We are a mathematical, theoretical, and computational lab in genetics
and evolution. Research in the lab addresses problems in evolutionary
biology and human genetics through a combination of mathematical
modeling, computer simulations, development of statistical methods, and
inference from population-genetic data.
Goldberg on the defense of her thesis "Mathematical and
statistical approaches to elucidate recent human evolutionary
history". Amy's thesis considers mechanistic mathematical models of
admixture, including the effect of sex-biased admixture on autosomes and
on the X chromosome, and the inference from ancient autosomes and X
chromosomes of sex-biased migration during prehistoric admixture events in
Europe. She also examines the human population size history of South
America on the basis of the density and location of archaeological
sites. Congratulations Amy!
4-24-2017 We congratulate
Goldberg on receiving the 2017 Sherwood Washburn Prize from
the American Association of Physical Anthropologists! This prize
recognizes the best student presentation at the AAPA annual
meeting. Amy spoke about her work on the contrast between Neolithic
and Bronze Age migrations in Europe in their levels of male and female
migration. [Read the paper]
that two ancient migration events in Europe involved different
proportions of male and female migrants, the earlier Neolithic
migration from Anatolia having similar numbers of males and females
and the later Pontic-Caspian migration having a greater proportion of
males. The result, relying on comparisons of ancient DNA patterns from
the X chromosome and the autosomes, builds on Amy's earlier work on
sex bias in genetic admixture models
study by postdoc alum Olga Kamneva evaluates the behavior
of several methods for inferring species networks when the
evolutionary process includes hybridization. The paper provides
much-needed information on the comparative performance of the
2-27-2017 Postdoc alum Olga Kamneva reports
in PLoS Computational Biology a
of the relationship between genome composition of microbes and the
co-occurrence of microbes in the environment. She finds that comparisons of
microbial genomes can contribute to predictions about whether microbes
are associated ecologically. Congrats Olga!
2-22-2017 We wish several members of the lab well in
their new positions.
Uricchio has reported an upper
bound on the size of gene tree sets required before all splits of a
species tree appear in a gene tree set with a specified probability. His
upper bound depends on a single parameter the shortest internal
branch in the species tree. The computation extends the lab's work on
methods for species tree inference from gene trees.
10-14-2016 Recent PhD
graduate Doc Edge has
devised a general mathematical model to understand how genotypic
differences between populations contribute to phenotypic differences
between populations. He uses the model to analyze the relationship of
genetics to "health disparities," concluding that health disparities
that all trend in the same direction are incompatible with neutral
genetic explanations. The work extends a simpler model of Doc's
, allowing for
diploidy, genetic drift, and general distributions of allele
10-7-2016 Postdoc Filippo Disanto continues the
lab's work on coalescent histories with
a study of the number
of coalescent histories for matching gene trees in caterpillar-like
families of species trees. Filippo's work solves an open problem from
earlier work in the lab
, showing that the
number of coalescent histories is asymptotic to a constant multiple of
the Catalan numbers. He uses clever iterative enumerations and
techniques of analytic combinatorics to obtain the result. See also
 for related
7-27-2016 We are pleased to announce that the
software MONOPHYLER is now available.
MONOPHYLER computes probabilities
that sets of lineages are monophyletic, both for general species trees and
for trees of small size. MONOPHYLER
is reported by PhD student Rohan Mehta. The software encodes
formulas from Rohan's
recent Proceedings of the National
Academy of Sciences paper.
7-22-2016 We congratulate PhD
student Doc Edge on his thesis
defense, "Pick up the pieces: combining information from multiple
genetic loci." Doc's thesis examines several problems in the
mathematical modeling of the genotype-to-phenotype relationship in
structured populations, mathematical properties of
the Fst measure of genetic differentiation, and
population-genetic aspects of forensic DNA testing and genetic association
studies. Doc has been recognized with the
Samuel Karlin Prize in Mathematical Biology, awarded by the Department of
Biology. Congratulations Doc!
7-19-2016 PhD student Rohan Mehta reports a
computation of the probability that a set of gene lineages on an
arbitrary species tree. The work generalizes earlier studies from the lab
that considered trees of
or three species. Rohan
illustrates the new formula with an application in maize.
The study is a contribution to
the Comparative Phylogeography volume of the "In the Light of Evolution"
special issue series of Proceedings of the National Academy of
- Nicolas Alcala Postdoc with Matthieu Foll, International
Agency for Research on Cancer, World Health Organization, Lyon.
- Filippo Disanto Junior faculty, Department of
Mathematics, University of Pisa (sponsored by the Rita Levi Montalcini
- Doc Edge Postdoc with Graham Coop, Department of
Evolution and Ecology, University of California, Davis.
- Olga Kamneva Bioinformatics Scientist, Affymetrix, Inc.
6-27-2016 We congratulate biology MS student Brian
Donovan on the completion of his PhD in science education "An
experimental exploration of how text-based instruction in school biology
affects belief in genetic essentialism of race in adolescent
populations." Brian defended his PhD in the Graduate School of
Education on May 26. He is continuing his studies as a postdoctoral fellow
at the Biological Sciences Curriculum Study in Colorado Springs.
6-17-2016 The lab reports
a study examining
the predicted distribution of gene tree shape under a birth-death
model of species divergence. The work suggests that gene trees are
expected to be more imbalanced than species trees, potentially
providing part of the explanation for an excess of imbalance
observed in inferred phylogenies.
and Jaehee Kim, who have received fellowships for
2016-2017 from the Stanford Center for Computational, Evolutionary, and
DeGiorgio reports on the consistency properties of species
tree inference methods in a model with ancestral population
structure. By introducing a model that includes population
subdivision in ancestral species,
introduces a new direction for studying consistency in species
tree inference. The work is related to several recent papers
from the lab on consistency of species tree methods
4-22-2016 Several projects from the lab have been in
4-5-2016 We congratulate PhD
student Amy Goldberg
on the publication of
her Nature article
entitled "Post-invasion demography of prehistoric humans in South
America." In this work, Amy and her colleagues use the locations and
dates of South American archaeological sites to estimate the time
trajectory of the human population size history of the
continent. Read the news
Edge, and Jaehee Kim report that forensic genetic
markers selected for their use in individual identification possess
a surprising level of information about genetic ancestry. Moreover, their
study finds that a general correlation holds for genetic
markers between their information about individual identity and
ancestry information. The result makes use of theory from the lab on the
connection between measures of genetic diversity and genetic
1-5-2016 The lab helps celebrate the centennial of the
student Amy Goldberg
develops a model for sex-biased admixture on the X-chromosome, a
curious mathematical sequence leads to an unexpected connection deep
in the Genetics archive.
Read about the oscillatory functions and
coupled recursions encountered in this scholarly adventure with a
surprise appearance of the Fibonacci numbers.
10-7-2015 PhD student Jonathan Kang has
analyzed a new approach for prioritizing individuals for whole-genome
sequencing. This approach, based on minimizing a quantity
the average distance to the closest leaf, seeks to identify a
set of samples that will provide optimal templates for imputing
genotypes in additional individuals. He compares the method to an
earlier algorithm, also from the lab: maximizing phylogenetic
Jonathan's article has been selected
for Genetics issue
9-30-2015 Postdoc Filippo Disanto reports a
study of the
number of coalescent histories for gene trees and species trees in
the lodgepole family. He uses connections with other
combinatorial structures from theoretical computer science to derive
exact results in the context of a new problem arising from
biology. The term "lodgepole" for the tree shape he considers is based
on a resemblance to the pattern in which lodgepole pine needles branch
off the main twig. The work follows earlier studies from the lab on
coalescent histories (,
9-24-2015 We report
an article on detecting
selective sweeps using a new statistic, the haplotype allele frequency
(HAF) score. This statistic tabulates the frequencies of alleles on a
haplotype, and it has distinctive patterns of change during a selective
sweep. The approach is related to previous articles from the lab that
examined haplotype properties for detecting a deviation from null
population-genetic models (
The lab reports two articles in this month's issue of Genetics.
Past news items
a study of the
effect of sex-biased admixture on the X chromosome. The study has a
number of surprises: (1) The admixture level on the X chromosome is not
simply a 2/3-and-1/3 linear combination of female and male
parameters. (2) A difference in X chromosomal and autosomal levels of
admixture need not imply male bias entering the admixed population from
one source and female bias from a second source: the bias can be in the
same direction in both source populations, but with different
magnitudes. (3) A third surprise involves the appearance of a sequence
related to the Fibonacci numbers! The paper follows two previous
articles from the lab on mechanistic models of admixture
- We report a review
of three cases in which differences in levels of genetic diversity
across populations contribute to population differences in societal
variables related to forensic testing, transplantation matching,
and genome-wide association. The study also considers a fourth scenario,
performing a reanalysis that contests a claim that within-population
genetic diversity has influenced global economic development. PhD
student Jonathan Kang contributed to the project.
to Genomes blog post from the Genetics Society of America]
SELECTED RECENT PUBLICATIONS
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 113:
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.
F Disanto, NA Rosenberg (2015) Coalescent histories for
lodgepole species trees. Journal of Computational Biology 22:
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.
NA Rosenberg, JTL Kang (2015) Genetic diversity and
societally important disparities. Genetics 201: 1-12.
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.
M Jakobsson, MD Edge, NA Rosenberg (2013) The
relationship between FST and the frequency of the
most frequent allele.
Genetics 193: 515-528.
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:
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.
ZA Szpiech, NA Rosenberg (2011) On the size
distribution of private microsatellite alleles. Theoretical
Population Biology 80: 100-113.