Ripan S Malhi

University of Illinois, Urbana-Champaign | UIUC · Department of Anthropology

Large canids (wolves, dogs, and coyote) and people form a close relationship in northern (subarctic and arctic) so-cioecological systems. Here, we document the antiquity of this bond and the multiple ways it manifested in interior Alaska, a region key to understanding the peopling of the Americas and early northern lifeways. We compile original and...

Multiple studies have demonstrated that European colonization of the Americas led to the death of nearly all North American dog mitochondrial lineages and replacement with European ones sometime between AD 1492 and the present day. Historical records indicate that colonists imported dogs from Europe to North America, where they became objects of in...

Mutually beneficial partnerships between genomics researchers and North American Indigenous Nations are rare yet becoming more common. Here, we present one such partnership that provides insight into the peopling of the Americas and furnishes another line of evidence that can be used to further treaty and Indigenous rights. We show that the genomic...

Cape lions (Panthera leo melanochaitus) formerly ranged throughout the grassland plains of the "Cape Flats" in what is today known as the Western Cape Province, South Africa. Cape lions were likely eradicated because of overhunting and habitat loss after European colonization. European naturalists originally described Cape lions as "Black-maned lio...

Modern humans carry both Neanderthal and Denisovan (archaic) genome elements that are part of the human gene pool and affect the life and health of living individuals. The impact of archaic DNA may be particularly evident in pharmacogenes—genes responsible for the processing of exogenous substances such as food, pollutants, and medications—as these...

Background Historical trauma experienced by Indigenous peoples of North America is correlated with health disparities and is hypothesized to be associated with DNA methylation. Massive group traumas such as genocide, loss of land and foodways, and forced conversion to Western lifeways may be embodied and affect individuals, families, communities, c...

Extinct Cape lions ( Panthera leo melanochaitus ) formerly ranged throughout the grassland plains of the "Cape Flats" in what is today known as the Western Cape Province, South Africa. Cape lions were likely eradicated because of overhunting and habitat loss after European colonization. European naturalists originally described Cape lions as "Black...

In the United States, the Native American Graves Protection and Repatriation Act (NAGPRA) provides a specific framework for the disposition of Native American Ancestral remains within its purview. However, samples such as a bone fragment, tooth, or other biological tissue taken from the remains of these Ancestors have been treated by institutions a...

Objectives: The field of paleogenomics has rapidly grown, influencing a range of scientific fields and drawing notice from the public. In the United States, this work is especially salient for Native Americans, who are frequently the subject of ancient DNA analyses, but are less frequently included as researchers, collaborators, or advisors. This...

Non-invasive biological samples benefit studies that investigate rare, elusive, endangered, or dangerous species. Integrating genomic techniques that use non-invasive biological sampling with advances in computational approaches can benefit and inform wildlife conservation and management. Here, we used non-invasive fecal DNA samples to generate low...

The ethics of the scientific study of Ancestors has long been debated by archaeologists, bioanthropologists, and, more recently, ancient DNA (aDNA) researchers. This article responds to the article “Ethics of DNA research on human remains: five globally applicable guidelines” published in 2021 in Nature by a large group of aDNA researchers and coll...

Nuclear mitochondrial pseudogenes (numts) may hinder the reconstruction of mtDNA genomes and affect the reliability of mtDNA datasets for phylogenetic and population genetic comparisons. Here, we present the program Numt Parser, which allows for the identification of DNA sequences that likely originate from numt pseudogene DNA. Sequencing reads are...

Non-invasive biological samples benefit studies that investigate rare, elusive, endangered, and/or dangerous species. Integrating genomic techniques that use non-invasive biological samples with advances in computational approaches can benefit and inform wildlife conservation and management. Here we present a molecular pipeline that uses non-invasi...

Canine microbiome studies are often limited in the geographic and temporal scope of samples studied. This results in a paucity of data on the canine microbiome around the world, especially in contexts where dogs may not be pets or human associated. Here, we present the shotgun sequences of fecal microbiomes of pet dogs from South Africa, shelter an...

Nuclear mitochondrial pseudogenes (numts) may hinder the reconstruction of mtDNA genomes and affect the reliability of mtDNA datasets for phylogenetic and population genetic comparisons. Here, we present the program NUMT PARSER, which allows for the identification of DNA sequences that likely originate from numt pseudogene DNA. Sequencing reads are...

Significance California supports a high cultural and linguistic diversity of Indigenous peoples. In a partnership of researchers with the Muwekma Ohlone tribe, we studied genomes of eight present-day tribal members and 12 ancient individuals from two archaeological sites in the San Francisco Bay Area, spanning ∼2,000 y. We find that compared to gen...

This study presents genetic data for nine Native American populations from northern North America. Analyses of genetic variation focus on the Pacific Northwest (PNW). Using mitochondrial, Y chromosomal, and autosomal DNA variants, we aimed to more closely address the relationships of geography and language with present genetic diversity among the r...

Modern humans carry Neanderthal and Denisovan (archaic) genome elements which may have been a result of environmental adaptation. These effects may be particularly evident in pharmacogenes - genes responsible for the processing of exogenous substances such as food, pollutants, and medications. However, the health implications and contribution of ar...

The ‘social microbiome’ can fundamentally shape the costs and benefits of group-living, but understanding social transmission of microbes in free-living animals is challenging due to confounding effects of kinship and shared environments (e.g. highly associated individuals often share the same spaces, food and water). Here, we report evidence for c...

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)...

An amendment to this paper has been published and can be accessed via a link at the top of the paper.

Paleofeces or coprolites are often used to reconstruct diet at archaeological sites, usually using macroscopic analyses or targeted DNA amplification and sequencing. Here we present an integrative analysis of dog coprolites, combining macroscopic analyses, stable isotope measurements, and DNA shotgun sequencing to examine diet and health status. Do...

The oldest known shipwreck in southern Africa was found in Namibia in 2008. Forty tons of cargo, including gold and silver coins, helped identify the ship as the BomJesus, a Portuguese nau (trading vessel) lost in 1533 while headed to India. The cargo included >100 elephant tusks which we examined using paleogenomic and stable isotope analyses. Nuc...

Advances in the isolation and sequencing of ancient DNA have begun to reveal the population histories of both people and dogs. Over the last 10,000 y, the genetic signatures of ancient dog remains have been linked with known human dispersals in regions such as the Arctic and the remote Pacific. It is suspected, however, that this relationship has a...

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...

Sex estimation of skeletons is fundamental to many archaeological studies. Currently, three approaches are available to estimate sex–osteology, genomics, or proteomics, but little is known about the relative reliability of these methods in applied settings. We present matching osteological, shotgun-genomic, and proteomic data to estimate the sex of...

Objectives Long‐tailed macaques (Macaca fascicularis ) are widely distributed throughout the mainland and islands of Southeast Asia, making them a useful model for understanding the complex biogeographical history resulting from drastic changes in sea levels throughout the Pleistocene. Past studies based on mitochondrial genomes (mitogenomes) of lo...

Addressing Indigenous rights and interests in genetic resources has become increasingly challenging in an open science environment that promotes unrestricted access to genomic data. Although Indigenous experiences with genetic research have been shaped by a series of negative interactions, there is increasing recognition that equitable benefits can...

Sex identification of ancient animal biological remains can benefit our understanding of historical population structure, demography and social behavior. Traditional methods for sex identification (e.g. osteological and morphometric comparisons) may be ineffective when animal remains are not well preserved, when sex distinguishing characteristics h...

Grey wolves (Canis lupus) are one of the few large terrestrial carnivores that have maintained a wide geographic distribution across the Northern Hemisphere throughout the Pleistocene and Holocene. Recent genetic studies have suggested that, despite this continuous presence, major demographic changes occurred in wolf populations between the late Pl...

Illegal hunting is a major threat to the elephants of Africa, with more elephants killed by poachers than die from natural causes. DNA from tusks has been used to infer the source populations for confiscated ivory, relying on nuclear genetic markers. However, mitochondrial DNA (mtDNA) sequences can also provide information on the geographic origins...

Automated, high-throughput technologies are becoming increasingly common in microbiome studies to decrease costs and increase efficiency. However, in microbiome studies, small differences in methodology - including storage conditions, wet lab methods, sequencing platforms and data analysis - can influence the reproducibility and comparability of da...

Northeastern Siberia has been inhabited by humans for more than 40,000 years but its deep population history remains poorly understood. Here we investigate the late Pleistocene population history of northeastern Siberia through analyses of 34 newly recovered ancient genomes that date to between 31,000 and 600 years ago. We document complex populati...

Archaeologists often struggle with the challenge of linking historic-period artifact assemblages with specific communities. In particular, small home sites discovered on historic plantations are often difficult to identify as an African American or white tenant house since the material culture appears similar. The discipline also struggles with how...

Complex processes in the settling of the Americas The expansion into the Americas by the ancestors of present day Native Americans has been difficult to tease apart from analyses of present day populations. To understand how humans diverged and spread across North and South America, Moreno-Mayar et al. sequenced 15 ancient human genomes from Alaska...

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...

Some recent academic and popular literature implies that the problem of the colonization of the Americas has been largely resolved in favor of one specific model: a Pacific coastal migration, dependent on high marine productivity, from the Bering Strait to South America, thousands of years before Clovis, the earliest widespread cultural manifestati...

DNA metabarcoding is a powerful tool for assessing the diets of wild animals, but there is no clear consensus on which proposed plant barcoding marker is most suitable for dietary analysis. This study compares two DNA plant barcoding markers that are commonly used for dietary analyses from degraded DNA, rbcL and trnL, to detailed dietary observatio...

Relative abundance of rbcL sequences assigned specific taxa for the entire study period. (XLSX)

ecotag output for rbcL sequences with taxonomic annotations. (TXT)

Detailed methods for the bioinformatic analyses. (DOCX)

Relative abundance of trnL sequences assigned specific taxa for the entire study period. (XLSX)

ecotag output for trnL sequences with taxonomic annotations. (TXT)

Percentage of observed feeding and foraging time spent consuming plant species in each month. (XLSX)

Correlations between observed percentage of feeding and foraging time on plant families and both frequency of occurrence and relative abundances of rbcL and trnL sequences. (XLSX)

Founder effects in modern populations The genomes of ancient humans can reveal patterns of early human migration (see the Perspective by Achilli et al. ). Iceland has a genetically distinct population, despite relatively recent settlement (∼1100 years ago). Ebenesersdóttir et al. examined the genomes of ancient Icelandic people, dating to near the...

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...

Ancestral remains should be regarded not as “artifacts” but as human relatives who deserve respect

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...

The Sumatran rhinoceros (Dicerorhinus sumatrensis), once widespread across Southeast Asia, now consists of as few as 30 individuals within Sumatra and Borneo. To aid in conservation planning, we sequenced 218 bp of control region mitochondrial (mt) DNA, identifying 17 distinct mitochondrial haplotypes across modern (N = 13) and museum (N = 26) samp...

Seven fish vertebrae were chosen for analysis from the 49-KEN-147 archaeological site in the Kenai Peninsula, Alaska. Mitochondrial DNA analysis of the ancient fish bones revealed that they were from sockeye and coho salmon. Here, we report the ancient mitochondrial genomes for three sockeye salmon and one coho salmon fish bone.

Despite broad agreement that the Americas were initially populated via Beringia, the land bridge that connected far northeast Asia with northwestern North America during the Pleistocene epoch, when and how the peopling of the Americas occurred remains unresolved1–5. Analyses of human remains from Late Pleistocene Alaska are important to resolving t...

Supplemental Data for Terminal Pleistocene Alaskan genome reveals first founding population of Native Americans

The field of paleogenomics (the study of ancient genomes) is rapidly advancing, with more robust methods of isolating ancient DNA and increasing access to next-generation DNA sequencing technology. As these studies progress, many important ethical issues have emerged that should be considered when ancient Native American remains, whom we refer to a...

The curse of ancient Egyptian DNA was lifted by a recent study which sequenced the mitochondrial genomes (mtGenome) of 90 ancient Egyptians from the archaeological site of Abusir el-Meleq. Surprisingly, these ancient inhabitants were more closely related to those from the Near East than to contemporary Egyptians. It has been accepted that the timel...

The field of paleogenomics (the study of ancient genomes) is rapidly advancing, with more robust methods of isolating ancient DNA and increasing access to next-generation DNA sequencing technology. As these studies progress, many important ethical issues have emerged that should be considered when ancient Native American remains, whom we refer to a...

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...