Evolutionary Anthropology
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| Publications of Amy Goldberg :chronological alphabetical combined listing:
%% Book Sections/Chapters
@misc{fds355710,
Author = {Agusto, F and Goldberg, A and Ortega, O and Ponce, J and Zaytseva, S and Sindi, S and Blower, S},
Title = {How Do Interventions Impact Malaria Dynamics Between
Neighboring Countries? A Case Study with Botswana and
Zimbabwe},
Volume = {22},
Pages = {83-109},
Booktitle = {Association for Women in Mathematics Series},
Year = {2021},
Month = {January},
url = {http://dx.doi.org/10.1007/978-3-030-57129-0_5},
Abstract = {Malaria is a vector-borne disease that is responsible for
over 400,000 deaths per year. Although countries around the
world have taken measures to decrease the incidence of
malaria, many regions remain endemic. Indeed, progress
towards elimination has stalled in multiple countries. While
control efforts are largely focused at the national level,
the movement of individuals between countries may complicate
the efficacy of elimination efforts. Here, we consider the
case of neighboring countries Botswana and Zimbabwe,
connected by human mobility. Both have improved malaria
interventions in recent years with differing success. We use
a two-patch Ross-MacDonald model with Lagrangian human
mobility to examine the coupled disease dynamics between
these two countries. In particular, we are interested in the
impact that interventions for controlling malaria applied in
one country can have on the incidence of malaria in the
other country. We find that dynamics and interventions in
Zimbabwe can dramatically influence pathways to elimination
in Botswana, largely driven by Zimbabwe’s population size
and larger basic reproduction number.},
Doi = {10.1007/978-3-030-57129-0_5},
Key = {fds355710}
}
%% Journal Articles
@article{fds369942,
Author = {Hamid, I and Korunes, KL and Schrider, DR and Goldberg,
A},
Title = {Localizing Post-Admixture Adaptive Variants with Object
Detection on Ancestry-Painted Chromosomes.},
Journal = {Molecular biology and evolution},
Volume = {40},
Number = {4},
Pages = {msad074},
Publisher = {Oxford University Press (OUP)},
Editor = {Rogers, R},
Year = {2023},
Month = {April},
url = {http://dx.doi.org/10.1093/molbev/msad074},
Abstract = {Gene flow between previously differentiated populations
during the founding of an admixed or hybrid population has
the potential to introduce adaptive alleles into the new
population. If the adaptive allele is common in one source
population, but not the other, then as the adaptive allele
rises in frequency in the admixed population, genetic
ancestry from the source containing the adaptive allele will
increase nearby as well. Patterns of genetic ancestry have
therefore been used to identify post-admixture positive
selection in humans and other animals, including examples in
immunity, metabolism, and animal coloration. A common method
identifies regions of the genome that have local ancestry
"outliers" compared with the distribution across the rest of
the genome, considering each locus independently. However,
we lack theoretical models for expected distributions of
ancestry under various demographic scenarios, resulting in
potential false positives and false negatives. Further,
ancestry patterns between distant sites are often not
independent. As a result, current methods tend to infer wide
genomic regions containing many genes as under selection,
limiting biological interpretation. Instead, we develop a
deep learning object detection method applied to images
generated from local ancestry-painted genomes. This approach
preserves information from the surrounding genomic context
and avoids potential pitfalls of user-defined summary
statistics. We find the method is robust to a variety of
demographic misspecifications using simulated data. Applied
to human genotype data from Cabo Verde, we localize a known
adaptive locus to a single narrow region compared with
multiple or long windows obtained using two other
ancestry-based methods.},
Doi = {10.1093/molbev/msad074},
Key = {fds369942}
}
@article{fds364954,
Author = {Korunes, KL and Soares-Souza, GB and Bobrek, K and Tang, H and Araújo,
II and Goldberg, A and Beleza, S},
Title = {Sex-biased admixture and assortative mating shape genetic
variation and influence demographic inference in admixed
Cabo Verdeans.},
Journal = {G3 (Bethesda, Md.)},
Volume = {12},
Number = {10},
Pages = {jkac183},
Year = {2022},
Month = {September},
url = {http://dx.doi.org/10.1093/g3journal/jkac183},
Abstract = {Genetic data can provide insights into population history,
but first, we must understand the patterns that complex
histories leave in genomes. Here, we consider the admixed
human population of Cabo Verde to understand the patterns of
genetic variation left by social and demographic processes.
First settled in the late 1400s, Cabo Verdeans are admixed
descendants of Portuguese colonizers and enslaved West
African people. We consider Cabo Verde's well-studied
historical record alongside genome-wide SNP data from 563
individuals from 4 regions within the archipelago. We use
genetic ancestry to test for patterns of nonrandom mating
and sex-specific gene flow, and we examine the consequences
of these processes for common demographic inference methods
and genetic patterns. Notably, multiple population genetic
tools that assume random mating underestimate the timing of
admixture, but incorporating nonrandom mating produces
estimates more consistent with historical records. We
consider how admixture interrupts common summaries of
genomic variation such as runs of homozygosity. While
summaries of runs of homozygosity may be difficult to
interpret in admixed populations, differentiating runs of
homozygosity by length class shows that runs of homozygosity
reflect historical differences between the islands in their
contributions from the source populations and postadmixture
population dynamics. Finally, we find higher African
ancestry on the X chromosome than on the autosomes,
consistent with an excess of European males and African
females contributing to the gene pool. Considering these
genomic insights into population history in the context of
Cabo Verde's historical record, we can identify how
assumptions in genetic models impact inference of population
history more broadly.},
Doi = {10.1093/g3journal/jkac183},
Key = {fds364954}
}
@article{fds362923,
Author = {Gopalan, S and Smith, SP and Korunes, K and Hamid, I and Ramachandran,
S and Goldberg, A},
Title = {Human genetic admixture through the lens of population
genomics.},
Journal = {Philosophical transactions of the Royal Society of London.
Series B, Biological sciences},
Volume = {377},
Number = {1852},
Pages = {20200410},
Year = {2022},
Month = {June},
url = {http://dx.doi.org/10.1098/rstb.2020.0410},
Abstract = {Over the past 50 years, geneticists have made great strides
in understanding how our species' evolutionary history gave
rise to current patterns of human genetic diversity
classically summarized by Lewontin in his 1972 paper, 'The
Apportionment of Human Diversity'. One evolutionary process
that requires special attention in both population genetics
and statistical genetics is admixture: gene flow between two
or more previously separated source populations to form a
new admixed population. The admixture process introduces
ancestry-based structure into patterns of genetic variation
within and between populations, which in turn influences the
inference of demographic histories, identification of
genetic targets of selection and prediction of complex
traits. In this review, we outline some challenges for
admixture population genetics, including limitations of
applying methods designed for populations without recent
admixture to the study of admixed populations. We highlight
recent studies and methodological advances that aim to
overcome such challenges, leveraging genomic signatures of
admixture that occurred in the past tens of generations to
gain insights into human history, natural selection and
complex trait architecture. This article is part of the
theme issue 'Celebrating 50 years since Lewontin's
apportionment of human diversity'.},
Doi = {10.1098/rstb.2020.0410},
Key = {fds362923}
}
@article{fds361870,
Author = {Voinson, M and Nunn, CL and Goldberg, A},
Title = {Primate malarias as a model for cross-species parasite
transmission.},
Journal = {eLife},
Volume = {11},
Pages = {e69628},
Year = {2022},
Month = {January},
url = {http://dx.doi.org/10.7554/elife.69628},
Abstract = {Parasites regularly switch into new host species,
representing a disease burden and conservation risk to the
hosts. The distribution of these parasites also gives
insight into characteristics of ecological networks and
genetic mechanisms of host-parasite interactions. Some
parasites are shared across many species, whereas others
tend to be restricted to hosts from a single species.
Understanding the mechanisms producing this distribution of
host specificity can enable more effective interventions and
potentially identify genetic targets for vaccines or
therapies. As ecological connections between human and local
animal populations increase, the risk to human and wildlife
health from novel parasites also increases. Which of these
parasites will fizzle out and which have the potential to
become widespread in humans? We consider the case of primate
malarias, caused by <i>Plasmodium</i> parasites, to
investigate the interacting ecological and evolutionary
mechanisms that put human and nonhuman primates at risk for
infection. <i>Plasmodium</i> host switching from nonhuman
primates to humans led to ancient introductions of the most
common malaria-causing agents in humans today, and new
parasite switching is a growing threat, especially in Asia
and South America. Based on a wild host-<i>Plasmodium</i>
occurrence database, we highlight geographic areas of
concern and potential areas to target further sampling. We
also discuss methodological developments that will
facilitate clinical and field-based interventions to improve
human and wildlife health based on this eco-evolutionary
perspective.},
Doi = {10.7554/elife.69628},
Key = {fds361870}
}
@article{fds359963,
Author = {Ai, H and Zhang, M and Yang, B and Goldberg, A and Li, W and Ma, J and Brandt,
D and Zhang, Z and Nielsen, R and Huang, L},
Title = {Human-Mediated Admixture and Selection Shape the Diversity
on the Modern Swine (Sus scrofa) Y Chromosomes.},
Journal = {Molecular biology and evolution},
Volume = {38},
Number = {11},
Pages = {5051-5065},
Year = {2021},
Month = {October},
url = {http://dx.doi.org/10.1093/molbev/msab230},
Abstract = {Throughout its distribution across Eurasia, domestic pig
(Sus scrofa) populations have acquired differences through
natural and artificial selection, and have often interbred.
We resequenced 80 Eurasian pigs from nine different Asian
and European breeds; we identify 42,288 reliable SNPs on the
Y chromosome in a panel of 103 males, among which 96.1% are
newly detected. Based on these new data, we elucidate the
evolutionary history of pigs through the lens of the Y
chromosome. We identify two highly divergent haplogroups:
one present only in Asia and one fixed in Europe but present
in some Asian populations. Analyzing the European haplotypes
present in Asian populations, we find evidence of three
independent waves of introgression from Europe to Asia in
last 200 years, agreeing well with the literature and
historical records. The diverse European lineages were
brought in China by humans and left significant imprints not
only on the autosomes but also on the Y chromosome of
geographically and genetically distinct Chinese pig breeds.
We also find a general excess of European ancestry on Y
chromosomes relative to autosomes in Chinese pigs, an
observation that cannot be explained solely by sex-biased
migration and genetic drift. The European Y haplotype is
associated with leaner meat production, and we hypothesize
that the European Y chromosome increased in frequency in
Chinese populations due to artificial selection. We find
evidence of Y chromosomal gene flow between Sumatran wild
boar and Chinese pigs. Our results demonstrate how
human-mediated admixture and selection shaped the
distribution of modern swine Y chromosomes.},
Doi = {10.1093/molbev/msab230},
Key = {fds359963}
}
@article{fds355709,
Author = {Kim, J and Edge, MD and Goldberg, A and Rosenberg,
NA},
Title = {Skin deep: The decoupling of genetic admixture levels from
phenotypes that differed between source populations.},
Journal = {American journal of physical anthropology},
Volume = {175},
Number = {2},
Pages = {406-421},
Year = {2021},
Month = {June},
url = {http://dx.doi.org/10.1002/ajpa.24261},
Abstract = {<h4>Objectives</h4>In genetic admixture processes, source
groups for an admixed population possess distinct patterns
of genotype and phenotype at the onset of admixture.
Particularly in the context of recent and ongoing admixture,
such differences are sometimes taken to serve as markers of
ancestry for individuals-that is, phenotypes initially
associated with the ancestral background in one source
population are assumed to continue to reflect ancestry in
that population. Such phenotypes might possess ongoing
significance in social categorizations of individuals, owing
in part to perceived continuing correlations with ancestry.
However, genotypes or phenotypes initially associated with
ancestry in one specific source population have been seen to
decouple from overall admixture levels, so that they no
longer serve as proxies for genetic ancestry. Here, we aim
to develop an understanding of the joint dynamics of
admixture levels and phenotype distributions in an admixed
population.<h4>Methods</h4>We devise a mechanistic model,
consisting of an admixture model, a quantitative trait
model, and a mating model. We analyze the behavior of the
mechanistic model in relation to the model
parameters.<h4>Results</h4>We find that it is possible for
the decoupling of genetic ancestry and phenotype to proceed
quickly, and that it occurs faster if the phenotype is
driven by fewer loci. Positive assortative mating attenuates
the process of dissociation relative to a scenario in which
mating is random with respect to genetic admixture and with
respect to phenotype.<h4>Conclusions</h4>The mechanistic
framework suggests that in an admixed population, a trait
that initially differed between source populations might
serve as a reliable proxy for ancestry for only a short
time, especially if the trait is determined by few loci. It
follows that a social categorization based on such a trait
is increasingly uninformative about genetic ancestry and
about other traits that differed between source populations
at the onset of admixture.},
Doi = {10.1002/ajpa.24261},
Key = {fds355709}
}
@article{fds366028,
Author = {Voinson, M and Nunn, C and Goldberg, A},
Title = {Primate malarias as a model for cross-species parasite
transmission},
Year = {2021},
Month = {April},
url = {http://dx.doi.org/10.32942/osf.io/zk2dq},
Abstract = {<p>Parasites regularly switch into new host species,
representing a disease burden and conservation risk to the
hosts. The distribution of these parasites also gives
insight into characteristics of ecological networks and
genetic mechanisms of host-parasite interactions. Some
parasites are shared across many species, whereas others
tend to be restricted to hosts from a single species.
Understanding the mechanisms producing this distribution of
host specificity can enable more effective interventions and
potentially identify genetic targets for vaccines or
therapies. With increasing ecological connections to local
animal populations, the risk to human health is increasing.
Which of these parasites will fizzle out and which have
potential to become widespread in humans? We consider the
case of primate malarias, caused by Plasmodium parasites, to
understand the interacting ecological and evolutionary
mechanisms that put humans at risk for disease. Plasmodium
host switching from primates to humans led to ancient
introductions of the most common malaria-causing agents in
humans today, and new parasite switching is a growing
threat, especially in Asia and South America. Based on a
wild host-Plasmodium occurrence database, we highlight
geographic areas of concern and potential areas to target
further sampling. Finally, we discuss methodological
developments that will facilitate clinical and field-based
interventions to improve human health based on this
eco-evolutionary perspective.</p>},
Doi = {10.32942/osf.io/zk2dq},
Key = {fds366028}
}
@article{fds355550,
Author = {Korunes, KL and Goldberg, A},
Title = {Human genetic admixture.},
Journal = {PLoS genetics},
Volume = {17},
Number = {3},
Pages = {e1009374},
Year = {2021},
Month = {March},
url = {http://dx.doi.org/10.1371/journal.pgen.1009374},
Abstract = {Throughout human history, large-scale migrations have
facilitated the formation of populations with ancestry from
multiple previously separated populations. This process
leads to subsequent shuffling of genetic ancestry through
recombination, producing variation in ancestry between
populations, among individuals in a population, and along
the genome within an individual. Recent methodological and
empirical developments have elucidated the genomic
signatures of this admixture process, bringing previously
understudied admixed populations to the forefront of
population and medical genetics. Under this theme, we
present a collection of recent PLOS Genetics publications
that exemplify recent progress in human genetic admixture
studies, and we discuss potential areas for future
work.},
Doi = {10.1371/journal.pgen.1009374},
Key = {fds355550}
}
@article{fds354581,
Author = {Hamid, I and Korunes, KL and Beleza, S and Goldberg,
A},
Title = {Rapid adaptation to malaria facilitated by admixture in the
human population of Cabo Verde.},
Journal = {eLife},
Volume = {10},
Pages = {e63177},
Year = {2021},
Month = {January},
url = {http://dx.doi.org/10.7554/elife.63177},
Abstract = {Humans have undergone large migrations over the past
hundreds to thousands of years, exposing ourselves to new
environments and selective pressures. Yet, evidence of
ongoing or recent selection in humans is difficult to
detect. Many of these migrations also resulted in gene flow
between previously separated populations. These recently
admixed populations provide unique opportunities to study
rapid evolution in humans. Developing methods based on
distributions of local ancestry, we demonstrate that this
sort of genetic exchange has facilitated detectable
adaptation to a malaria parasite in the admixed population
of Cabo Verde within the last ~20 generations. We estimate
that the selection coefficient is approximately 0.08, one of
the highest inferred in humans. Notably, we show that this
strong selection at a single locus has likely affected
patterns of ancestry genome-wide, potentially biasing
demographic inference. Our study provides evidence of
adaptation in a human population on historical
timescales.},
Doi = {10.7554/elife.63177},
Key = {fds354581}
}
@article{fds349408,
Author = {Goldberg, A and Rastogi, A and Rosenberg, NA},
Title = {Assortative mating by population of origin in a mechanistic
model of admixture.},
Journal = {Theoretical population biology},
Volume = {134},
Pages = {129-146},
Year = {2020},
Month = {August},
url = {http://dx.doi.org/10.1016/j.tpb.2020.02.004},
Abstract = {Populations whose mating pairs have levels of similarity in
phenotypes or genotypes that differ systematically from the
level expected under random mating are described as
experiencing assortative mating. Excess similarity in mating
pairs is termed positive assortative mating, and excess
dissimilarity is negative assortative mating. In humans,
empirical studies suggest that mating pairs from various
admixed populations - whose ancestry derives from two or
more source populations - possess correlated ancestry
components that indicate the occurrence of positive
assortative mating on the basis of ancestry. Generalizing a
two-sex mechanistic admixture model, we devise a model of
one form of ancestry-assortative mating that occurs through
preferential mating based on source population. Under the
model, we study the moments of the admixture fraction
distribution for different assumptions about mating
preferences, including both positive and negative
assortative mating by population. We demonstrate that
whereas the mean admixture under assortative mating is
equivalent to that of a corresponding randomly mating
population, the variance of admixture depends on the level
and direction of assortative mating. We consider two special
cases of assortative mating by population: first, a single
admixture event, and second, constant contributions to the
admixed population over time. In contrast to standard
settings in which positive assortment increases variation
within a population, certain assortative mating scenarios
allow the variance of admixture to decrease relative to a
corresponding randomly mating population: with the three
populations we consider, the variance-increasing effect of
positive assortative mating within a population might be
overwhelmed by a variance-decreasing effect emerging from
mating preferences involving other pairs of populations. The
effect of assortative mating is smaller on the X chromosome
than on the autosomes because inheritance of the X in males
depends only on the mother's ancestry, not on the mating
pair. Because the variance of admixture is informative about
the timing of admixture and possibly about sex-biased
admixture contributions, the effects of assortative mating
are important to consider in inferring features of
population history from distributions of admixture values.
Our model provides a framework to quantitatively study
assortative mating under flexible scenarios of admixture
over time.},
Doi = {10.1016/j.tpb.2020.02.004},
Key = {fds349408}
}
@article{fds349643,
Author = {Kemp, ME and Mychajliw, AM and Wadman, J and Goldberg,
A},
Title = {7000 years of turnover: historical contingency and human
niche construction shape the Caribbean's Anthropocene
biota.},
Journal = {Proceedings. Biological sciences},
Volume = {287},
Number = {1927},
Pages = {20200447},
Year = {2020},
Month = {May},
url = {http://dx.doi.org/10.1098/rspb.2020.0447},
Abstract = {The human-mediated movement of species across biogeographic
boundaries-whether intentional or accidental-is dramatically
reshaping the modern world. Yet humans have been reshaping
ecosystems and translocating species for millennia, and
acknowledging the deeper roots of these phenomena is
important for contextualizing present-day biodiversity loss,
ecosystem functioning and management needs. Here, we present
the first database of terrestrial vertebrate species
introductions spanning the entire anthropogenic history of a
system: the Caribbean. We employ this approximately
7000-year dataset to assess the roles of historical
contingency and priority effects in shaping present-day
community structure and conservation outcomes, finding that
serial human colonization events contributed to habitat
modifications and species extinctions that shaped the
trajectories of subsequent species introductions by other
human groups. We contextualized spatial and temporal
patterns of species introductions within cultural practices
and population histories of Indigenous, colonial and modern
human societies, and show that the taxonomic and
biogeographic diversity of introduced species reflects
diversifying reasons for species introductions through time.
Recognition of the complex social and economic structures
across the 7000-year human history of the Caribbean provides
the necessary context for interpreting the formation of an
Anthropocene biota.},
Doi = {10.1098/rspb.2020.0447},
Key = {fds349643}
}
@article{fds354167,
Author = {Hamid, I and Korunes, K and Beleza, S and Goldberg,
A},
Title = {Rapid adaptation to malaria facilitated by admixture in the
human population of Cabo Verde},
Year = {2020},
url = {http://dx.doi.org/10.1101/2020.09.01.278226},
Abstract = {Humans have undergone large migrations over the past
hundreds to thousands of years, exposing ourselves to new
environments and selective pressures. Yet, evidence of
ongoing or recent selection in humans is difficult to
detect. Many of these migrations also resulted in gene flow
between previously separated populations. These recently
admixed populations provide unique opportunities to study
rapid evolution in humans. Developing methods based on
distributions of local ancestry, we demonstrate that this
sort of genetic exchange has facilitated detectable
adaptation to a malaria parasite in the admixed population
of Cabo Verde within the last ∼20 generations. We estimate
the selection coefficient is approximately 0.08, one of the
highest inferred in humans. Notably, we show that this
strong selection at a single locus has likely affected
patterns of ancestry genome-wide, potentially biasing
demographic inference. Our study provides evidence of
adaptation in a human population on historical
timescales.},
Doi = {10.1101/2020.09.01.278226},
Key = {fds354167}
}
@article{fds366029,
Author = {Korunes, K and Soares-Souza, GB and Bobrek, K and Tang, H and Araújo,
II and Goldberg, A and Beleza, S},
Title = {Sex-biased admixture and assortative mating shape genetic
variation and influence demographic inference in admixed
Cabo Verdeans},
Year = {2020},
url = {http://dx.doi.org/10.1101/2020.12.14.422766},
Abstract = {Genetic data can provide insights into population history,
but first we must understand the patterns that complex
histories leave in genomes. Here, we consider the admixed
human population of Cabo Verde to understand the patterns of
genetic variation left by social and demographic processes.
First settled in the late 1400s, Cabo Verdeans are admixed
descendants of Portuguese colonizers and enslaved West
African people. We consider Cabo Verde’s well-studied
historical record alongside genome-wide SNP data from 563
individuals from 4 regions within the archipelago. We use
genetic ancestry to test for patterns of nonrandom mating
and sex-specific gene flow, and we examine the consequences
of these processes for common demographic inference methods
and for genetic patterns. Notably, multiple population
genetic tools that assume random mating underestimate the
timing of admixture, but incorporating non-random mating
produces estimates more consistent with historical records.
We consider how admixture interrupts common summaries of
genomic variation such as runs-of-homozygosity (ROH). While
summaries of ROH may be difficult to interpret in admixed
populations, differentiating ROH by length class shows that
ROH reflect historical differences between the islands in
their contributions from the source populations and
post-admixture population dynamics. Finally, we find higher
African ancestry on the X chromosome than on the autosomes,
consistent with an excess of European males and African
females contributing to the gene pool. Considering these
genomic insights into population history in the context of
Cabo Verde’s historical record, we can identify how
assumptions in genetic models impact inference of population
history more broadly.},
Doi = {10.1101/2020.12.14.422766},
Key = {fds366029}
}
@article{fds366768,
Author = {Alcala, N and Goldberg, A and Ramakrishnan, U and Rosenberg,
NA},
Title = {Coalescent Theory of Migration Network Motifs.},
Journal = {Molecular biology and evolution},
Volume = {36},
Number = {10},
Pages = {2358-2374},
Year = {2019},
Month = {October},
url = {http://dx.doi.org/10.1093/molbev/msz136},
Abstract = {Natural populations display a variety of spatial
arrangements, each potentially with a distinctive impact on
genetic diversity and genetic differentiation among
subpopulations. Although the spatial arrangement of
populations can lead to intricate migration networks,
theoretical developments have focused mainly on a small
subset of such networks, emphasizing the island-migration
and stepping-stone models. In this study, we investigate all
small network motifs: the set of all possible migration
networks among populations subdivided into at most four
subpopulations. For each motif, we use coalescent theory to
derive expectations for three quantities that describe
genetic variation: nucleotide diversity, FST, and half-time
to equilibrium diversity. We describe the impact of network
properties on these quantities, finding that motifs with a
high mean node degree have the largest nucleotide diversity
and the longest time to equilibrium, whereas motifs with low
density have the largest FST. In addition, we show that the
motifs whose pattern of variation is most strongly
influenced by loss of a connection or a subpopulation are
those that can be split easily into disconnected components.
We illustrate our results using two example data sets-sky
island birds of genus Sholicola and Indian
tigers-identifying disturbance scenarios that produce the
greatest reduction in genetic diversity; for tigers, we also
compare the benefits of two assisted gene flow scenarios.
Our results have consequences for understanding the effect
of geography on genetic diversity, and they can assist in
designing strategies to alter population migration networks
toward maximizing genetic variation in the context of
conservation of endangered species.},
Doi = {10.1093/molbev/msz136},
Key = {fds366768}
}
@article{fds346384,
Author = {Kim, J and Edge, M and Goldberg, A and Rosenberg,
N},
Title = {Assortative mating and the dynamical decoupling of genetic
admixture levels from phenotypes that differ between source
populations},
Year = {2019},
Month = {September},
url = {http://dx.doi.org/10.1101/773663},
Abstract = {Abstract Source populations for an admixed population can
possess distinct patterns of genotype and pheno-type at the
beginning of the admixture process. Such differences are
sometimes taken to serve as markers of ancestry—that is,
phenotypes that are initially associated with the ancestral
background in one source population are taken to reflect
ancestry in that population. Examples exist, however, in
which genotypes or phenotypes initially associated with
ancestry in one source population have decoupled from
overall admixture levels, so that they no longer serve as
proxies for genetic ancestry. We develop a mechanistic model
for describing the joint dynamics of admixture levels and
phenotype distributions in an admixed population. The
approach includes a quantitative-genetic model that relates
a phenotype to underlying loci that affect its trait value.
We consider three forms of mating. First, individuals might
assort in a manner that is independent of the overall
genetic admixture level. Second, individuals might assort by
a quantitative phenotype that is initially correlated with
the genetic admixture level. Third, individuals might assort
by the genetic admixture level itself. Under the model, we
explore the relationship between genetic admixture level and
phenotype over time, studying the effect on this
relationship of the genetic architecture of the phenotype.
We find that the decoupling of genetic ancestry and
phenotype can occur surprisingly quickly, especially if the
phenotype is driven by a small number of loci. We also find
that positive assortative mating attenuates the process of
dissociation in relation to a scenario in which mating is
random with respect to genetic admixture and with respect to
phenotype. The mechanistic framework suggests that in an
admixed population, a trait that initially differed between
source populations might be a reliable proxy for ancestry
for only a short time, especially if the trait is determined
by relatively few loci. The results are potentially relevant
in admixed human populations, in which phenotypes that have
a perceived correlation with ancestry might have social
significance as ancestry markers, despite declining
correlations with ancestry over time. Author Summary Admixed
populations are populations that descend from two or more
populations that had been separated for a long time at the
beginning of the admixture process. The source populations
typically possess distinct patterns of genotype and
phenotype. Hence, early in the admixture process, phenotypes
of admixed individuals can provide information about the
extent to which these individuals possess ancestry in a
specific source population. To study correlations between
admixture levels and phenotypes that differ between source
populations, we construct a genetic and phenotypic model of
the dynamical process of admixture. Under the model, we show
that correlations between admixture levels and these
phenotypes dissipate over time—especially if the genetic
architecture of the phenotypes involves only a small number
of loci, or if mating in the admixed population is random
with respect to both the admixture levels and the
phenotypes. The result has the implication that a trait that
once reflected ancestry in a specific source population
might lose this ancestry correlation. As a consequence, in
human populations, after a sufficient length of time,
salient phenotypes that can have social meaning as ancestry
markers might no longer bear any relationship to genome-wide
genetic ancestry.},
Doi = {10.1101/773663},
Key = {fds346384}
}
@article{fds345875,
Author = {Goldberg, A and Rastogi, A and Rosenberg, N},
Title = {Assortative mating by population of origin in a mechanistic
model of admixture},
Year = {2019},
Month = {August},
url = {http://dx.doi.org/10.1101/743476},
Abstract = {Abstract Populations whose mating pairs have levels of
similarity in phenotypes or genotypes that differ
systematically from the level expected under random mating
are described as experiencing assortative mating. Excess
similarity in mating pairs is termed positive assortative
mating, and excess dissimilarity is negative assortative
mating. In humans, empirical studies suggest that mating
pairs from various admixed populations—whose ancestry
derives from two or more source populations—possess
correlated ancestry components that indicate the occurrence
of positive assortative mating on the basis of ancestry.
Generalizing a two-sex mechanistic admixture model, we
devise a model of one form of ancestry-assortative mating
that occurs through preferential mating based on source
population. Under the model, we study the moments of the
admixture fraction distribution for different assumptions
about mating preferences, including both positive and
negative assortative mating by population. We consider the
special cases of assortative mating by population that
involve a single admixture event and that consider a model
of constant contributions to the admixed population over
time. We demonstrate that whereas the mean admixture under
assortative mating is equivalent to that of a corresponding
randomly mating population, the variance of admixture
depends on the level and direction of assortative mating. In
contrast to standard settings in which positive assortment
increases variation within a population, certain assortative
mating scenarios allow the variance of admixture to decrease
relative to a corresponding randomly mating population: with
the three populations we consider, the variance-increasing
effect of positive assortative mating within a population
might be overwhelmed by a variance-decreasing effect
emerging from mating preferences involving other pairs of
populations. The effect of assortative mating is smaller on
the X chromosome than the autosomes because inheritance of
the X in males depends only on the mother’s ancestry, not
on the mating pair. Because the variance of admixture is
informative about the timing of admixture and possibly about
sex-biased admixture contributions, the effects of
assortative mating are important to consider in inferring
features of population history from distributions of
admixture values. Our model provides a framework to
quantitatively study assortative mating under flexible
scenarios of admixture over time.},
Doi = {10.1101/743476},
Key = {fds345875}
}
@article{fds354168,
Author = {Agusto, F and Goldberg, A and Ortega, O and Ponce, J and Zaytseva, S and Sindi, S and Blower, S},
Title = {How do interventions impact malaria dynamics between
neighboring countries? A case study with Botswana and
Zimbabwe},
Year = {2019},
url = {http://dx.doi.org/10.1101/19013631},
Abstract = {Malaria is a vector-borne disease that is responsible for
over 400,000 deaths per year. Although countries around the
world have taken measures to decrease the incidence of
malaria, many regions remain endemic. Indeed, progress
towards elimination has stalled in multiple countries. While
control efforts are largely focused at the national level,
the movement of individuals between countries may complicate
the efficacy of elimination efforts. Here, we consider the
case of neighboring countries Botswana and Zimbabwe,
connected by human mobility. Both have improved malaria
rates in recent years with differing success. We use a
two-patch Ross-MacDonald Model with Lagrangian human
mobility to examine the coupled disease dynamics between
these two countries. In particular, we are interested in the
impact that interventions for controlling malaria applied in
one country can have on the incidence of malaria in the
other country. We find that dynamics and interventions in
Zimbabwe can dramatically influence pathways to elimination
in Botswana, largely driven by Zimbabwe’s population size
and larger basic reproduction number.},
Doi = {10.1101/19013631},
Key = {fds354168}
}
@article{fds354020,
Author = {Damgaard, PDB and Marchi, N and Rasmussen, S and Peyrot, M and Renaud,
G and Korneliussen, T and Moreno-Mayar, JV and Pedersen, MW and Goldberg, A and Usmanova, E and Baimukhanov, N and Loman, V and Hedeager, L and Pedersen, AG and Nielsen, K and Afanasiev, G and Akmatov, K and Aldashev, A and Alpaslan, A and Baimbetov, G and Bazaliiskii, VI and Beisenov, A and Boldbaatar, B and Boldgiv, B and Dorzhu, C and Ellingvag, S and Erdenebaatar, D and Dajani, R and Dmitriev, E and Evdokimov, V and Frei, KM and Gromov, A and Goryachev,
A and Hakonarson, H and Hegay, T and Khachatryan, Z and Khaskhanov, R and Kitov, E and Kolbina, A and Kubatbek, T and Kukushkin, A and Kukushkin,
I and Lau, N and Margaryan, A and Merkyte, I and Mertz, IV and Mertz, VK and Mijiddorj, E and Moiyesev, V and Mukhtarova, G and Nurmukhanbetov, B and Orozbekova, Z and Panyushkina, I and Pieta, K and Smrčka, V and Shevnina, I and Logvin, A and Sjögren, K-G and Štolcová, T and Taravella, AM and Tashbaeva, K and Tkachev, A and Tulegenov, T and Voyakin, D and Yepiskoposyan, L and Undrakhbold, S and Varfolomeev,
V and Weber, A and Wilson Sayres and MA and Kradin, N and Allentoft, ME and Orlando, L and Nielsen, R and Sikora, M and Heyer, E and Kristiansen, K and Willerslev, E},
Title = {137 ancient human genomes from across the Eurasian
steppes.},
Journal = {Nature},
Volume = {557},
Number = {7705},
Pages = {369-374},
Year = {2018},
Month = {May},
url = {http://dx.doi.org/10.1038/s41586-018-0094-2},
Abstract = {For thousands of years the Eurasian steppes have been a
centre of human migrations and cultural change. Here we
sequence the genomes of 137 ancient humans (about 1×
average coverage), covering a period of 4,000 years, to
understand the population history of the Eurasian steppes
after the Bronze Age migrations. We find that the genetics
of the Scythian groups that dominated the Eurasian steppes
throughout the Iron Age were highly structured, with diverse
origins comprising Late Bronze Age herders, European farmers
and southern Siberian hunter-gatherers. Later, Scythians
admixed with the eastern steppe nomads who formed the
Xiongnu confederations, and moved westward in about the
second or third century BC, forming the Hun traditions in
the fourth-fifth century AD, and carrying with them plague
that was basal to the Justinian plague. These nomads were
further admixed with East Asian groups during several
short-term khanates in the Medieval period. These historical
events transformed the Eurasian steppes from being inhabited
by Indo-European speakers of largely West Eurasian ancestry
to the mostly Turkic-speaking groups of the present day, who
are primarily of East Asian ancestry.},
Doi = {10.1038/s41586-018-0094-2},
Key = {fds354020}
}
@article{fds336364,
Author = {Goldberg, A and Günther, T and Rosenberg, NA and Jakobsson,
M},
Title = {Reply to Lazaridis and Reich: Robust model-based inference
of male-biased admixture during Bronze Age migration from
the Pontic-Caspian Steppe.},
Journal = {Proceedings of the National Academy of Sciences of the
United States of America},
Volume = {114},
Number = {20},
Pages = {E3875-E3877},
Year = {2017},
Month = {May},
url = {http://dx.doi.org/10.1073/pnas.1704442114},
Doi = {10.1073/pnas.1704442114},
Key = {fds336364}
}
@article{fds336365,
Author = {Goldberg, A and Günther, T and Rosenberg, NA and Jakobsson,
M},
Title = {Ancient X chromosomes reveal contrasting sex bias in
Neolithic and Bronze Age Eurasian migrations.},
Journal = {Proceedings of the National Academy of Sciences of the
United States of America},
Volume = {114},
Number = {10},
Pages = {2657-2662},
Year = {2017},
Month = {March},
url = {http://dx.doi.org/10.1073/pnas.1616392114},
Abstract = {Dramatic events in human prehistory, such as the spread of
agriculture to Europe from Anatolia and the late
Neolithic/Bronze Age migration from the Pontic-Caspian
Steppe, can be investigated using patterns of genetic
variation among the people who lived in those times. In
particular, studies of differing female and male demographic
histories on the basis of ancient genomes can provide
information about complexities of social structures and
cultural interactions in prehistoric populations. We use a
mechanistic admixture model to compare the
sex-specifically-inherited X chromosome with the autosomes
in 20 early Neolithic and 16 late Neolithic/Bronze Age human
remains. Contrary to previous hypotheses suggested by the
patrilocality of many agricultural populations, we find no
evidence of sex-biased admixture during the migration that
spread farming across Europe during the early Neolithic. For
later migrations from the Pontic Steppe during the late
Neolithic/Bronze Age, however, we estimate a dramatic male
bias, with approximately five to 14 migrating males for
every migrating female. We find evidence of ongoing,
primarily male, migration from the steppe to central Europe
over a period of multiple generations, with a level of sex
bias that excludes a pulse migration during a single
generation. The contrasting patterns of sex-specific
migration during these two migrations suggest a view of
differing cultural histories in which the Neolithic
transition was driven by mass migration of both males and
females in roughly equal numbers, perhaps whole families,
whereas the later Bronze Age migration and cultural shift
were instead driven by male migration, potentially connected
to new technology and conquest.},
Doi = {10.1073/pnas.1616392114},
Key = {fds336365}
}
@article{fds354021,
Author = {Algee-Hewitt, BFB and Goldberg, A},
Title = {Better together: Thinking anthropologically about
genetics.},
Journal = {American journal of physical anthropology},
Volume = {160},
Number = {4},
Pages = {557-560},
Year = {2016},
Month = {August},
url = {http://dx.doi.org/10.1002/ajpa.23022},
Abstract = {What are the effects that genetics has had on
Anthropological research and how can we think
anthropologically about Genetics? Just as genetic data have
encouraged new hypotheses about human phenotypic variation,
evolutionary history, population interaction, and
environmental effects, so too has Anthropology offered to
genetic studies a new interpretive locus in its history and
perspective. This introduction examines how the fields of
Anthropology and Genetics have arrived at a crucial moment
at which their interaction requires careful examination and
critical reflection. The papers discussed here exemplify how
we may engage in such a trans-disciplinary conversation.
They speak to the future of thoughtful interaction between
genetic and anthropological literature and seek a new
integration that embodies the holism of the human biological
sciences.},
Doi = {10.1002/ajpa.23022},
Key = {fds354021}
}
@article{fds340695,
Author = {Goldberg, A and Mychajliw, AM and Hadly, EA},
Title = {Post-invasion demography of prehistoric humans in South
America.},
Journal = {Nature},
Volume = {532},
Number = {7598},
Pages = {232-235},
Publisher = {Springer Science and Business Media LLC},
Year = {2016},
Month = {April},
url = {http://dx.doi.org/10.1038/nature17176},
Abstract = {As the last habitable continent colonized by humans, the
site of multiple domestication hotspots, and the location of
the largest Pleistocene megafaunal extinction, South America
is central to human prehistory. Yet remarkably little is
known about human population dynamics during colonization,
subsequent expansions, and domestication. Here we
reconstruct the spatiotemporal patterns of human population
growth in South America using a newly aggregated database of
1,147 archaeological sites and 5,464 calibrated radiocarbon
dates spanning fourteen thousand to two thousand years ago
(ka). We demonstrate that, rather than a steady exponential
expansion, the demographic history of South Americans is
characterized by two distinct phases. First, humans spread
rapidly throughout the continent, but remained at low
population sizes for 8,000 years, including a 4,000-year
period of 'boom-and-bust' oscillations with no net growth.
Supplementation of hunting with domesticated crops and
animals had a minimal impact on population carrying
capacity. Only with widespread sedentism, beginning ~5 ka,
did a second demographic phase begin, with evidence for
exponential population growth in cultural hotspots,
characteristic of the Neolithic transition worldwide. The
unique extent of humanity's ability to modify its
environment to markedly increase carrying capacity in South
America is therefore an unexpectedly recent
phenomenon.},
Doi = {10.1038/nature17176},
Key = {fds340695}
}
@article{fds354022,
Author = {Kang, JTL and Goldberg, A and Edge, MD and Behar, DM and Rosenberg,
NA},
Title = {Consanguinity Rates Predict Long Runs of Homozygosity in
Jewish Populations.},
Journal = {Human heredity},
Volume = {82},
Number = {3-4},
Pages = {87-102},
Year = {2016},
Month = {January},
url = {http://dx.doi.org/10.1159/000478897},
Abstract = {<h4>Objectives</h4>Recent studies have highlighted the
potential of analyses of genomic sharing to produce insight
into the demographic processes affecting human populations.
We study runs of homozygosity (ROH) in 18 Jewish
populations, examining these groups in relation to 123
non-Jewish populations sampled worldwide.<h4>Methods</h4>By
sorting ROH into 3 length classes (short, intermediate, and
long), we evaluate the impact of demographic processes on
genomic patterns in Jewish populations.<h4>Results</h4>We
find that the portion of the genome appearing in long ROH -
the length class most directly related to recent
consanguinity - closely accords with data gathered from
interviews during the 1950s on frequencies of consanguineous
unions in various Jewish groups.<h4>Conclusion</h4>The high
correlation between 1950s consanguinity levels and coverage
by long ROH explains differences across populations in ROH
patterns. The dissection of ROH into length classes and the
comparison to consanguinity data assist in understanding a
number of additional phenomena, including similarities of
Jewish populations to Middle Eastern, European, and Central
and South Asian non-Jewish populations in short ROH
patterns, relative lengths of identity-by-descent tracts in
different Jewish groups, and the "population isolate" status
of the Ashkenazi Jews.},
Doi = {10.1159/000478897},
Key = {fds354022}
}
@article{fds354023,
Author = {Goldberg, A and Rosenberg, NA},
Title = {Beyond 2/3 and 1/3: The Complex Signatures of Sex-Biased
Admixture on the X Chromosome.},
Journal = {Genetics},
Volume = {201},
Number = {1},
Pages = {263-279},
Year = {2015},
Month = {September},
url = {http://dx.doi.org/10.1534/genetics.115.178509},
Abstract = {Sex-biased demography, in which parameters governing
migration and population size differ between females and
males, has been studied through comparisons of X
chromosomes, which are inherited sex-specifically, and
autosomes, which are not. A common form of sex bias in
humans is sex-biased admixture, in which at least one of the
source populations differs in its proportions of females and
males contributing to an admixed population. Studies of
sex-biased admixture often examine the mean ancestry for
markers on the X chromosome in relation to the autosomes. A
simple framework noting that in a population with equally
many females and males, two-thirds of X chromosomes appear
in females, suggests that the mean X-chromosomal admixture
fraction is a linear combination of female and male
admixture parameters, with coefficients 2/3 and 1/3,
respectively. Extending a mechanistic admixture model to
accommodate the X chromosome, we demonstrate that this
prediction is not generally true in admixture models,
although it holds in the limit for an admixture process
occurring as a single event. For a model with constant
ongoing admixture, we determine the mean X-chromosomal
admixture, comparing admixture on female and male X
chromosomes to corresponding autosomal values. Surprisingly,
in reanalyzing African-American genetic data to estimate
sex-specific contributions from African and European
sources, we find that the range of contributions compatible
with the excess African ancestry on the X chromosome
compared to autosomes has a wide spread, permitting
scenarios either without male-biased contributions from
Europe or without female-biased contributions from
Africa.},
Doi = {10.1534/genetics.115.178509},
Key = {fds354023}
}
@article{fds336366,
Author = {Goldberg, A and Rosenberg, N},
Title = {Beyond 2/3 and 1/3: the complex signatures of sex-biased
admixture on the X chromosome},
Year = {2015},
Month = {March},
url = {http://dx.doi.org/10.1101/016543},
Abstract = {Sex-biased demography, in which parameters governing
migration and population size differ between females and
males, has been studied through comparisons of X
chromosomes, which are inherited sex-specifically, and
autosomes, which are not. A common form of sex bias in
humans is sex-biased admixture, in which at least one of the
source populations differs in its proportions of females and
males contributing to an admixed population. Studies of
sex-biased admixture often examine the mean ancestry for
markers on the X chromosome in relation to the autosomes. A
simple framework noting that in a population with equally
many females and males, 2/3 of X chromosomes appear in
females, suggests that the mean X-chromosomal admixture
fraction is a linear combination of female and male
admixture parameters, with coefficients 2/3 and 1/3,
respectively. Extending a mechanistic admixture model to
accommodate the X chromosome, we demonstrate that this
prediction is not generally true in admixture models, though
it holds in the limit for an admixture process occurring as
a single event. For a model with constant ongoing admixture,
we determine the mean X-chromosomal admixture, comparing
admixture on female and male X chromosomes to corresponding
autosomal values. Surprisingly, in reanalyzing
African-American genetic data to estimate sex-specific
contributions from African and European sources, we find
that the range of contributions compatible with the excess
African ancestry on the X chromosome compared to autosomes
has a wide spread, permitting scenarios either without
male-biased contributions from Europe or without
female-biased contributions from Africa.},
Doi = {10.1101/016543},
Key = {fds336366}
}
@article{fds354024,
Author = {Goldberg, A and Verdu, P and Rosenberg, NA},
Title = {Autosomal admixture levels are informative about sex bias in
admixed populations.},
Journal = {Genetics},
Volume = {198},
Number = {3},
Pages = {1209-1229},
Year = {2014},
Month = {November},
url = {http://dx.doi.org/10.1534/genetics.114.166793},
Abstract = {Sex-biased admixture has been observed in a wide variety of
admixed populations. Genetic variation in sex chromosomes
and functions of quantities computed from sex chromosomes
and autosomes have often been examined to infer patterns of
sex-biased admixture, typically using statistical approaches
that do not mechanistically model the complexity of a
sex-specific history of admixture. Here, expanding on a
model of Verdu and Rosenberg (2011) that did not include sex
specificity, we develop a model that mechanistically
examines sex-specific admixture histories. Under the model,
multiple source populations contribute to an admixed
population, potentially with their male and female
contributions varying over time. In an admixed population
descended from two source groups, we derive the moments of
the distribution of the autosomal admixture fraction from a
specific source population as a function of sex-specific
introgression parameters and time. Considering admixture
processes that are constant in time, we demonstrate that
surprisingly, although the mean autosomal admixture fraction
from a specific source population does not reveal a sex bias
in the admixture history, the variance of autosomal
admixture is informative about sex bias. Specifically, the
long-term variance decreases as the sex bias from a
contributing source population increases. This result can be
viewed as analogous to the reduction in effective population
size for populations with an unequal number of breeding
males and females. Our approach suggests that it may be
possible to use the effect of sex-biased admixture on
autosomal DNA to assist with methods for inference of the
history of complex sex-biased admixture processes.},
Doi = {10.1534/genetics.114.166793},
Key = {fds354024}
}
%% Papers Presented/Symposia/Abstracts
@article{fds342235,
Author = {Bobrek, K and Beleza, S and Goldberg, A},
Title = {Sex-biased admixture and geographic mating structure shape
genomic variation in Cape Verde},
Journal = {AMERICAN JOURNAL OF PHYSICAL ANTHROPOLOGY},
Volume = {168},
Pages = {23-23},
Publisher = {WILEY},
Year = {2019},
Month = {March},
Key = {fds342235}
}
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