If the alleged paternity would be supported, the six candidates expected to carry the largest amount of autosomal DNA are those closer in number of generations to Joseph Smith Jr. and Josephine Lyon (Fig. 2). Joseph Smith Jr. begat nine biological children with his first wife, Emma Hale. Four sons lived to adulthood, but only two of them, Joseph Smith III and Alexander Hale Smith, have known living biological posterity. All children and grandchildren of Joseph Smith Jr. were deceased at time of sampling. Five great-grandchildren were still alive and agreed to contribute a DNA sample (M652395, T177361, M298807, M309701 and M265410, expectedly carrying about 12.5% of Joseph Smith Jr.’s autosomal DNA). Josephine Lyon gave birth to ten children, with seven surviving to adulthood. Descendants from six children donated DNA samples to the current study, including the only grandchild that was still alive at time of sampling (M885071, with expected ˜25% of Josephine autosomal DNA). Under the assumption that Joseph Smith Jr. was the biological father of Josephine Lyon, her grandson M885071 would share an expected 1.563% of autosomal DNA (or approximately 106.25 cMs, Table 1) with Joseph Smith Jr.’s great grandchildren included in this study. Given the number of generations separating these individuals, it is unlikely that we can
confirm a biological paternity, but we should find strong evidence to either support or exclude it.
2.4 Kinship analysis
PLINKv1.9 was used to merge and convert the data from the UCSC build37 reference genome. A total of 227,200 SNPs were retained to compare all 56 individuals, after filtering for missing data (threshold = 0.01). It is worth mentioning that similar results (data not shown) were obtained when considering only 23andMe data, 52 samples and 501,495 filtered SNPs.
The kinship coefficient, defined as the probability that two randomly chosen alleles are identical by descent (IBD), provides an estimate of the relatedness between pairs of individuals; this coefficient can be measured using different algorithms implemented in several software. Here, the kinship coefficient was estimated in KING v1.4 96 (–kinship and –ibs flags), which allows checking for pair-wise relationships by assuming the existence of a population structure. Different ranges of the estimated kinship coefficients, i.e. [> 0.354], [0.177, 0.354], [0.0884, 0.177] and [0.0442, 0.0884], were used to infer different degrees of relationships, i.e. a duplicate sample, 1 st degree, 2nd degree and 3rd degree, respectively. Eventually, the kinship values were used first to build an UPGMA (Unweighted Pair Group Method with Arithmetic Mean) tree (based on Euclidean distances) using the hclust() function in R and then to create an heatmap with the pheatmap package.
The pairwise proportion of IBD was also investigated using the –genome flag in PLINKv1.9 and the results were plotted using ggplot2 package in R. We took into consideration the IBD score (or PI_HAT) in the form p(IBD = 2) + 0.5*p(IBD = 1).
Table 1Comparison between the Josephine Lyon’s grandson and five great grand-children of Joseph Smith Jr. (alleged father).
|Josephine Lyon’s grandson||Joseph Smith Jr’s great grandchildren||Alleged Relationship||Average Expected cMs||Avgs and ranges observed in Shared cM Project (v.3.0)||Actual cMs|
|M885071||T177361||Half 2C : half second cousin||106.25||117 (9-397)||0|
|M885071||M298807||Half 2C||106.25||117 (9-397)||0|
|M885071||M265410||Half 2C||106.25||117 (9-397)||0|
|M885071||M309701||Half 2C||106.25||117 (9-397)||0|
|M885071||M652395||Half 2C||106.25||117 (9-397)||0|
2.5 Pairwise likelihood ratio calculations
Pairwise Likelihood Ratios (LRs) were computed using SNP analyzer, a software package that performs kinship calculations using large sets of SNPs. LRs assess the probability of observing the genetic data under two competing hypotheses about the relatedness between two individuals and are calculated from IBD patterns within pedigrees. They are provided in several degrees of thinning (or pruning), choosing a minimum distance of 0.1–8 cM s between the SNPs considered for calculations. This naïve method aims to select enough markers but mitigating the possible effect of linkage disequilibrium (LD). Summary statistics were calculated from the ˜300,000 overlapping markers between the person of interest and the reference population. Population frequency data from Utah residents, with Northern and Western European ancestry, from the 1000 Genomes project were chosen as assumedly closest. Default settings were used (no genotyping error; minimum allele frequency = 0.4). A total of 162 calculations were performed on the 27 individuals considered to be the most informative to solve the paternity case.
3.2 Verifying the biological paternity of Josephine Lyon
Once the genealogical information on the two families was confirmed, the next step was a comparison between Josephine Lyon’s only surviving grandson with each of Joseph Smith Jr.’s great-grandchildren (Table 1
). None of the five Smith’s shared any amount of autosomal DNA with Josephine’s grandchild, while at the half second-degree cousin relationship, which the five descendants of Joseph Smith Jr. would allegedly share with Josephine’s grandchild, it is expected to observe an average of 106.25 cMs (based on a linear decrement) or 117 (9–397) cMs (based on The Shared cM Project, v. 3.0). As a positive control, the observed range for a similar relationship within each family was 27.7–177.5 cM s (twenty occurrences in the Smith family). Therefore, the observed absence of shared autosomal DNA between Josephine’s grandson and Joseph Smith Jr.’s five great-grandchildren indicates that the five Smiths are probably not biologically related within the alleged relationship degree.
In order to test the paternity of Windsor Lyon, we checked the autosomal DNA from Josephine Lyon’s grandson shared with five individuals related to Josephine through her mother Sylvia Sessions or through Windsor Lyon’s family, but bearing no apparent close relationship to the Smith family (Table 2
). Even if one of them (M535447) did not share any cMs, which is a likely possibility at those distant degrees of relationship (Half 2C1R), four individuals (M277648, M958130, M186496, and M267975) shared autosomal DNA with Josephine’s grandson, ranging from 19.8 to 117.5 cMs. The closeness of Josephine’s descendant M885071 with the Lyon family rather than the Smith pedigree was also confirmed by the average proportion of IBD fragments shared with Windsor Lyon’s that is significantly higher (Wilcoxon p-value
<0.05) than with the Joseph Smith Jr.’s descendants (Fig. S1).
Table 2Comparison between the Josephine Lyon’s grandson and five relatives of Windsor Lyon (biological father).
|Josephine Lyon’s grandson||Joseph Smith Jr’s great grandchildren||Alleged Relationship||Average Expected cMs||Avgs and ranges observed in Shared cM Project (v.3.0)||Actual cMs|
|M885071||M277648||Half 2C1R (half second cousin once removed)||53.13||73 (-341)||117.4|
|M885071||M958130||Half 2C1R||53.13||73 (-341)||84.2|
|M885071||M186496||3C1R (third cousin once removed)||26.56||48 (0-173)||30.1|
|M885071||M267975||Half 2C1R||53.13||73 (-341)||19.7|
|M885071||M535447||Half 2C1R||53.13||73 (-341)||0|
The overall results are well summarized by the UPGMA genetic tree based on kinship values showing a well-defined separation between Smiths and Lyons (Fig. 3). Notably, all the Josephine’s great and grand-sons fall in the group of Lyon family among the previously mentioned descendants of Sylvia Sessions (A281469, A004825) and Windsor Lyon (M535447, M267975, M958130, M277648 and M186496). The location of these samples in the UPGMA clustering tree, together with the relationship highlighted in the heatmap, further supports the relationship between Josephine and the Lyons. Moreover, genetic data are consistent with the genealogical relationships reported in Fig. 1 for both families, with one notable exception. In fact, sample M307597, which belongs to the Smith family, clusters with the Lyon family (the only pink square among the blue ones). A possible explanation is the distant relationship M307597 shares with Joseph Smith Jr., as he is a descendant of Joseph’s brother Hyrum through his first wife Jerusha Barden. According to the genealogical data provided, his closest Joseph Smith Jr.’s descendants tested in the current study would be his third cousin twice removed (3C2R). Table S1 shows that M307597 has extremely little or no DNA in common with the five Joseph Smith Sr.’s great grandchildren included in the current study. As both Hyrum Smith and Josephine Lyon’s descendants relocated and settled in the state of Utah, it is likely (although it has not been verified yet) that M307597 could have some common, more recent ancestors with the Lyons. This hypothesis would explain why M307597 clusters with the Lyon and not with the Smith family in Fig. 3.
3.3 Supporting our results with Pairwise LR
To corroborate our inferences, a total of 162 Pairwise LR comparisons were also performed to test the genetic relationships between the most informative offspring pairs. We started by comparing the 18 most informative descendants of Josephine Lyon (i.e
. her grandson M885071, and her 17 great grandchildren processed with 23andMe: M477183, M369031, M338915, M035925, M798210, M754500, M819905, M474845, M627809, M376930, M157517, M246659, M765786, M700418, M877227, M498236, M672512; Fig. 1
) and the five most informative descendants of Joseph Smith Jr. and Emma Hale (i.e
. their five great grandchildren M652395, M309701, M265410, T177361, M298807; Fig. 2
). None of the 90 pairwise comparisons supported the hypothesized genetic relationships of half second cousin (half 2C, for M885071) or half second cousin once removed (half 2C1R, for all others, respectively). Results were largely inconclusive and provided limited support (LR <<10) for either hypothesis with all marker selections, which may indicate that even more markers would be necessary to resolve this case. Thus, there is no evidence for the paternity of Joseph Smith Jr.
Exceedance probability simulations have shown that high LR results are possible in very distant true relations of individuals. This is demonstrated in the second batch of analyses. In fact, the LR results for the denser marker set favor genetic relations of the 18 descendants of Josephine Lyon (see above) to the four available descendants of Windsor Lyon and Suzanne E. Gee (i.e
. their four great great-grandchildren M535447, M267975, M958130, M277648) (Fig. 1
). Among the 72 pairwise comparisons performed, assuming half second cousin once removed (half 2C1R) relations for M885071 and half third cousin (half 3C) relations for all others, respectively, 40 yielded LR results >1,000, which is considered very strong support. In general, high LRs were yielded in comparisons including all the individuals, except for only three individuals related to Josephine Lyon through three of her children that showed no indication for the investigated relationship with the chosen markers. The results indicate strong evidence for relatedness between individuals through Windsor Lyon, thus also for the paternity hypothesis.
The proportion of pairwise comparisons between Josephine Lyon’s and Windsor Lyon’s descendants that did not yield high LR in favor of the putative relation were dispersed among individuals that yielded extremely high LRs with other individuals in the same tree, which likely pinpoints the variation in the small amount of shared cMs between very distantly related individuals. False rates, indicating the percentage of unrelated pairs that is falsely concluded as related (LR > 1000) were very low (< 0.02) (data not shown). In this context, it appears highly unlikely that the negative kinship results from all 90 pairwise comparisons between Josephine Lyon’s and Joseph Smith Jr.’s descendants (that, in addition, were putatively closer related than Windsor Lyon’s descendants) would be caused by this effect.
3.4 Completing the genetic profile of Joseph Smith Jr. with his mitogenome
In order to completely investigate the genetic profile of Joseph Smith Jr. we have also reconstructed his maternal lineage by sequencing the entire mitochondrial DNA (using the previously described protocol from a descendant of Katherine Smith, one of Joseph Smith Jr.’s sisters (Fig. S2). His maternal line is characterized by the haplotype 152C 263 G 315.1C 750 G 1438 G 2706 G 4769 G 7028 T 8860 G 9039A 14180C 15,326 G 16519C relative to the rCRS . It belongs to haplogroup HV18, a rare lineage (five samples in EMPOP v4/R12, https://empop.online/
) that has been defined for the first time by analyzing modern Iranians and that is nowadays present in Western Europe and the Middle East. It has been recently identified also in an ancient Iron Age from the South Baltic region.
In this project, a total of 56 individuals representing both Joseph Smith Jr.’s and Josephine Lyon’s families, including controls from other relatives, contributed samples for autosomal DNA testing to solve the highly debated question of the Joseph Smith Jr.’s alleged paternity of Josephine Lyon. Using pedigrees may be a pitfall, because they are necessarily assumptions from historical/genealogical data, which might lead to a plethora of possible errors, ranging from typos during pedigree transcriptions to possible extra-pair paternity or maternity events. Actually, this was an issue when preliminary genetic data from a small number of descendants (three Smiths and six Lyons) were published. DNA sharing between the Smith/Lyon family member pairs was observed, but it was quickly determined that it could have been the result of additional intermarriages and not necessarily from a Joseph and Sylvia alleged offspring. Here, a much larger number of individuals were tested and the reconstructed pedigrees were concordant with the results from autosomal SNPs, thus strengthening the genetic outcome.
Although a reconstruction of Joseph Smith Jr. and Josephine Lyon’s DNA through their descendants separated by three or more generations will never provide the same level of accuracy as a paternity test with DNA obtained directly from Joseph and Josephine, data presented in this study was consistent and offered the strongest evidence to date toward clarifying their alleged father/daughter relationship. Based on this analysis, it appears that Josephine did not share a biological tie with the founder of Mormonism and that perhaps what Sylvia Sessions told her daughter would mean something other than the biological relationship many historians have perceived. This is certainly an additional piece of genetic evidence in future researches on the subject of Joseph Smith Jr.’s practice of polygamy.
This study confirms that autosomal DNA testing is providing the opportunity to address many genealogical questions that could not be answered by analysis of autosomal STRs or the uniparental Y-chromosome and mitochondrial molecules. The weak signal of genetic inheritance of shared cM segments is here strengthened by the high number of individuals available from the well documented pedigrees, the high number of markers and the use of three methods independently. Errors could always be introduced in these types of studies by incorrectly transcribing genealogical records, lab errors or even illegitimacies. However, when a considerable number of individuals are carefully selected and tested for the same family history case, the strength of both the results and the study conclusions increase. This study proves that a considerable number of individuals carefully selected and tested for the same family history case might enable a result even when the “actual” individuals are not available.
Mitogenome sequence has been deposited in GenBank (xxxxx). To access the genotyped data, researchers should send a signed letter to A.A. containing the following text: (a) I will not distribute the data outside my collaboration; (b) I will not post the data publicly;(c) I will make no attempt to connect the genetic data to personal identifiers for the samples; (d) I will not use the data for any selection studies; (e) I will not use the data for medical or disease-related analyses; (f) I will not use the data for commercial purposes.’
This study would have not been possible without the support of key individuals in both Joseph Smith Jr.’s and Josephine Lyon’s families. We are especially grateful to all the fifty-six DNA donors. We are grateful to the generous individuals that made financial contributions through the crowdfunding website https://www.gofundme.com/JosephSmithDNA
. This funding was used for the DNA testing and tools needed for this project.
This study received support from: i) the University of Pavia strategic theme “Towards a governance model for international migration: an interdisciplinary and diachronic perspective” (MIGRAT-IN-G) (to A.A.); ii) the Italian Ministry of Education, University and Research (MIUR), i.e. Dipartimenti di Eccellenza Program (2018–2022) to the Dept. of Biology and Biotechnology “L. Spallanzani” at the University of Pavia (to A.A. and A.R.) and PRIN2017 project No. 20174BTC4R (to A.A.); iii) the European Research Council (ERC), i.e. Horizon 2020 Consolidator Grant CoG-2014 No. 648535 (to A.A.).
We are also grateful to Ann Turner and Blaine Bettinger for providing valuable feedback and suggestions to early drafts of this paper, and to the PhD programs of the University of Pavia and to Cristian Capelli at the Department of Zoology to the University of Oxford for facilitating the research visit of A.R..
We thank Daniel Kling (Dep. of Forensic Sciences, University Hospital Oslo, Oslo, Norway) for providing SNP analyzer and friendly support with using the software.
Other DNA articles:
- DNA Rules Out Joseph Smith has descendants from polygamist wives
- DNA Solves a Joseph Smith Mystery
- The Irish Mormon Prophet
- Resolving a 150-Year-Old paternity case in Mormon history using DTC autosomal DNA testing of distant relatives
- DNA shows Joseph Smith was Irish
- Joseph Smith Jr. now even more Irish
- Joseph Smith DNA Revealed: New Clues from the Prophet’s Genes
We thank the two anonymous reviewers for useful comments.