Logan J Kistler

Logan J Kistler
Smithsonian Institution · Department of Anthropology

PhD Anthropology

About

81
Publications
19,176
Reads
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1,543
Citations
Citations since 2016
65 Research Items
1459 Citations
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Introduction
I study plant domestication and evolutionary ecology in the human context using ancient DNA and genomics. In particular, the adaptability of maize and the domestication and movement of gourds and squashes. I also collaborate on issues of biodiversity and endemic ecosystem conservation in eastern Cuba, and on genomic research into Madagascar's giant, extinct, subfossil lemurs. Broadly, my work deals with human-environment interactions and human impacts on ancient and modern ecosystems.
Additional affiliations
August 2012 - August 2014
Pennsylvania State University
Position
  • PostDoc Position

Publications

Publications (81)
Article
Full-text available
Significance Bottle gourd, one of the most cross-culturally ubiquitous crops, had a pan-tropical distribution by the beginning of the Holocene. Our findings overturn a major component of the current model for bottle gourd’s early global dispersal, specifically regarding how it entered the Americas. Our findings also indicate that the domestication...
Article
Full-text available
The colonization of the human environment by plants, and the consequent evolution of domesticated forms is increasingly being viewed as a co-evolutionary plant–human process that occurred over a long time period, with evidence for the co-evolutionary relationship between plants and humans reaching ever deeper into the hominin past. This developing...
Article
Full-text available
Significance Squashes, pumpkins, and gourds belonging to the genus Cucurbita were domesticated on several occasions throughout the Americas, beginning around 10,000 years ago. The wild forms of these species are unpalatably bitter to humans and other extant mammals, but their seeds are present in mastodon dung deposits, demonstrating that they may...
Article
Full-text available
The persistence of DNA over archaeological and paleontological timescales in diverse environments has led to a revolutionary body of paleogenomic research, yet the dynamics of DNA degradation are still poorly understood. We analyzed 185 paleogenomic datasets and compared DNA survival with environmental variables and sample ages. We find cytosine de...
Article
The complexity of maize domestication Maize originated in what is now central Mexico about 9000 years ago and spread throughout the Americas before European contact. Kistler et al. applied genomic analysis to ancient and extant South American maize lineages to investigate the genetic changes that accompanied domestication (see the Perspective by Ze...
Article
Abbo and Gopher contend that we offer nothing new to the study of domestication in three recent papers (Bogaard et al., 2021; Allaby et al., 2021, Allaby et al., 2022b). They claim that we offer no “innovation, a new venue of research” and “use a new jargon to express old ideas.” They further claim as erroneous our key conclusions about domesticati...
Article
Full-text available
South America is a megadiverse continent that witnessed the domestication, translocation and cultivation of various plant species from seemingly contrasting ecosystems. It was the recipient and supplier of crops brought to and from Mesoamerica (such as maize and cacao, respectively), and Polynesia to where the key staple crop sweet potato was expor...
Article
Full-text available
The evidence from ancient crops over the past decade challenges some of our most basic assumptions about the process of domestication. The emergence of crops has been viewed as a technologically progressive process in which single or multiple localized populations adapt to human environments in response to cultivation. By contrast, new genetic and...
Chapter
As genetic and archaeological evidence has developed over the past few years, it has become apparent that our most basic assumptions about how crops became incorporated into human culture may be in need of fundamental revision. Conventionally, crop origins have been understood through a local founding model in which one or multiple centers of small...
Article
The genus Manihot, with around 120 known species, is native to a wide range of habitats and regions in the tropical and subtropical Americas. Its high species richness and recent diversification only ~6Mya have significantly complicated previous phylogenetic analyses. Several basic elements of Manihot evolutionary history therefore remain unresolve...
Article
Full-text available
Significance Based on “subfossil” skeletal remains it is known that multiple now-extinct giant lemur (primate) species with estimated body masses of up to ∼160 kg survived on Madagascar into the past millennium. In this study, we used ancient DNA methods to sequence the nuclear genome of one of these megafaunal lemurs, Megaladapis edwardsi (∼85 kg)...
Article
Significance The brightly colored feathers of macaws, amazons, and other neotropical parrots were one of the most important symbols of wealth, power, and sacredness in the pre-Columbian Americas. Andean highland and coastal societies imported these exotic goods from Amazonian tropical forests by little-understood mechanisms of exchange. The study o...
Article
Full-text available
Significance Maize is a global food staple with great economic and cultural importance. Archaeogenomic studies have revealed a process of protracted maize domestication and multiple waves of human-mediated dispersal in the Americas. Maize first arrived in South America as a partial domesticate, where the domestication syndrome became independently...
Preprint
Full-text available
No endemic Madagascar animal with body mass >10 kg survived a relatively recent wave of extinction on the island. From morphological and isotopic analyses of skeletal ‘subfossil’ remains we can reconstruct some of the biology and behavioral ecology of giant lemurs (primates; up to ~160 kg), elephant birds (up to ~860 kg), and other extraordinary Ma...
Article
Full-text available
Doggerland was a landmass occupying an area currently covered by the North Sea until marine inundation took place during the mid-Holocene, ultimately separating the British landmass from the rest of Europe. The Storegga Event, which triggered a tsunami reflected in sediment deposits in the northern North Sea, northeast coastlines of the British Isl...
Article
Full-text available
The ancient DNA revolution of the past 35 years has driven an explosion in the breadth, nuance, and diversity of questions that are approachable using ancient biomolecules, and plant research has been a constant, indispensable facet of these developments. Using archaeological, paleontological, and herbarium plant tissues, researchers have probed pl...
Article
Full-text available
Since the beginning of the ancient DNA revolution in the 1980s, archeological plant remains and herbarium specimens have been analyzed with molecular techniques to probe the evolutionary interface of plants and humans. In tandem with archeobotany, ethnobiology, and other methods, ancient DNA offers tremendous insights into the co-evolution of peopl...
Article
Full-text available
The ancient DNA revolution of the past 35 years has driven an explosion in the breadth, nuance, and diversity of questions that are approachable using ancient biomolecules, and plant research has been a constant, indispensable facet of these developments. Using archaeological, paleontological, and herbarium plant tissues, researchers have probed pl...
Preprint
Full-text available
Doggerland was a land mass occupying an area currently covered by the North Sea until marine inundation took place during the mid-Holocene, ultimately separating the British land mass from the rest of Europe. The Storegga Slide, which triggered a tsunami reflected in sediment deposits in the Northern North Sea, North East coastlines of the British...
Article
Full-text available
High-throughput DNA sequencing techniques enable time- and cost-effective sequencing of large portions of the genome. Instead of sequencing and annotating whole genomes, many phylogenetic studies focus sequencing effort on large sets of pre-selected loci, which further reduces costs and bioinformatic challenges while increasing coverage. One common...
Preprint
Full-text available
High-throughput DNA sequencing techniques enable time- and cost-effective sequencing of large portions of the genome. Instead of sequencing and annotating whole genomes, many phylogenetic studies focus sequencing efforts on large sets of pre-selected loci, which further reduces costs and bioinformatic challenges while increasing sequencing depth. O...
Preprint
Full-text available
High-throughput DNA sequencing techniques enable time- and cost-effective sequencing of large portions of the genome. Instead of sequencing and annotating whole genomes, many phylogenetic studies focus sequencing efforts on large sets of pre-selected loci, which further reduces costs and bioinformatic challenges while increasing sequencing depth. O...
Article
Full-text available
The evolution of domesticated cereals was a complex interaction of shifting selection pressures and repeated episodes of introgression. Genomes of archaeological crops have the potential to reveal these dynamics without being obscured by recent breeding or introgression. We report a temporal series of archaeogenomes of the crop sorghum (Sorghum bic...
Chapter
Ancient plant remains from archaeological sites, paleoenvironmental contexts, and herbaria provide excellent opportunities for interrogating plant genetics over Quaternary timescales using ancient DNA (aDNA)-based analyses. A variety of plant tissues, preserved primarily by desiccation and anaerobic waterlogging, have proven to be viable sources of...
Article
Ancient DNA analysis integrates the deep‐time perspective of archaeology and paleontology with the capacity of genetics to address questions of evolution, ecology, and population biology. This toolkit serves as a powerful complement to paleoethnobotany, the analysis of archaeological plant remains. Ancient DNA research with plant tissues has been d...
Chapter
The genetic history of domestic plants is complex, protracted, and unique to often very specific factors including location, human intent, and the wider environment. In addition to well-addressed questions of domestication syndrome, and conscious versus unconscious selection, the issue of domestication poses a plethora of more nuanced questions, in...
Article
Full-text available
Significance Archaeogenomic analysis of scarlet macaw bones demonstrates that the genetic diversity of these birds acquired by people in the southwestern United States (SW) between 900 and 1200 CE was exceedingly low. Only one mitochondrial DNA haplogroup (Haplo6) is present of the five historically known haplogroups in the lowland forests of Mexic...
Article
Full-text available
Domesticated crops show a reduced level of diversity that is commonly attributed to the ‘domestication bottleneck’; a drastic reduction in the population size associated with sub‐sampling the wild progenitor species and the imposition of selection pressures associated with the domestication syndrome. A prediction of the domestication bottleneck is...
Article
Full-text available
Motivation: Massively parallel capture of short tandem repeats (STRs, or microsatellites) provides a strategy for population genomic and demographic analyses at high resolution with or without a reference genome. However, the high Polymerase Chain Reaction (PCR) cycle numbers needed for target capture experiments create genotyping noise through pol...
Preprint
Full-text available
The evolution of domesticated cereals was a complex interaction of shifting selection pressures and repeated introgressions. Genomes of archaeological crops have the potential to reveal these dynamics without being obscured by recent breeding or introgression. We report a temporal series of archaeogenomes of the crop sorghum (Sorghum bicolor) from...
Article
Full-text available
Significance Maize was initially domesticated in the Balsas region of Mexico ∼9,000 y ago, but it remains unclear when this globally important cultigen became a staple crop in the Americas. We demonstrate that highly productive maize varieties were present in Central America outside the natural distribution of ancestral teosinte populations [ Zea m...
Article
Several taxonomically distinct mammalian groups-certain microbats and cetaceans (e.g., dolphins)-share both morphological adaptations related to echolocation behavior and strong signatures of convergent evolution at the amino acid level across seven genes related to auditory processing. Aye-ayes (Daubentonia madagascariensis) are nocturnal lemurs w...
Article
Full-text available
Short tandem repeat (STR) variants are highly polymorphic markers that facilitate powerful population genetic analyses. STRs are especially valuable in conservation and ecological genetic research, yielding detailed information on population structure and short-term demographic fluctuations. Massively parallel sequencing has not previously been lev...
Article
Full-text available
The persistence of DNA over archaeological and paleontological timescales in diverse environments has led to revolutionary body of paleogenomic research, yet the dynamics of DNA degradation are still poorly understood. We analyzed 185 paleogenomic datasets and compared DNA survival with environmental variables and sample ages. We find cytosine deam...
Chapter
Full-text available
In this chapter, we summarize recent contributions made by archaeologists and researchers in other disciplines toward understanding the many factors involved in the domestication of Chenopodium berlandieri in North America and Chenopodium quinoa in South America. We focus on studies of seed morphology and molecular genetics, which have aided in cla...
Article
Full-text available
For societies with writing systems, hereditary leadership is documented as one of the hallmarks of early political complexity and governance. In contrast, it is unknown whether hereditary succession played a role in the early formation of prehistoric complex societies that lacked writing. Here we use an archaeogenomic approach to identify an elite...
Data
List of ancient samples, sequencing results, genetic sex results, and osteological analysis.
Data
List of modern mitogenome accession numbers, geographic origins, and Pueblo Bonito Room 33 samples.
Data
Supplementary Figures, Supplementary Tables, and Supplementary Notes
Preprint
Full-text available
Short tandem repeat (STRs or microsatellites) variants, are highly polymorphic markers that facilitate powerful, high-precision population genetic analyses. STRs are especially valuable in conservation and ecological genetic research, yielding detailed information on population structure and short-term demographic flux. However, STR marker developm...
Preprint
Full-text available
Several taxonomically distinct mammalian groups – certain microbats and cetaceans (e.g. dolphins) – share both morphological adaptations related to echolocation behavior and strong signatures of convergent evolution at the amino acid level across seven genes related to auditory processing. Aye-ayes ( Daubentonia madagascariensis ) are nocturnal lem...
Article
Full-text available
Debate on the adaptive origins of primates has long focused on the functional ecology of the primate visual system. For example, it is hypothesized that variable expression of short- (SWS1) and middle-to-long-wavelength sensitive (M/LWS) opsins, which confer color vision, can be used to infer ancestral activity patterns and therefore selective ecol...