# Full Text: CryptoJews

> Extracted from `2015_CryptoJews.pdf`

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## Page 1

GENERAL COMMENTARY
published: 07 August 2015
doi: 10.3389/fgene.2015.00261
Frontiers in Genetics | www.frontiersin.org
1
August 2015 | Volume 6 | Article 261
Edited by:
Badri Padhukasahasram,
Illumina, Inc., USA
Reviewed by:
Luca Pagani,
University of Cambridge, UK
Jill Bennett Gaieski,
University of Pennsylvania, USA
*Correspondence:
Daniel A. Friedman,
danielarifriedman@gmail.com
Specialty section:
This article was submitted to
Evolutionary and Population Genetics,
a section of the journal
Frontiers in Genetics
Received: 31 March 2015
Accepted: 23 July 2015
Published: 07 August 2015
Citation:
Marcus AW, Ebel ER and Friedman
DA (2015) Commentary: Portuguese
crypto-Jews: the genetic heritage of a
complex history. Front. Genet. 6:261.
doi: 10.3389/fgene.2015.00261
Commentary: Portuguese
crypto-Jews: the genetic heritage of
a complex history
Alexander W. Marcus 1, Emily R. Ebel 2 and Daniel A. Friedman 2*
1 Department of Religious Studies, Stanford University, Stanford, CA, USA, 2 Department of Biology, Stanford University,
Stanford, CA, USA
Keywords: Jewish genetics, haplotypes, crypto-Jews, Iberian Peninsula, admixture, demographic history
A commentary on
Portuguese crypto-Jews: the genetic heritage of a complex history
by Nogueiro, I., Teixeira, J. C., Amorim, A., Gusmão, L., and Alvarez, L. (2015). Front. Genet. 6:12.
doi: 10.3389/fgene.2015.00012
Introduction
Nogueiro et al. (2015) utilize Y chromosome and mitochondrial genotype data from a
contemporary Iberian and non-Iberian human populations to explore the genetic identity of
Portuguese “crypto-Jews.” In the first section of the paper, a historical introduction reviews the
plight of Jews in the Iberian Peninsula from the earliest archaeological evidence, through the
Inquisition, to the current day. In the second section, Y chromosome and mtDNA population
genetic data from many previous studies are reviewed, along with a reanalysis of data from
two Portuguese Jewish populations. In the final section, a historical narrative of the Portuguese
crypto-Jews is presented, caveats to the analysis are discussed, and future directions are
suggested.
Critique 1
Many of the data reviewed suffer from methodological issues that weaken or invalidate the
conclusions made. Specifically, the data are ambiguous with regards to the inference of Jewish
ancestry and do not identify diagnostic patrilineal or matrilineal markers.
Critique 2
The authors suggest that the data may support a history of “complex mating strategies” in Jewish
populations, but fail to test this hypothesis against models of even simple demographic histories
or admixture events. Without consideration of alternative hypotheses, it is not possible to draw
inferences about how the crypto-Jews must have “belong[ed] to a distinctive community,” especially
with regards to belief and practice.

## Page 2

Marcus et al.
Commentary: Portuguese crypto-Jews
Explanation of Critique 1
The analysis of Nogueiro et al. (2015) uses previous work on
uniparental markers (Y chromosomal and mtDNA) to explore
the possibility of a diagnostic genetic pattern of Jewish ancestry.
We have reservations about the strength of the matrilineal
(mtDNA) and patrilineal (Y chromosomal) data reviewed and
presented in this analysis. A recent study (Tofanelli et al.,
2014) finds that Jewish haplotype motifs in much previous
work are inadequate for “forensic or genealogical purposes,”
because ambiguity in the molecular clock, along with haplotype
polyphyly, preclude their usage as “reliable Jewish ancestry
predictors.” Furthermore, the cited studies do not, even amongst
themselves, find a diagnostic Jewish “genetic profile.” Many of
the “Jewish” haplotypes cited by Nogueiro et al. (Gonçalves et al.,
2005; Pacheco et al., 2005) are pan-Middle Eastern markers—
common in self-identified Jews, but also in multiple Arabic
lineages. Thus, these haplotypes are of ambiguous ancestry—they
could be of Jewish ancestry, Arab ancestry, or observed at high
frequencies due to more complex demographic scenarios.
Nogueiro et al. acknowledge that “the inference of a genetic
profile for the Portuguese Jews was not possible” from a study
of self-defined Sephardic Jews (Adams et al., 2008), and instead
focus their analysis on two smaller Jewish populations. Their
acknowledgment that there is no diagnostic Jewish genetic
profile, which is supported by the data presented, appears to
contradict the major conclusion of the paper: that Iberian Jews
have “succeeded in maintaining a genetic heritage of their own.”
Explanation of Critique 2
To answer questions of medical and cultural relevance,
population-level genetic analyses must carefully control for
population structure using complex statistical methodologies
on high-quality, whole-genome scale datasets (Pickrell and
Pritchard, 2012). This is to ensure that observed genetic patterns
are not merely false-positives stemming from situations where
human demography violates certain simple assumptions (Liu
et al., 2013). Admixture is one of the central forces in shaping
global patterns of human genetic diversity, and is difficult to
estimate with confidence (Hellenthal et al., 2014). Even in very
recent admixture events where whole-genome data is available,
findings can be ambiguous (Jin et al., 2012). Small sample sizes of
uniparental markers, as used in Nogueiro et al. (2015), are unable
to draw robust conclusions.
Inferring historical admixture patterns in contemporary
populations is a quantitative, empirical question. However,
the analysis of Nogueiro et al. rests on qualitative patterns
of diversity, which are not tested against any models of
human demography. For example, patterns of diversity in both
mitochondrial and Y-chromosome haplotypes in the Bragança
Jews more closely resemble patterns in the Portuguese population
than in the Belmonte Jews. Although Nogueiro et al. call
this “extremely surprising,” given their expectation of severe
inbreeding, they attribute it to “complex mating strategies and/or
a very heterogeneous genetic pool in their origin.” These findings
are “extremely surprising” only when they are “translated
in a conscience of belonging to a distinctive community”—
the author’s pre-existing model of crypto-Jew reproductive
isolation.
Hypotheses of admixture in the Bragança Jews and a
bottleneck in the Belmonte Jews could be statistically evaluated
using extant demographic models. Together with historical data,
quantitative estimates of admixture could be used to infer the
interesting and potentially unique histories of these populations.
However, this opportunity is missed by focusing primarily on
diagnosing a Jewish genetic signature.
Conclusion
Nogueiro
et
al.
(2015)
interpret
many
ambiguous
and
contradictory population genetic findings within an a priori
model of Portuguese crypto-Jew reproductive isolation. The
results and analysis offer no concrete support for specific
statements about the mating habits, beliefs, and/or praxis of
these historical Jewish populations. Our critique is consistent
with the previously-recognized difficulty of making claims
about both Jewish haplotype motifs and late-antique and early-
medieval Iberia (Astren, 2004; Tofanelli et al., 2014; Falk, 2015).
Textual and material evidence dating from the period following
the Inquisition provide a complex picture of both inter-marriage
and communal isolation in the Iberian Peninsula (Nirenberg,
2014). Given the synchronic and diachronic complexities
of Iberian population dynamics, as well as the ambiguous
interpretation of molecular markers, the claim of the persistence
of “crypto-Judaism”—a secret adherence to Jewish belief and
practice across generations—is one that requires more careful
examination. Especially when statements are of political or
cultural relevance, human population genetic researchers must
be careful to draw only data-supported conclusions.
Funding
This work was supported by a National Science Foundation
Graduate Research Fellowship to EE (DGE-1247312) and an
Urbanek Family Stanford Graduate Fellowship to DF.
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## Page 3

Marcus et al.
Commentary: Portuguese crypto-Jews
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Conflict of Interest Statement: The authors declare that the research was
conducted in the absence of any commercial or financial relationships that could
be construed as a potential conflict of interest.
Copyright © 2015 Marcus, Ebel and Friedman. This is an open-access article
distributed under the terms of the Creative Commons Attribution License (CC BY).
The use, distribution or reproduction in other forums is permitted, provided the
original author(s) or licensor are credited and that the original publication in this
journal is cited, in accordance with accepted academic practice. No use, distribution
or reproduction is permitted which does not comply with these terms.
Frontiers in Genetics | www.frontiersin.org
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*Extraction method: pymupdf*