity between two populations exceeded by the allele-sharing dissimilarity of a population with itself? Statistical Applications in Genetics and Molecular Biology 22: 2023004. [Abstract] [PDF]
E Lappo, NA Rosenberg, MW Feldman (2023) Cultural transmission of move choice in chess. Proceedings of the Royal Society B: Biological Sciences 290: 37964528. [Abstract] [PDF] [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. [Abstract] [PDF] [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. [Abstract] [PDF] [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. Genetics 224: iyad079. [Abstract] [PDF] [Supplement]
S Mathur, NA Rosenberg (2023) All galls are divided into three or more parts: recursive enumeration of labeled histories for galled trees. Algorithms for Molecular Biology 18:1. [Abstract] [PDF]
F Disanto, M Fuchs, AR Paningbatan, NA Rosenberg (2022) The distributions under two species-tree models of the number of root ancestral configurations for matching gene trees and species trees. Annals of Applied Probability 32: 4426-4458. [Abstract] [PDF]
E Lappo, NA Rosenberg (2022) Approximations to the expectations and variances of ratios of tree properties under the coalescent. G3: Genes, Genomes, Genetics 12: jkac205. [Abstract] [PDF]
ML Morrison, N Alcala, NA Rosenberg (2022) FSTruct: an F_ST-based tool for measuring ancestry variation in inference of population structure. Molecular Ecology Resources 22: 2614-2626. [Abstract] [PDF] [Supplement]
DJ Cotter, AL Severson, S Carmi, NA Rosenberg (2022) Limiting distribution of X-chromosomal coalescence times under first-cousin consanguineous mating. Theoretical Population Biology 147: 1-15. [Abstract]
N Alcala, NA Rosenberg (2022) Mathematical constraints on F_ST: multiallelic markers in arbitrarily many populations. Philosophical Transactions of the Royal Society B: Biological Sciences 377: 20200414. [Abstract] [PDF] [Supplement]
E Alimpiev, NA Rosenberg (2022) A compendium of covariances and correlation coefficients of coalescent tree properties. Theoretical Population Biology 143: 1-13. [Abstract ] [PDF]
DJ Cotter, AL Severson, NA Rosenberg The effect of consanguinity on coalescence times on the X chromosome. Theoretical Population Biology 140: 32-43 (2021). [Abstract]
AL Severson, S Carmi, NA Rosenberg (2021) Variance and limiting distribution of coalescence times in a diploid model of a consanguineous population. Theoretical Population Biology 139: 50-65. [Abstract ]
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). [Abstract]
G Greenbaum, MW Feldman, NA Rosenberg, J Kim (2021) Designing gene drives to limit spillover to non-target populations. PLoS Genetics 17: e1009278. [Abstract] [PDF] [Supplement]
SM Boca, L Huang, NA Rosenberg (2020) On the heterozygosity of an admixed population. Journal of Mathematical Biology 81: 1217-1250. [Abstract]
A Goldberg, A Rastogi, NA Rosenberg (2020) Assortative mating by population of origin in a mechanistic model of admixture. Theoretical Population Biology 134: 129-146. [Abstract]
RS Mehta, NA Rosenberg (2020) Modelling anti-vaccine sentiment as a cultural pathogen. Evolutionary Human Sciences 2: e21. [Abstract] [PDF] [Supplement]
IM Arbisser, NA Rosenberg (2020) F_ST and the triangle inequality for biallelic markers. Theoretical Population Biology 133: 117-129. [Abstract]
NA Rosenberg, DM Zulman (2020) Measures of care fragmentation: mathematical insights from population genetics. Health Services Research 55: 318-327. [Abstract]
JTL Kang, NA Rosenberg (2019) Mathematical properties of linkage disequilibrium statistics defined by normalization of the coefficient D=p_AB-p_Ap_B. Human Heredity 84: 127-143. [Abstract] [PDF]
G Greenbaum, A Rubin, AR Templeton, NA Rosenberg (2019) Network-based hierarchical population structure analysis for large genomic datasets. Genome Research 29: 2020-2033. [Abstract] [PDF] [Supplement]
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. [Abstract] [PDF] [Supplement]
RS Mehta, NA Rosenberg (2019) The probability of reciprocal monophyly of gene lineages in three and four species. Theoretical Population Biology 129: 133-147. [Abstract] [PDF]
N Alcala, A Goldberg, U Ramakrishnan, NA Rosenberg (2019) Coalescent theory of migration network motifs. Molecular Biology and Evolution 36: 2358-2374. [Abstract] [PDF] [Supplement]
RS Mehta, AF Feder, SM Boca, NA Rosenberg (2019) The relationship between haplotype-based F_ST and haplotype length. Genetics 213: 281-295. [Abstract] [PDF] [Supplementary Figure 1] [Supplementary Figure 2] [Supplementary Figure 3] [Supplementary Figure 4]
AL Severson, S Carmi, NA Rosenberg (2019) The effect of consanguinity on between-individual identity-by-descent sharing. Genetics 212: 305-316. [Abstract] [PDF]
N Alcala, NA Rosenberg (2019) G^'_ST, Jost's D, and F_ST are similarly constrained by allele frequencies: a mathematical, simulation, and empirical study. Molecular Ecology 28: 1624-1636. [Abstract] [PDF] [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. [Abstract] [PDF] [Supplement]
AJ Aw, NA Rosenberg (2018) Bounding measures of genetic similarity and diversity using majorization. Journal of Mathematical Biology 77: 711-737. [Abstract] [PDF]
NA Rosenberg (2018) Variance-partitioning and classification in human population genetics. In RG Winther, ed. Phylogenetic Inference, Selection Theory, and History of Science: Selected Papers of A. W. F. Edwards with Commentaries, pp. 399-403. Cambridge: Cambridge University Press. [PDF]
IM Arbisser, EM Jewett, NA Rosenberg (2018) On the joint distribution of tree height and tree length under the coalescent. Theoretical Population Biology 122: 46-56. [Abstract] [PDF]
N Alcala, NA Rosenberg (2017) Mathematical constraints on F_ST: biallelic markers in arbitrarily many populations. Genetics 206: 1581-1600. [Abstract] [PDF] [File S1] [File S2]
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. [Abstract] [PDF] [Supplement] [Software]
NA Rosenberg (2016) Admixture models and the breeding systems of H. S. Jennings: a GENETICS connection. Genetics 202: 9-13. [PDF]
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. [Abstract] [PDF] [Supplement]
A Goldberg, NA Rosenberg (2015) Beyond 2/3 and 1/3: the complex signatures of sex-biased admixture on the X chromosome. Genetics 201: 263-279. [Abstract] [PDF]
MD Edge, NA Rosenberg (2015) Implications of the apportionment of human genetic diversity for the apportionment of human phenotypic diversity. Studies in History and Philosophy of Biological and Biomedical Sciences 52: 32-45. [Abstract] [PDF]
NR Garud, NA Rosenberg (2015) Enhancing the mathematical properties of new haplotype homozygosity statistics for the detection of selective sweeps. Theoretical Population Biology 102: 94-101. [Abstract] [PDF]
A Goldberg, P Verdu, NA Rosenberg (2014) Autosomal admixture levels are informative about sex bias in admixed populations. Genetics 198: 1209-1229. [Abstract] [PDF]
MD Edge, NA Rosenberg (2014) Upper bounds on F_ST in terms of the frequency of the most frequent allele and total homozygosity: the case of a specified number of alleles. Theoretical Population Biology 97: 20-34. [Abstract ] [PDF]
EM Jewett, NA Rosenberg (2014) Theory and applications of a deterministic approximation to the coalescent model. Theoretical Population Biology 93: 14-29. [Abstract] [PDF]
NA Rosenberg (2013) Coalescent histories for caterpillar-like families. IEEE/ACM Transactions on Computational Biology and Bioinformatics 10: 1253-1262. [Abstract] [PDF]
NA Rosenberg (2013) Discordance of species trees with their most likely gene trees: a unifying principle. Molecular Biology and Evolution 30: 2709-2713. [Abstract] [Full-text at journal website] [PDF]
L Huang, EO Buzbas, NA Rosenberg (2013) Genotype imputation in a coalescent model with infinitely-many-sites mutation. Theoretical Population Biology 87: 62-74. [Abstract] [PDF]
CV Than, NA Rosenberg (2013) Mathematical properties of the deep coalescence cost. IEEE/ACM Transactions on Computational Biology and Bioinformatics 10: 61-72. [Abstract] [PDF]
M Jakobsson, MD Edge, NA Rosenberg (2013) The relationship between F_ST and the frequency of the most frequent allele. Genetics 193: 515-528. [Abstract] [PDF]
M DeGiorgio, NA Rosenberg (2013) Geographic sampling scheme as a determinant of the major axis of genetic variation in principal components analysis. Molecular Biology and Evolution 30: 480-488. [Abstract] [PDF]
NM Kopelman, L Stone, O Gascuel, NA Rosenberg (2013) The behavior of admixed populations in neighbor-joining inference of population trees. Pacific Symposium on Biocomputing 18: 273-284. [Abstract] [PDF]
JH Degnan, NA Rosenberg, T Stadler (2012) A characterization of the set of species trees that produce anomalous ranked gene trees. IEEE/ACM Transactions on Computational Biology and Bioinformatics 9: 1558-1568. [Abstract] [PDF]
EM Jewett*, M Zawistowski*, NA Rosenberg, S Zöllner (2012) A coalescent model for genotype imputation. Genetics 191: 1239-1255. [Abstract] [PDF]
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. [Abstract] [PDF] [Supplement]
LJ Helmkamp, EM Jewett, NA Rosenberg (2012) Improvements to a class of distance matrix methods for inferring species trees from gene trees. Journal of Computational Biology 19: 632-649. [Abstract] [PDF]
EM Jewett, NA Rosenberg (2012) iGLASS: an improvement to the GLASS method for estimating species trees from gene trees. Journal of Computational Biology 19: 293-315. [Abstract] [PDF]
SB Reddy, NA Rosenberg (2012) Refining the relationship between homozygosity and the frequency of the most frequent allele. Journal of Mathematical Biology 64: 87-108. [Abstract] [PDF]
JH Degnan, NA Rosenberg, T Stadler (2012) The probability distribution of ranked gene trees on a species tree. Mathematical Biosciences 235: 45-55. [Abstract] [PDF]
P Verdu, NA Rosenberg (2011) A general mechanistic model for admixture histories of hybrid populations. Genetics 189: 1413-1426. [Abstract] [PDF] [Supplementary Text] [Supplementary Figure 1] [Supplementary Table 1]
M DeGiorgio, JH Degnan, NA Rosenberg (2011) Coalescence-time distributions in a serial founder model of human evolutionary history. Genetics 189: 579-593. [Abstract] [PDF]
SM Boca, NA Rosenberg (2011) Mathematical properties of F_st between admixed populations and their parental source populations. Theoretical Population Biology 80: 208-216. [Abstract] [PDF]
ZA Szpiech, NA Rosenberg (2011) On the size distribution of private microsatellite alleles. Theoretical Population Biology 80: 100-113. [Abstract] [PDF]
EO Buzbas, P Joyce, NA Rosenberg (2011) Inference on the strength of balancing selection for epistatically interacting loci. Theoretical Population Biology 79: 102-113. [Abstract] [PDF]
CV Than, NA Rosenberg (2011) Consistency properties of species tree inference by minimizing deep coalescences. Journal of Computational Biology 18: 1-15. [Abstract] [PDF]
M DeGiorgio*, I Jankovic*, NA Rosenberg (2010) Unbiased estimation of gene diversity in samples containing related individuals: exact variance and arbitrary ploidy. Genetics 186: 1367-1387. [Abstract] [PDF]
NA Rosenberg, JH Degnan (2010) Coalescent histories for discordant gene trees and species trees. Theoretical Population Biology 77: 145-151. [Abstract] [PDF]
JH Degnan, NA Rosenberg (2009) Gene tree discordance, phylogenetic inference and the multispecies coalescent. Trends in Ecology and Evolution 24: 332-340. [Abstract] [PDF] [Supplement]
JH Degnan, M DeGiorgio, D Bryant, NA Rosenberg (2009) Properties of consensus methods for inferring species trees from gene trees. Systematic Biology 58: 35-54. [Abstract] [PDF]
S Ramachandran, NA Rosenberg, MW Feldman, J Wakeley (2008) Population differentiation and migration: coalescence times in a two-sex island model for autosomal and X-linked loci. Theoretical Population Biology 74: 291-301. [Abstract] [PDF]
NA Rosenberg, M Jakobsson (2008) The relationship between homozygosity and the frequency of the most frequent allele. Genetics 179: 2027-2036. [Abstract] [PDF]
JM VanLiere, NA Rosenberg (2008) Mathematical properties of the r² measure of linkage disequilibrium. Theoretical Population Biology 74: 130-137. [Abstract] [PDF]
JM Macpherson, J Gonzalez, DM Witten, JC Davis, NA Rosenberg, AE Hirsh, DA Petrov (2008) Nonadaptive explanations for signatures of partial selective sweeps in Drosophila. Molecular Biology and Evolution 25: 1025-1042. [Abstract] [PDF]
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. [Abstract] [PDF] [Supplement]
K Zhang, NA Rosenberg (2007) On the genealogy of a duplicated microsatellite. Genetics 177: 2109-2122. [Abstract] [PDF]
MGB Blum, NA Rosenberg (2007) Estimating the number of ancestral lineages using a maximum likelihood method based on rejection sampling. Genetics 176: 1741-1757. [Abstract] [PDF]
NA Rosenberg, MGB Blum (2007) Sampling properties of homozygosity-based statistics for linkage disequilibrium. Mathematical Biosciences 208: 33-47. [Abstract] [PDF]
M Jakobsson, NA Rosenberg (2007) The probability distribution under a population divergence model of the number of genetic founding lineages of a population or species. Theoretical Population Biology 71: 502-523. [Abstract] [PDF]
NA Rosenberg (2007) Statistical tests for taxonomic distinctiveness from observations of monophyly. Evolution 61: 317-323. [Abstract] [PDF]
JH Degnan, NA Rosenberg (2006) Discordance of species trees with their most likely gene trees. PLoS Genetics 2: 762-768. [Abstract] [PDF]
NA Rosenberg (2006) The mean and variance of the numbers of r-pronged nodes and r-caterpillars in Yule-generated genealogical trees. Annals of Combinatorics 10: 129-146. [Abstract] [PDF]
NA Rosenberg (2005) A sharp minimum on the mean number of steps taken in adaptive walks. Journal of Theoretical Biology 237: 17-22. [Abstract] [PDF]
H Innan, K Zhang, P Marjoram, S Tavaré, NA Rosenberg (2005) Statistical tests of the coalescent model based on the haplotype frequency distribution and the number of segregating sites. Genetics 169: 1763-1777. [Abstract] [PDF] [Software]
NA Rosenberg, PP Calabrese (2004) Polyploid and multilocus extensions of the Wahlund inequality. Theoretical Population Biology 66: 381-391. [Abstract] [PDF]
MM Tanaka, NA Rosenberg, PM Small (2004) The control of copy number of IS6110 in Mycobacterium tuberculosis. Molecular Biology and Evolution 21: 2195-2201. [Abstract] [PDF]
S Ramachandran, NA Rosenberg, LA Zhivotovsky, MW Feldman (2004) Robustness of the inference of human population structure: a comparison of X-chromosomal and autosomal microsatellites. Human Genomics 1: 87-97. [Abstract] [PDF]
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. [Abstract] [PDF] [Supplement] [Microsatellite data] [SNP data] [SNP data readme] [Solution to Problem 11039 required in appendix of paper (American Mathematical Monthly 112: 572-573, 2005)] [Software]
NA Rosenberg, AE Hirsh (2003) On the use of star-shaped genealogies in inference of coalescence times. Genetics 164: 1677-1682. [Abstract] [PDF]
NA Rosenberg (2003) The shapes of neutral gene genealogies in two species: probabilities of monophyly, paraphyly, and polyphyly in a coalescent model. Evolution 57: 1465-1477. [Abstract] [PDF]
NA Rosenberg, M Nordborg (2002) Genealogical trees, coalescent theory, and the analysis of genetic polymorphisms. Nature Reviews Genetics 3: 380-390. [Abstract] [PDF]
NA Rosenberg (2002) The probability of topological concordance of gene trees and species trees. Theoretical Population Biology 61: 225-247. [Abstract] [PDF]
NA Rosenberg, MW Feldman (2002) The relationship between coalescence times and population divergence times. Chapter 9 in M Slatkin and M Veuille, eds. Modern Developments in Theoretical Population Genetics. Oxford: Oxford University Press, pp. 130-164. [Abstract] [PDF of final version]

Gene trees and species trees; mathematical phylogenetics

L Agranat-Tamir, M Fuchs, B Gittenberger, NA Rosenberg (2024) Asymptotic enumeration of rooted binary unlabeled galled trees with a fixed number of galls. In C. Mailler, S. Wild, eds. Proceedings of the 35th International Conference on Probabilistic, Combinatorial and Asymptotic Methods for the Analysis of Algorithms (AofA 2024). Leibniz International Proceedings in Informatics (LIPIcs) 302: 27. Schloss Dagstuhl — Leibniz-Zentrum für Informatik. [Abstract] [PDF]
M Doboli, H-K Hwang, NA Rosenberg (2024) Periodic behavior of the minimal Colijn-Plazzotta rank for trees with a fixed number of leaves. In C. Mailler, S. Wild, eds. Proceedings of the 35th International Conference on Probabilistic, Combinatorial and Asymptotic Methods for the Analysis of Algorithms (AofA 2024). Leibniz International Proceedings in Informatics (LIPIcs) 302: 18. Schloss Dagstuhl — Leibniz-Zentrum für Informatik. [Abstract] [PDF]
E Lappo, NA Rosenberg (2024) A lattice structure for ancestral configurations arising from the relationship between gene trees and species trees. Discrete Applied Mathematics 343: 65-81. [Abstract] [PDF]
ARP Maranca, NA Rosenberg (2024) Bijections between the multifurcating unlabeled rooted trees and the positive integers. Advances in Applied Mathematics 153: 102612. [Abstract] [PDF].
F Disanto, M Fuchs, C-Y Huang, AR Pangingbatan, NA Rosenberg (2024) The distributions under two species-tree models of the total number of ancestral configurations for matching gene trees and species trees. Advances in Applied Mathematics 152: 102594. [Abstract]
RS Mehta, M Steel, NA Rosenberg (2022) The probability of joint monophyly of samples of gene lineages for all species in an arbitrary species tree. Journal of Computational Biology 27: 679-703. [Abstract]
JA Palacios, A Bhaskar, F Disanto, NA Rosenberg (2022) Enumeration of binary trees compatible with a perfect phylogeny. Journal of Mathematical Biology 84: 54. [Abstract] [PDF]
MC King, NA Rosenberg (2021) A simple derivation of the mean of the Sackin index of tree balance under the uniform model on rooted binary labeled trees. Mathematical Biosciences 342: 108688. [PDF]
J Kim, NA Rosenberg, JA Palacios (2020) Distance metrics for ranked evolutionary trees. Proceedings of the National Academy of Sciences 117: 28876-28886. [Abstract] [PDF] [Supplement]
A Kim, NA Rosenberg, JH Degnan (2020) Probabilities of unranked and ranked anomaly zones under birth-death models. Molecular Biology and Evolution 37: 1480-1494. [Abstract]
ZM Himwich, NA Rosenberg (2020) Roadblocked monotonic paths and the enumeration of coalescent histories for non-matching caterpillar gene trees and species trees. Advances in Applied Mathematics 113: 101939. [Abstract]
F Disanto, NA Rosenberg (2019) Enumeration of compact coalescent histories for matching gene trees and species trees. Journal of Mathematical Biology 78: 155-188. [Abstract] [PDF]
F Disanto, NA Rosenberg (2019) On the number of non-equivalent ancestral configurations for matching gene trees and species trees. Bulletin of Mathematical Biology 81: 384-407. [Abstract] [PDF]
NA Rosenberg (2019) Enumeration of lonely pairs of gene trees and species trees by means of antipodal cherries. Advances in Applied Mathematics 102: 1-17. [Abstract] [PDF]
F Disanto, NA Rosenberg (2017) Enumeration of ancestral configurations for matching gene trees and species trees. Journal of Computational Biology 24: 831-850. [Abstract] [PDF]
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. [Abstract] [PDF] [File S1 Table S1] [File S2 Sequences] [File S3 Table S2] [File S4 Figures S1-S11] [File S5 Table S3] [File S6 R code]
OK Kamneva, NA Rosenberg (2017) Simulation-based evaluation of hybridization network reconstruction methods in the presence of incomplete lineage sorting. Evolutionary Bioinformatics 13: 1176934317691935. [Abstract] [PDF] [Supplement]
LH Uricchio, T Warnow, NA Rosenberg (2016) An analytical upper bound on the number of loci required for all splits of a species tree to appear in a set of gene trees. BMC Bioinformatics 17: 417. [Abstract] [PDF]
F Disanto, NA Rosenberg (2016) Asymptotic properties of the number of matching coalescent histories for caterpillar-like families of species trees. IEEE/ACM Transactions on Computational Biology and Bioinformatics 13: 913-925. [Abstract] [PDF]
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. [Abstract] [PDF] [Supplement] [Software]
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. [Abstract] [PDF] [Supplement]
M DeGiorgio, NA Rosenberg (2016) Consistency and inconsistency of consensus methods for inferring species trees from gene trees in the presence of ancestral population structure. Theoretical Population Biology 110: 12-24. [Abstract] [PDF]
F Disanto, NA Rosenberg (2015) Coalescent histories for lodgepole species trees. Journal of Computational Biology 22: 918-929. [Abstract] [PDF]
F Disanto, NA Rosenberg (2014) On the number of ranked species trees producing anomalous ranked gene trees. IEEE/ACM Transactions on Computational Biology and Bioinformatics 11: 1229-1238. [Abstract] [PDF]
CV Than, NA Rosenberg (2014) Mean deep coalsescence cost under exchangeable probability distributions. Discrete Applied Mathematics 174: 11-26. [Abstract] [PDF]
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. [Abstract] [PDF] [Supplementary File 1 (.xlsx, accession numbers)] [Supplementary File 2 (.pdf, supplementary analyses)] [Supplementary File 3 (.zip, data)]
NA Rosenberg (2013) Coalescent histories for caterpillar-like families. IEEE/ACM Transactions on Computational Biology and Bioinformatics 10: 1253-1262. [Abstract] [PDF]
NA Rosenberg (2013) Discordance of species trees with their most likely gene trees: a unifying principle. Molecular Biology and Evolution 30: 2709-2713. [Abstract] [Full-text at journal website] [PDF]
CV Than, NA Rosenberg (2013) Mathematical properties of the deep coalescence cost. IEEE/ACM Transactions on Computational Biology and Bioinformatics 10: 61-72. [Abstract] [PDF]
JH Degnan, NA Rosenberg, T Stadler (2012) A characterization of the set of species trees that produce anomalous ranked gene trees. IEEE/ACM Transactions on Computational Biology and Bioinformatics 9: 1558-1568. [Abstract] [PDF]
EO Buzbas (2012) On the article titled "Estimating species trees using approximate Bayesian computation" (Fan and Kubatko, Molecular Phylogenetics and Evolution 59:354-363). Molecular Phylogenetics and Evolution 65: 1014-1016 (2012). [PDF]
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. [Abstract] [PDF] [Supplement]
LJ Helmkamp, EM Jewett, NA Rosenberg (2012) Improvements to a class of distance matrix methods for inferring species trees from gene trees. Journal of Computational Biology 19: 632-649. [Abstract] [PDF]
EM Jewett, NA Rosenberg (2012) iGLASS: an improvement to the GLASS method for estimating species trees from gene trees. Journal of Computational Biology 19: 293-315. [Abstract] [PDF]
JH Degnan, NA Rosenberg, T Stadler (2012) The probability distribution of ranked gene trees on a species tree. Mathematical Biosciences 235: 45-55. [Abstract] [PDF]
CV Than, NA Rosenberg (2011) Consistency properties of species tree inference by minimizing deep coalescences. Journal of Computational Biology 18: 1-15. [Abstract] [PDF]
NA Rosenberg, JH Degnan (2010) Coalescent histories for discordant gene trees and species trees. Theoretical Population Biology 77: 145-151. [Abstract] [PDF]
M DeGiorgio, JH Degnan (2010) Fast and consistent estimation of species trees using supermatrix rooted triples. Molecular Biology and Evolution 27: 552-569. [Abstract] [PDF]
JH Degnan, NA Rosenberg (2009) Gene tree discordance, phylogenetic inference and the multispecies coalescent. Trends in Ecology and Evolution 24: 332-340. [Abstract] [PDF] [Supplement]
JH Degnan, M DeGiorgio, D Bryant, NA Rosenberg (2009) Properties of consensus methods for inferring species trees from gene trees. Systematic Biology 58: 35-54. [Abstract] [PDF]
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. [Abstract] [PDF] [Supplement]
NA Rosenberg (2007) Counting coalescent histories. Journal of Computational Biology 14: 360-377. [Abstract] [PDF]
JH Degnan, NA Rosenberg (2006) Discordance of species trees with their most likely gene trees. PLoS Genetics 2: 762-768. [Abstract] [Full-text at journal website] [PDF]
NA Rosenberg (2003) The shapes of neutral gene genealogies in two species: probabilities of monophyly, paraphyly, and polyphyly in a coalescent model. Evolution 57: 1465-1477. [Abstract] [PDF]
NA Rosenberg, M Nordborg (2002) Genealogical trees, coalescent theory, and the analysis of genetic polymorphisms. Nature Reviews Genetics 3: 380-390. [Abstract] [PDF]
NA Rosenberg (2002) The probability of topological concordance of gene trees and species trees. Theoretical Population Biology 61: 225-247. [Abstract] [PDF]
NA Rosenberg, MW Feldman (2002) The relationship between coalescence times and population divergence times. Chapter 9 in M Slatkin and M Veuille, eds. Modern Developments in Theoretical Population Genetics. Oxford: Oxford University Press, pp. 130-164. [Abstract] [PDF of final version]

Human variation and inference of human evolutionary history from genetic markers

L Agranat-Tamir, JA Mooney, NA Rosenberg (2024). Counting the genetic ancestors from source populations in members of an admixed population. Genetics 226: iyae011. [Abstract] [PDF] [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. [Abstract] [PDF] [Supplement]
E Lappo, NA Rosenberg (2024). Solving the Arizona search problem by imputation. iScience 27: 108831. [Abstract] [PDF] [Supplement]
X Liu, Z Ahsan, TK Martheswaran, NA Rosenberg (2023) When is the allele-sharing dissimilarity between two populations exceeded by the allele-sharing dissimilarity of a population with itself? Statistical Applications in Genetics and Molecular Biology 22: 2023004. [Abstract] [PDF]
J Kim, NA Rosenberg (2023) Record-matching of STR profiles with fragmentary genomic SNP data. European Journal of Human Genetics 31: 1283-1290. [Abstract] [PDF] [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. Genetics 224: iyad079. [Abstract] [PDF] [Supplement]
R Laurent, ZA Szpiech, SS da Cosa, V Thouzeau, CA Fortes-Lima, F Dessarps-Freichey, L Lémée, J Utgé, NA Rosenberg, M Baptista, P Verdu (2023) A genetic and linguistic analysis of the admixture histories of the islands of Cabo Verde. eLife 12: e79827. [Abstract] [PDF]
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. [Abstract] [PDF] [Supplement]
ML Morrison, N Alcala, NA Rosenberg (2022) FSTruct: an F_ST-based tool for measuring ancestry variation in inference of population structure. Molecular Ecology Resources 22: 2614-2626. [Abstract] [PDF] [Supplement]
X Liu, NA Rosenberg, G Greenbaum (2022) Extracting hierarchical features of cultural variation using network-based clustering. Evolutionary Human Sciences 4: e18. [Abstract] [PDF] [Supplement] [Supplementary code] [Supplementary data]
N Alcala, NA Rosenberg (2022) Mathematical constraints on F_ST: multiallelic markers in arbitrarily many populations. Philosophical Transactions of the Royal Society B: Biological Sciences 377: 20200414. [Abstract] [PDF] [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. [Abstract] [PDF] [Supplement]
SM Boca, L Huang, NA Rosenberg (2020) On the heterozygosity of an admixed population. Journal of Mathematical Biology 81: 1217-1250. [Abstract]
AL Fortier, J Kim, NA Rosenberg (2020) Human-genetic ancestry inference and false positives in forensic familial searching. G3: Genes, Genomes, Genetics 10: 2893-2902. [Abstract] [PDF] [Supplement]
IM Arbisser, NA Rosenberg (2020) F_ST and the triangle inequality for biallelic markers. Theoretical Population Biology 133: 117-129. [Abstract]
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. [Abstract
JTL Kang, NA Rosenberg (2019) Mathematical properties of linkage disequilibrium statistics defined by normalization of the coefficient D=p_AB-p_Ap_B. Human Heredity 84: 127-143. [Abstract] [PDF]
G Greenbaum, A Rubin, AR Templeton, NA Rosenberg (2019) Network-based hierarchical population structure analysis for large genomic datasets. Genome Research 29: 2020-2033. [Abstract] [PDF] [Supplement]
RS Mehta, AF Feder, SM Boca, NA Rosenberg (2019) The relationship between haplotype-based F_ST and haplotype length. Genetics 213: 281-295. [Abstract] [PDF] [Supplementary Figure 1] [Supplementary Figure 2] [Supplementary Figure 3] [Supplementary Figure 4]
AL Severson, S Carmi, NA Rosenberg (2019) The effect of consanguinity on between-individual identity-by-descent sharing. Genetics 212: 305-316. [Abstract] [PDF]
NA Rosenberg, MD Edge, JK Pritchard, MW Feldman (2019) Interpreting polygenic scores, polygenic adaptation, and human phenotypic differences. Evolution, Medicine, and Public Health 2019: 26-34. [Abstract] [PDF]
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. [Abstract] [PDF] [PDF] [Code]
NA Rosenberg (2018) Variance-partitioning and classification in human population genetics. In RG Winther, ed. Phylogenetic Inference, Selection Theory, and History of Science: Selected Papers of A. W. F. Edwards with Commentaries, pp. 399-403. [PDF]
A Goldberg, LH Uricchio, NA Rosenberg (2018) Natural selection in human populations. Oxford Bibliographies in Evolutionary Biology doi:10.1093/OBO/9780199941728-0112. [PDF]
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. [Abstract] [PDF] [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. [Abstract] [PDF] [Supplement]
N Alcala, NA Rosenberg (2017) Mathematical constraints on F_ST: biallelic markers in arbitrarily many populations. Genetics 206: 1581-1600. [Abstract] [PDF] [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. [Abstract] [PDF] [Supplement]
A Goldberg, T Günther, NA Rosenberg, M Jakobsson (2017) Robust model-based inference of male-biased admixture during Bronze Age migration from the Pontic-Caspian Steppe. Proceedings of the National Academy of Sciences USA 114: E3875-E3877. [PDF]
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. [Abstract] [PDF] [Supplement]
JTL Kang, A Goldberg, MD Edge, DM Behar, NA Rosenberg (2016) Consanguinity rates predict long runs of homozygosity in Jewish populations. Human Heredity 82: 87-102. [Abstract] [PDF]
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. [Abstract] [PDF] [Supplement]
MD Edge, NA Rosenberg (2015) A general model of the relationship between the apportionment of human genetic diversity and the apportionment of human phenotypic diversity. Human Biology 87: 313-337. [Abstract] [PDF]
A Goldberg, NA Rosenberg (2015) Beyond 2/3 and 1/3: the complex signatures of sex-biased admixture on the X chromosome. Genetics 201: 263-279. [Abstract] [PDF]
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. [Abstract] [PDF] [Supplement] [Software]
MD Edge, NA Rosenberg (2015) Implications of the apportionment of human genetic diversity for the apportionment of human phenotypic diversity. Studies in History and Philosophy of Biological and Biomedical Sciences 52: 32-45. [Abstract] [PDF]
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. [Abstract] [PDF] [Supplementary Appendix] [Supplementary Data S1] [Supplementary Data S2] [Supplementary Data S3]
EO Buzbas, NA Rosenberg (2015) AABC: approximate approximate Bayesian computation for inference in population-genetic models. Theoretical Population Biology 99: 31-42. [Abstract] [PDF]
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. [Abstract] [PDF] [Supplement]
TJ Pemberton, NA Rosenberg (2014) Population-genetic influences on genomic estimates of the inbreeding coefficient: a global perspective. Human Heredity 77: 37-48. [Abstract] [PDF] [Supplementary Figure 1] [Supplementary Figure 2] [Supplementary Table 1] [Supplementary Table 2] [Supplementary Table 3]
DM Behar*, M Metspalu*, Y Baran, NM Kopelman, B Yunusbayev, A Gladstein, S Tzur, H Sahakyan, A Bahmanimehr, L Yepiskoposyan, K Tambets, EK Khusnutdinova, A Kushniarevich, O Balanovsky, E Balanovsky, L Kovacevic, D Marjanovic, E Mihailov, A Kouvatsi, C Triantaphyllidis, RJ King, O Semino, A Torroni, MF Hammer, E Metspalu, K Skorecki, S Rosset, E Halperin, R Villems, NA Rosenberg (2013) No evidence from genome-wide data of a Khazar origin for the Ashkenazi Jews. Human Biology 85: 859-900. [Abstract] [PDF]
PJ Oefner, G Hölzl, P Shen, I Shpirer, D Gefel, T Lavi, E Woolf, J Cohen, C Cinnioglu, PA Underhill, NA Rosenberg, J Hochrein, JM Granka, J Hillel, MW Feldman (2013) Genetics and the history of the Samaritans: Y-chromosomal microsatellites and genetic affinity between Samaritans and Cohanim. Human Biology 85: 825-857. [Abstract] [PDF]
NA Rosenberg, TJ Pemberton, JZ Li, JW Belmont (2013) Runs of homozygosity and parental relatedness. Genetics in Medicine 15: 753-754. [PDF]
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. [Abstract] [PDF] [Supplement] [Data]
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. [Abstract] [Full-text at journal website] [PDF] [Supplement] [Data (.zip) - File S1]
M Jakobsson, MD Edge, NA Rosenberg (2013) The relationship between F_ST and the frequency of the most frequent allele. Genetics 193: 515-528. [Abstract] [PDF]
M DeGiorgio, NA Rosenberg (2013) Geographic sampling scheme as a determinant of the major axis of genetic variation in principal components analysis. Molecular Biology and Evolution 30: 480-488. [Abstract] [PDF]
NM Kopelman, L Stone, O Gascuel, NA Rosenberg (2013) The behavior of admixed populations in neighbor-joining inference of population trees. Pacific Symposium on Biocomputing 18: 273-284. [Abstract] [PDF]
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. [Abstract] [Full-text at journal website] [PDF] [Supplement] [Software]
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. [Abstract] [Full-text at journal website] [PDF] [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. [Abstract] [PDF] [Supplement (.docx)] [Data]
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. [Abstract] [PDF] [Main Supplement] [Supplementary Table 2 (.zip)] [Supplementary Table 3 (.zip)] [Supplementary Table 4 (.zip)] [Supplementary Table 5 (.zip)]
FA San Lucas, NA Rosenberg, P Scheet (2012) Haploscope: a tool for the graphical display of haplotype structure in populations. Genetic Epidemiology 35: 17-21. [Abstract] [PDF]
NA Rosenberg (2011) A population-genetic perspective on the similarities and differences among worldwide human populations. Human Biology 83: 659-684. [Abstract] [PDF]
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. [Abstract] [PDF] [Supplement] [Data]
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. [Abstract] [PDF] [Supplementary Figure 1] [Supplementary Figure 2] [Supplementary Tables]
M DeGiorgio, JH Degnan, NA Rosenberg (2011) Coalescence-time distributions in a serial founder model of human evolutionary history. Genetics 189: 579-593. [Abstract] [PDF]
SM Boca, NA Rosenberg (2011) Mathematical properties of F_st between admixed populations and their parental source populations. Theoretical Population Biology 80: 208-216. [Abstract] [PDF]
ZA Szpiech, NA Rosenberg (2011) On the size distribution of private microsatellite alleles. Theoretical Population Biology 80: 100-113. [Abstract] [PDF]
EO Buzbas, P Joyce, NA Rosenberg (2011) Inference on the strength of balancing selection for epistatically interacting loci. Theoretical Population Biology 79: 102-113. [Abstract] [PDF]
M DeGiorgio*, I Jankovic*, NA Rosenberg (2010) Unbiased estimation of gene diversity in samples containing related individuals: exact variance and arbitrary ploidy. Genetics 186: 1367-1387. [Abstract] [PDF]
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. [Abstract] [PDF] [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. [Abstract] [PDF] [Supplementary Figure 1] [Supplementary Table 1] [Supplementary Table 2] [Supplementary Methods]
C Wang, ZA Szpiech, JH Degnan, M Jakobsson, TJ Pemberton, JA Hardy, AB Singleton, NA Rosenberg (2010) Comparing spatial maps of human population-genetic variation using Procrustes analysis. Statistical Applications in Genetics and Molecular Biology 9: 13. [Abstract] [PDF]
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. [PDF] [Supplement]
TJ Pemberton, CI Sandefur, M Jakobsson, NA Rosenberg (2009) Sequence determinants of human microsatellite variability. BMC Genomics 10: 612. [Abstract] [Full text at journal website] [PDF] [Supplementary table 1 (XLS)] [Supplementary table 2 (XLS)] [Supplementary tables 3-6 (PDF)] [Data]
NM Kopelman, L Stone, C Wang, D Gefel, MW Feldman, J Hillel, NA Rosenberg (2009) Genomic microsatellites identify shared Jewish ancestry intermediate between Middle Eastern and European populations. BMC Genetics 10: 80. [Abstract] [Full text at journal website] [PDF] [Data]
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. [Abstract] [PDF] [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. [Abstract] [PDF] [Supplement]
M DeGiorgio, NA Rosenberg (2009) An unbiased estimator of gene diversity in samples containing related individuals. Molecular Biology and Evolution 26: 501-512. [Abstract] [PDF]
S Ramachandran, NA Rosenberg, MW Feldman, J Wakeley (2008) Population differentiation and migration: coalescence times in a two-sex island model for autosomal and X-linked loci. Theoretical Population Biology 74: 291-301. [Abstract] [PDF]
ZA Szpiech, M Jakobsson, NA Rosenberg (2008) ADZE: a rarefaction approach for counting alleles private to combinations of populations. Bioinformatics 24: 2498-2504. [Abstract] [ Full text at journal website] [PDF] [Software]
O François, MGB Blum, M Jakobsson, NA Rosenberg (2008) Demographic history of European populations of Arabidopsis thaliana. PLoS Genetics 4: e1000075. [Abstract] [Full text at journal website] [PDF] [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. [Abstract] [PDF] [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. [Abstract] [PDF] [Supplement] [Data] [Readme for datafile]
M Jakobsson, NA Rosenberg (2007) CLUMPP: a cluster matching and permutation program for dealing with label switching and multimodality in analysis of population structure. Bioinformatics 23: 1801-1806. [Abstract] [Full text at journal website] [PDF] [Software]
MGB Blum, NA Rosenberg (2007) Estimating the number of ancestral lineages using a maximum likelihood method based on rejection sampling. Genetics 176: 1741-1757. [Abstract] [PDF]
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. [Abstract] [PDF] [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. [Abstract] [PDF] [Supplementary Tables 1-3 (DOC)] [Supplementary Tables 1-3 (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. [Abstract] [PDF] [Supplement (methods, note, and figures)] [Supplementary Table 1] [Data]
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. [Abstract] [PDF] [Supplement] [Data] [Spreadsheet with recommended subsets (txt format)] [Spreadsheet with recommended subsets (xls format)]
NA Rosenberg, S Mahajan, S Ramachandran, C Zhao, JK Pritchard, MW Feldman (2005) Clines, clusters, and the effect of study design on the inference of human population structure. PLoS Genetics 1: 660-671. [Abstract] [PDF] [Data]
NA Rosenberg (2005) Algorithms for selecting informative marker panels for population assignment. Journal of Computational Biology 12: 1183-1201. [Abstract] [PDF]
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. [Abstract] [PDF] [Supplementary Figure 6] [Supplementary Table 2] [Supplementary text] [Data]
M Nordborg, TT Hu, Y Ishino, J Jhaveri, C Toomajian, H Zheng, E Bakker, P Calabrese, J Gladstone, R Goyal, M Jakobsson, S Kim, Y Morozov, B Padhukasahasram, V Plagnol, NA Rosenberg, C Shah, JD Wall, J Wang, K Zhao, T Kalbfleisch, V Schulz, M Kreitman, J Bergelson (2005) The pattern of polymorphism in Arabidopsis thaliana. PLoS Biology 3: 1289-1299. [Abstract] [PDF]
H Innan, K Zhang, P Marjoram, S Tavaré, NA Rosenberg (2005) Statistical tests of the coalescent model based on the haplotype frequency distribution and the number of segregating sites. Genetics 169: 1763-1777. [Abstract] [PDF] [Software]
NA Rosenberg, PP Calabrese (2004) Polyploid and multilocus extensions of the Wahlund inequality. Theoretical Population Biology 66: 381-391. [Abstract] [PDF]
S Ramachandran, NA Rosenberg, LA Zhivotovsky, MW Feldman (2004) Robustness of the inference of human population structure: a comparison of X-chromosomal and autosomal microsatellites. Human Genomics 1: 87-97. [Abstract] [PDF]
NA Rosenberg (2004) Distruct: a program for the graphical display of population structure. Molecular Ecology Notes 4: 137-138. [Abstract] [PDF] [Software]
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. [Abstract] [PDF] [Supplement] [Microsatellite data] [SNP data] [SNP data readme] [Solution to Problem 11039 required in appendix of paper (American Mathematical Monthly 112: 572-573, 2005)] [Software]
NA Rosenberg, AE Hirsh (2003) On the use of star-shaped genealogies in inference of coalescence times. Genetics 164: 1677-1682. [Abstract] [PDF]
NA Rosenberg, JK Pritchard, JL Weber, HM Cann, KK Kidd, LA Zhivotovsky, MW Feldman (2003) Response to comment on "Genetic structure of human populations." Science 300: 1877. [Abstract] [PDF] [Data]
LA Zhivotovsky, NA Rosenberg, MW Feldman (2003) Features of evolution and expansion of modern humans, inferred from genomewide microsatellite markers. American Journal of Human Genetics 72: 1171-1186. [Abstract] [PDF] [Data]
NA Rosenberg, JK Pritchard, JL Weber, HM Cann, KK Kidd, LA Zhivotovsky, MW Feldman (2002) Genetic structure of human populations. Science 298: 2381-2385. [Abstract] [Full Text at Science website] [PDF] [Supplement] [Data in structure and NEXUS formats] [Software for drawing figures] [Español]
NA Rosenberg, M Nordborg (2002) Genealogical trees, coalescent theory, and the analysis of genetic polymorphisms. Nature Reviews Genetics 3: 380-390. [Abstract] [PDF]
NA Rosenberg, MW Feldman (2002) The relationship between coalescence times and population divergence times. Chapter 9 in M Slatkin and M Veuille, eds. Modern Developments in Theoretical Population Genetics. Oxford: Oxford University Press, pp. 130-164. [Abstract] [PDF of final version]
NA Rosenberg, T Burke, K Elo, MW Feldman, P Friedlin, MAM Groenen, J Hillel, A Mäki-Tanila, M Tixier-Boichard, A Vignal, K Wimmers, S Weigend (2001) Empirical evaluation of genetic clustering methods using multilocus genotypes from 20 chicken breeds. Genetics 159: 699-713. [Abstract] [PDF] [Data] [Photo]
NA Rosenberg, E Woolf, JK Pritchard, T Schaap, D Gefel, I Shpirer, U Lavi, B Bonné-Tamir, J Hillel, MW Feldman (2001) Distinctive genetic signatures in the Libyan Jews. Proceedings of the National Academy of Sciences, USA 98: 858-863. [Abstract] [PDF] [Data]
L Jin , ML Baskett, LL Cavalli-Sforza, LA Zhivotovsky, MW Feldman, NA Rosenberg (2000) Microsatellite evolution in modern humans: a comparison of two data sets from the same populations. Annals of Human Genetics 64: 117-134. [Abstract] [PDF] [Data]

The relationship of human population genetics to the search for disease-susceptibility genes

NA Rosenberg, MD Edge, JK Pritchard, MW Feldman (2019) Interpreting polygenic scores, polygenic adaptation, and human phenotypic differences. Evolution, Medicine, and Public Health 2019: 26-34. [Abstract] [PDF]
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. [Abstract] [PDF] [Supplement]
MD Edge, NA Rosenberg (2015) A general model of the relationship between the apportionment of human genetic diversity and the apportionment of human phenotypic diversity. Human Biology 87: 313-337. [Abstract] [PDF]
JTL Kang, P Zhang, S Zöllner, NA Rosenberg (2015) Choosing subsamples for sequencing studies by minimizing the average distance to the closest leaf. Genetics 201: 499-511. [Abstract] [PDF]
MD Edge, P Gorroochurn, NA Rosenberg (2013) Windfalls and pitfalls: applications of population genetics to the search for disease genes. Evolution, Medicine, and Public Health 2013: 254-272. [Abstract] [Full-text at journal website] [PDF]
P Zhang, X Zhan, NA Rosenberg, S Zöllner (2013) Genotype imputation reference panel selection using maximal phylogenetic diversity. Genetics 195: 319-330. [Abstract] [PDF]
L Huang, EO Buzbas, NA Rosenberg (2013) Genotype imputation in a coalescent model with infinitely-many-sites mutation. Theoretical Population Biology 87: 62-74. [Abstract] [PDF]
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. [Abstract] [PDF] [Supplement] [Data]
EM Jewett*, M Zawistowski*, NA Rosenberg, S Zöllner (2012) A coalescent model for genotype imputation. Genetics 191: 1239-1255. [Abstract] [PDF]
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. [Abstract] [PDF] [Main Supplement] [Supplementary Table 2 (.zip)] [Supplementary Table 3 (.zip)] [Supplementary Table 4 (.zip)] [Supplementary Table 5 (.zip)]
FA San Lucas, NA Rosenberg, P Scheet (2012) Haploscope: a tool for the graphical display of haplotype structure in populations. Genetic Epidemiology 35: 17-21. [Abstract] [PDF]
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. [Abstract] [PDF] [Supplement] [Data]
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. [Abstract] [PDF] [Supplementary Figure 1] [Supplementary Table 1] [Supplementary Table 2] [Supplementary Methods]
NA Rosenberg, L Huang*, EM Jewett*, ZA Szpiech*, I Jankovic*, M Boehnke (2010) Genome-wide association studies in diverse populations. Nature Reviews Genetics 11: 356-366. [Abstract] [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. [Abstract] [PDF] [Supplement]
NA Rosenberg, JM VanLiere (2009) Replication of genetic associations as pseudoreplication due to shared genealogy. Genetic Epidemiology 33: 479-487. [Abstract] [PDF]
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. [Abstract] [PDF] [Supplement]
TJ Pemberton*, M Jakobsson*, DF Conrad, G Coop, JD Wall, JK Pritchard, PI Patel, NA Rosenberg (2008) Using population mixtures to optimize the utility of genomic databases: linkage disequilibrium and association study design in India. Annals of Human Genetics 72: 535-546. [Abstract] [PDF] [Data]
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. [Abstract] [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. [Abstract] [PDF] [Supplement (methods, note, and figures] [Supplementary Table 1] [Data]
NA Rosenberg, M Nordborg (2006) A general population-genetic model for the production by population structure of spurious genotype-phenotype associations in discrete, admixed or spatially distributed populations. Genetics 173: 1665-1678. [Abstract] [PDF]
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. [Abstract] [PDF] [Supplement] [Microsatellite data] [SNP data] [SNP data readme] [Solution to Problem 11039 required in appendix of paper (American Mathematical Monthly 112: 572-573, 2005)] [Software]
NA Rosenberg, JK Pritchard, JL Weber, HM Cann, KK Kidd, LA Zhivotovsky, MW Feldman (2002) Genetic structure of human populations. Science 298: 2381-2385. [Abstract] [Full Text at Science website] [PDF] [Supplement] [Data in structure and NEXUS formats] [Software for drawing figures] [Español]
JK Pritchard, M Stephens, NA Rosenberg, P Donnelly (2000) Association mapping in structured populations. American Journal of Human Genetics 67: 170-181. [Abstract] [PDF]
JK Pritchard, NA Rosenberg (1999) Use of unlinked genetic markers to detect population stratification in association studies. American Journal of Human Genetics 65: 220-228. [Abstract] [PDF]

Some recent papers

On the joint distribution of tree height and tree length under the coalescent (2018).
No evidence from genome-wide data of a Khazar origin for the Ashkenazi Jews (2013).
Asymptotic properties of the number of matching coalescent histories for caterpillar-like families of species trees (2016).
Enumeration of lonely pairs of gene trees and species trees by means of antipodal cherries (2019).
Natural selection in human populations (2018).