Rosenberg lab - corrigenda

Typos and thinkos

Inexhaustive list of known errors of a nontrivial nature in published papers.

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]

In the first paragraph on page 6, the last line should read "For the genealogy in Fig. 3A, Fig. 3B shows the perfect phylogeny of the data observed at its tips."
The last paragraph at the bottom of page 25 is erroneously placed in the main text. This paragraph belongs as a footnote to Table 1.

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]

On page 5676, the BEAGLE setting maxlr=50,000 should instead be maxlr=5,000.

A Goldberg, P Verdu, NA Rosenberg (2014) Autosomal admixture levels are informative about sex bias in admixed populations. Genetics 198: 1209-1229. [Abstract] [PDF]

On page 1214, in eq. 21, fifth line of the equation, the expression P[L=HS₁] should instead be P[L=HH].

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: 263-274. [Abstract] [PDF]

The characterization of additive trees in Section 4.1 is too strong, and additive trees do not necessarily have the shape described in Figure 3B. The error is corrected in Appendix B and Figure 12 of Kim et al. (Bull Math Biol 81:452-493, 2019).

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]

In the caption for Figure 1, the symbol for the San population was omitted. Individuals from this population are represented as open orange squares.

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]

On page 771, column 2, second full paragraph, line 11, the figure reference should be to Figure 7, not Figure 10.

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]

On page 1422, in Figure 7, some of the parameters are misspecified in the legend so that they do not reflect the curves plotted. In part a, the correct value of s₂ is 0.03. In part b, the correct value of s₁ is 0.03. In the caption, the correct long-term limit of the variance is 10/1045 ≈ 0.096 (rather than 60/5523, corresponding to the misspecified parameter value of 0.3).

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]

This paper unfortunately had a very large number of printer's typos in our section on estimating allele age. A complete list of typos (in this section only) is available here.

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]

Affiliations for two authors were listed incorrectly. Affiliation 9 should read "Facultad de Medicina and Laboratorios de Investigación y Desarrollo, Universidad Peruana Cayetano Heredia, Lima, Peru". Giovanni Poletti should be listed with affiliation 8.
In Table 2 on page 2053, the mean heterozygosity for Huilliche should read 0.667.

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]

On page 671 it was stated that θ was estimated using equation 5.12 of Weir (1996). This is not correct. Actually, θ was estimated using the GDA (Genetic Data Analysis) software of P. O. Lewis and D. Zaykin. The computation was therefore done by separately computing for each allele at each locus the numerator and the denominator of the first equation on p. 173. The overall estimate of θ was then obtained as the ratio of the mean of the numerators and the mean of the denominators.

NA Rosenberg, AE Hirsh (2003) On the use of star-shaped genealogies in inference of coalescence times. Genetics 164: 1677-1682. [Abstract] [PDF]

In the denominator of eq. 4, (n-1/n) should be (n-1)/n.

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]

On page 1468, line 6, H_{k-1} and k-1 should be replaced with H_k and k respectively. In the following equation line, H_{k-1} should be replaced with H_k. The equation marked (10) is correct. This error and its correction are discussed in the supplementary material of Mehta et al. (PNAS 113:8002-8009, 2016), eq. S2.

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 Excel] [Data in structure and NEXUS formats] [Software for drawing figures] [Español]

In Supplementary Figure 1A, the yellow component of the pie chart (1.33%) should refer to "Africa, Central/South Asia, Europe, Middle East". The percent associated with "Africa, Central/South Asia, East Asia, Middle East" is 1.00%.

NA Rosenberg (2002) The probability of topological concordance of gene trees and species trees. Theoretical Population Biology 61: 225-247. [Abstract] [PDF]

Eqs. 11-13 and the associated 6th and 7th columns of Table 2 are not correct. The problem arises from omitting some cases. The numerical magnitude of the error is generally small. The error is fixed in Appendix A.1 of Mehta and Rosenberg (Theor Pop Biol 129:133-147, 2019), which describes the correct formulas and gives replacements for the table entries in its Table 3.

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]

A superscript 1 should have been added to indicate that author K Elo was part of the alphabetical list.

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]

In the note below Table 3, reference (27) should be (29).