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Duke University

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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{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{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},
   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{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},
   Month = {September},
   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{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 of the Royal Society B: 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{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},
   Month = {December},
   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{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{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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