John Lindo

John Lindo
Emory University | EU · Department of Anthropology

JD, PhD

About

36
Publications
14,723
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958
Citations
Introduction
Specialize in Ancient DNA, Population Genetics, and Functional Genomics.
Additional affiliations
July 2017 - present
Emory University
Position
  • Professor (Assistant)
August 2015 - August 2017
University of Chicago
Position
  • PostDoc Position
August 2010 - August 2015
University of Illinois, Urbana-Champaign
Position
  • PhD Student

Publications

Publications (36)
Article
The increasing availability of next generation sequencing techniques in recent decades has led to new discoveries, and sometimes the redefinition of conventional hypotheses, regarding many complex human‐pathogen evolutionary relationships. These new discoveries are particularly poignant in studies of the Americas, where research into Indigenous anc...
Preprint
An increasing body of archaeological and genomic evidence has hinted to a complex settlement process of the Americas. This is especially true for South America, where unexpected ancestral signals have raised perplexing scenarios for the early migrations into different regions of the continent. Here we present ancient genomes from the archaeological...
Article
Full-text available
The prehistory of the people of Uruguay is greatly complicated by the dramatic and severe effects of European contact, as with most of the Americas. After the series of military campaigns that exterminated the last remnants of nomadic peoples, Uruguayan official history masked and diluted the former Indigenous ethnic diversity into the narrative of...
Article
Full-text available
The gene-culture coevolution (GCC) framework has gained increasing prominence in the social and biological sciences. While most studies on human GCC concern the evolution of low-level physiological traits, attempts have also been made to apply GCC to complex human traits, including social behavior and cognition. One major methodologi-cal challenge...
Preprint
Full-text available
The prehistory of the people of Uruguay is greatly complicated by the dramatic and severe effects of European contact, as with most of the Americas. After the series of military campaigns that exterminated the last remnants of nomadic peoples, Uruguayan official history masked and diluted the former indigenous ethnic diversity into the narrative of...
Poster
Full-text available
Allele frequencies of oxytocin receptor gene (OXTR) polymorphisms are known to vary across primate species and across human populations. Yet, specific evolutionary mechanisms and phenotypic correlates of these observed differences are unclear. We hypothesized that OXTR variants were selected for their effects on receptor expression in specific brai...
Article
Full-text available
The South American continent is remarkably diverse in its ecological zones, spanning the Amazon rainforest, the high-altitude Andes, and Tierra del Fuego. Yet the original human populations of the continent successfully inhabited all these zones, well before the buffering effects of modern technology. Therefore, it is likely that the various cultur...
Article
Full-text available
Chimpanzees (Pan troglodytes) and bonobos (Pan paniscus) diverged into distinct species approximately 1.7 million years ago when the ancestors of modern‐day bonobo populations were separated by the Congo River. This geographic boundary separates the two species today and the associated ecological factors, including resource distribution and feeding...
Article
Full-text available
The peopling of the Andean highlands above 2500 m in elevation was a complex process that included cultural, biological, and genetic adaptations. Here, we present a time series of ancient whole genomes from the Andes of Peru, dating back to 7000 calendar years before the present (BP), and compare them to 42 new genome-wide genetic variation dataset...
Article
Research using exome analysis to address questions of interest to biological anthropologists is just beginning. These early studies use exomes to address demographic and evolutionary questions in humans. As biotechnological advances continue to lower the costs of DNA sequencing, the use of exomes is likely to increase for biological anthropologists...
Preprint
Full-text available
The peopling of the Andean highlands above 2500m in elevation was a complex process that included cultural, biological and genetic adaptations. Here we present a time series of ancient whole genomes from the Andes of Peru, dating back to 7,000 calendar years before present (BP), and compare them to 64 new genome-wide genetic variation datasets from...
Article
Full-text available
Little is known regarding the first people to enter the Americas and their genetic legacy. Genomic analysis of the oldest human remains from the Americas showed a direct relationship between a Clovis-related ancestral population and all modern Central and South Americans as well as a deep split separating them from North Americans in Canada. We pre...
Article
Full-text available
Little is known regarding the first people to enter the Americas and their genetic legacy.Genomic analysis of the oldest human remains from the Americas showed a direct relationship between a Clovis-related ancestral population and all modern Central and South Americans as well as a deep split separating them from North Americans in Canada.We prese...
Article
Full-text available
The effects of European colonization on the genomes of Native Americans may have produced excesses of potentially deleterious features, mainly due to the severe reductions in population size and corresponding losses of genetic diversity. This assumption, however, neither considers actual genomic patterns that existed before colonization nor does it...
Article
Full-text available
RESUMEN CG14E01 " Isla Larga " es un sitio con estructu-ra monticular (" cerrito de indios ") localizado en el depar-tamento de Rocha (Uruguay), con una cronología que se extiende de 3600 años AP al siglo XVII. En este sitio se registran evidencias vinculadas con diversos contactos inte-rétnicos en la forma de dos urnas Tupiguaraní y cuentas de vid...
Chapter
Full-text available
Despite the 'Age of Genomics', many scholars who study race and the law resist biological insights into human psychology and behaviour. Contemporary developments make this resistance increasingly untenable. This chapter synthesizes recent findings in genomics and evolutionary psychology, which suggest cause for concern over how racial concepts func...
Article
Full-text available
Recent genomic studies of both ancient and modern indigenous people of the Americas have shed light on the demographic processes involved during the first peopling. The Pacific Northwest Coast proves an intriguing focus for these studies because of its association with coastal migration models and genetic ancestral patterns that are difficult to re...
Article
Full-text available
CG14E01 “Isla Larga” es un sitio con estructura monticular (“cerrito de indios”) localizado en el departamento de Rocha (Uruguay), con una cronología que se extiende de 3600 años AP al siglo XVII. En este sitio se registran evidencias vinculadas con diversos contactos interétnicos en la forma de dos urnas Tupiguaraní y cuentas de vidrio de origen e...
Article
Full-text available
Recent genome-wide studies of both ancient and modern indigenous people of the Americas have shed light on the demographic processes involved during the first peopling. The Pacific northwest coast proves an intriguing focus for these studies due to its association with coastal migration models and genetic ancestral patterns that are difficult to re...
Article
Full-text available
A major factor for the population decline of Native Americans after European contact has been attributed to infectious disease susceptibility. To investigate whether a pre-existing genetic component contributed to this phenomenon, here we analyse 50 exomes of a continuous population from the Northwest Coast of North America, dating from before and...
Data
Supplementary Figures 1-12, Supplementary Tables 1-10, Supplementary Notes 1-8 and Supplementary References
Article
Full-text available
The susceptibility of Native Americans to infectious disease has been postulated as a major factor for their population decline after European contact. To investigate if a preexisting genetic component contributed to this phenomenon, we analyzed 50 exomes of both ancient and modern individuals from the Northwest Coast of North America, dating from...
Article
Full-text available
Based on mitochondrial DNA (mtDNA), it has been estimated that at least 15 founder haplogroups peopled the Americas. Subhaplogroup C1d3 was defined based on the mitogenome of a living individual from Uruguay that carried a lineage previously identified in hypervariable region I sequences from ancient and modern Uruguayan individuals. When complete...
Research
Full-text available
How and when the Americas were populated remains contentious. Using ancient and modern genome-wide data, we find that the ancestors of all present-day Native Americans, including Athabascans and Amerindians, entered the Americas as a single migration wave from Siberia no earlier than 23 thousand years ago (KYA), and after no more than 8,000-year is...
Article
Full-text available
How and when the Americas were populated remains contentious. Using ancient and modern genome-wide data, we found that the ancestors of all present-day Native Americans, including Athabascans and Amerindians, entered the Americas as a single migration wave from Siberia no earlier than 23 thousand years ago (ka) and after no more than an 8000-year i...
Article
Full-text available
Prüfer and Meyer raise concerns over the mitochondrial DNA (mtDNA) results we reported for the Hoyo Negro individual, citing failure of a portion of these data to conform to their expectations of ancient DNA (aDNA). Because damage patterns in aDNA vary, outright rejection of our findings on this basis is unwarranted, especially in light of our othe...
Article
Full-text available
We describe the complete mitochondrial genome sequence of an adult male skeleton, discovered at Cañadón Misioneros (Santa Cruz Province, Argentina), and dated 70 ± 30 years before present. The DNA sequence corresponded to haplogroup D4h3a5, native to the Americas and exclusive to the south of Patagonia, where it has been observed both in ancient an...
Article
We describe the complete mitochondrial genome sequence of an adult male skeleton, discovered at Cañadón Misioneros (Santa Cruz Province, Argentina), and dated 70 ± 30 years before present. The DNA sequence corresponded to haplogroup D4h3a5, native to the Americas and exclusive to the south of Patagonia, where it has been observed both in ancient an...
Article
Full-text available
To gain a better understanding of North American population history, complete mitochondrial genomes (mitogenomes) were generated from four ancient and three living individuals of the northern Northwest Coast of North America, specifically the north coast of British Columbia, Canada, current home to the indigenous Tsimshian, Haida, and Nisga'a. The...
Data
DNA damage signatures. The graphs demonstrate an excess of purines at the genomic coordinates located right before the sequence start. This pattern is indicative of ancient DNA, where post-mortem depurination occurs followed by a subsequent fragmentation (Briggs, Stenzel, Johnson, et al. 2007). The Perl script, mapDamage 0.36, measured this pattern...
Article
Discovered in the early 16th century by European colonists, Bermuda is an isolated set of islands located in the mid-Atlantic. Shortly after its discovery, Bermuda became the first English colony to forcibly import its labor by trafficking in enslaved Africans, white ethnic minorities, and indigenous Americans. Oral traditions circulating today amo...

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Projects

Projects (4)
Project
This project aims to investigate the roles of the oxytocin receptor genes (OXTR) in the evolution of uniquely human sociality as well as cross-population differences in various social phenotypes. Central to this project is 1) to quantify the specific intermediate phenotypes of OXTR in the human brain (e.g., region-specific gene expression) and to 2) use them to explore possible signatures of species-level or local adaptation in humans.
Project
Understanding ancient migrations and genetic patterns among Native American groups in California and adjacent regions