Maria C Avila-Arcos

• PhD
• Professor (Assistant) at National Autonomous University of Mexico

Admixture between populations is a common feature of human history. Admixture events introduce new genetic variation that can fuel evolution. Characterizing the significance of admixture events on the evolution of a population across various species is of great interest to evolutionary geneticists. Local Ancestry Inference (LAI) methods infer genet...

Paleogenomic data has informed us about the movements, growth, and relationships of ancient populations. It has also given us context for medically relevant adaptations that appear in present-day humans due to introgression from other hominids, and it continues to help us characterize the evolutionary history of humans. However, ancient DNA (aDNA)...

The strategic location of North Africa has made the region the core of a wide range of human demographic events, including migrations, bottlenecks, and admixture processes. This has led to a complex and heterogeneous genetic and cultural landscape, which remains poorly studied compared to other world regions. Whole-exome sequencing (WES) is particu...

Ancient DNA (aDNA) has added a wealth of information about our species’ history, including insights on genetic origins, migrations and gene flow, genetic admixture, and health and disease. Much early work has focused on continental-level questions, leaving many regional questions, especially those relevant to the Global South, comparatively underex...

Paleogenomic data has informed us about the movements, growth, and relationships of ancient populations. It has also given us context for medically relevant adaptations that appear in present-day humans due to introgression from other hominids, and it continues to help us characterize the evolutionary history of humans. However, ancient DNA (aDNA)...

We study the gene MUC19, for which modern humans carry a Denisovan-like haplotype. MUC19 is a mucin, a glycoprotein that forms gels with various biological functions. We find the diagnostic variants for the Denisovan-like MUC19 haplotype at high frequencies in admixed Latin American individuals among global populations, and at highest frequency in...

The island of St Helena played a crucial role in the suppression of the transatlantic slave trade. Strategically located in the middle of the South Atlantic, it served as a staging post for the Royal Navy and reception point for enslaved Africans who had been "liberated" from slave ships intercepted by the British. In total, St Helena received appr...

Ethical discussions around ancient DNA (aDNA) research predate the technological breakthroughs that led to the accelerated generation of ancient genomic data, revealing a long-due need to address these aspects in the field. Given the diverse conflicts that genomics has raised towards the communities associated with the Non-living Human Ancestors un...

Aridoamerica and Mesoamerica are two distinct cultural areas in northern and central Mexico, respectively, that hosted numerous pre-Hispanic civilizations between 2500 BCE and 1521 CE. The division between these regions shifted southward because of severe droughts ~1100 years ago, which allegedly drove a population replacement in central Mexico by...

In this Journal Club article, María Ávila-Arcos discusses a paper on a medically relevant genetic variant that was found exclusively in Indigenous populations from the Americas. She describes how this work served as inspiration for the inclusion of more diverse populations in the 1000 Genomes Project.

Human populations have been shaped by catastrophes that may have left long-lasting signatures in their genomes. One notable example is the second plague pandemic that entered Europe in ca. 1,347 CE and repeatedly returned for over 300 years, with typical village and town mortality estimated at 10%–40%.¹ It is assumed that this high mortality affect...

Aridoamerica and Mesoamerica are two distinct cultural areas that hosted numerous pre-Hispanic civilizations between 2,500 BCE and 1,521 CE. The division between these regions shifted southward due to severe droughts ca. 1,100 years ago, allegedly driving demographic changes and population replacement in some sites in central Mexico. Here, we prese...

Paleogenomics - the study of ancient genomes - has made significant contributions, especially to our understanding of the evolutionary history of humans. This knowledge influx has been a direct result of the coupling of next-generation sequencing with improved methods for DNA recovery and analysis of ancient samples. The appeal of ancient DNA studi...

Although Brazil was inhabited by more than 3,000 Indigenous populations prior to European colonization, today’s Indigenous peoples represent less than 1% of Brazil’s census population. Some of the decimated communities belonged to the so-called “Botocudos” from central-eastern Brazil. These peoples are thought to represent a case of long-standing g...

Although the first ancient DNA molecules were extracted more than three decades ago, the first ancient nuclear genomes could only be characterized after high-throughput sequencing was invented. Genome-scale data have now been gathered from thousands of ancient archaeological specimens, and the number of ancient biological tissues amenable to genome...

Polynesia was settled in a series of extraordinary voyages across an ocean spanning one third of the Earth¹, but the sequences of islands settled remain unknown and their timings disputed. Currently, several centuries separate the dates suggested by different archaeological surveys2–4. Here, using genome-wide data from merely 430 modern individuals...

The ‘red complex’ is an aggregate of three oral bacteria ( Tannerella forsythia , Porphyromonas gingivalis and Treponema denticola ) responsible for severe clinical manifestation of periodontal disease. Here, we report the first direct evidence of ancient T. forsythia DNA in dentin and dental calculus samples from archaeological skeletal remains th...

The possibility of voyaging contact between prehistoric Polynesian and Native American populations has long intrigued researchers. Proponents have pointed to the existence of New World crops, such as the sweet potato and bottle gourd, in the Polynesian archaeological record, but nowhere else outside the pre-Columbian Americas1–6, while critics have...

After the European colonization of the Americas there was a dramatic population collapse of the Indigenous inhabitants caused in part by the introduction of new pathogens. Although there is much speculation on the etiology of the Colonial epidemics, direct evidence for the presence of specific viruses during the Colonial era is lacking. To uncover...

Abstract Evolutionary processes, including selection, can be indirectly inferred based on patterns of genomic variation among contemporary populations or species. However, this often requires unrealistic assumptions of ancestral demography and selective regimes. Sequencing ancient DNA from temporally spaced samples can inform about past selection p...

Native American genetic variation remains underrepresented in most catalogs of human genome sequencing data. Previous genotyping efforts have revealed that Mexico's indigenous population is highly differentiated and substructured, thus potentially harboring higher proportions of private genetic variants of functional and biomedical relevance. Here...

From 1500 to 1900, an estimated 12 million Africans were transported to the Americas as part of the transatlantic slave trade. Following Britain's abolition of slave trade in 1807, the Royal Navy patrolled the Atlantic and intercepted slave ships that continued to operate. During this period, the island of St Helena in the South Atlantic served as...

Native American genetic variation remains underrepresented in most catalogs of human genome sequencing data. Previous genotyping efforts have revealed that Mexico′s indigenous population is highly differentiated and substructured, thus potentially harboring higher proportions of private genetic variants of functional and biomedical relevance. Here...

Abstract Background As most ancient biological samples have low levels of endogenous DNA, it is advantageous to enrich for specific genomic regions prior to sequencing. One approach—in-solution capture-enrichment—retrieves sequences of interest and reduces the fraction of microbial DNA. In this work, we implement a capture-enrichment approach targe...

Significance The acquisition of agricultural techniques during the so-called Neolithic revolution has been one of the major steps forward in human history. Using next-generation sequencing and ancient-DNA techniques, we directly test whether Neolithization in North Africa occurred through the transmission of ideas or by demic diffusion. We show tha...

Significance Recent genomic studies of ancient and modern humans from the Americas have given a comprehensive view of the peopling of the continent. However, regional characterization of ancient and modern individuals is lacking, being key to unveiling fine-scale differences within the continent. We present genome-wide analyses of ancient and moder...

Over a decade ago, the Atacama humanoid skeleton (Ata) was discovered in the Atacama region of Chile. The Ata specimen carried a strange phenotype-6-in stature, fewer than expected ribs, elongated cranium, and accelerated bone age-leading to speculation that this was a preserved nonhuman primate, human fetus harboring genetic mutations, or even an...

Significance Ancient DNA has revolutionized the field of archaeology, but in the Caribbean and other tropical regions of the world, the work has been hampered by poor DNA preservation. We present an ancient human genome from the Caribbean and use it to shed light on the early peopling of the islands. We demonstrate that the ancestors of the so-call...

The extent to which prehistoric migrations of farmers influenced the genetic pool of western North Africans remains unclear. Archaeological evidence suggests the Neolithization process may have happened through the adoption of innovations by local Epipaleolithic communities, or by demic diffusion from the Eastern Mediterranean shores or Iberia. Her...

Background As most ancient biological samples have low levels of endogenous DNA, it is advantageous to enrich for specific genomic regions prior to sequencing. One approach – in-solution capture-enrichment – retrieves sequences of interest and reduces the fraction of microbial DNA. In this work, we implement a capture-enrichment approach targeting...

DNA extraction and library preparation are crucial steps in any ancient DNA study. Although palaeogenomic researchers are facing a growing choice of DNA extraction and sequencing library preparation methods, how their performance varies with DNA preservation remains unclear. To help elucidate this question, we compared the performance of two common...

In ancient DNA (aDNA) research, evolutionary and archaeological questions are often investigated using the genomic sequences of organelles: mitochondrial and chloroplast DNA. Organellar genomes are found in multiple copies per living cell, increasing their chance of recovery from archaeological samples, and are inherited from one parent without gen...

Analysing population genomic data from killer whale ecotypes, which we estimate have globally radiated within less than 250,000 years, we show that genetic structuring including the segregation of potentially functional alleles is associated with socially inherited ecological niche. Reconstruction of ancestral demographic history revealed bottlenec...

Details of fixed non-synonymous changes in the exons of protein coding genes, including the per-individual and per-population read count for each allele.

D-statistic (ABBA-BABA test) values and standard error estimates for the inference of ancient admixture.

Supplementary Figures 1-17, Supplementary Tables 1-10, Supplementary Note 1 and Supplementary References

Pairwise genetic distance estimates and 100 bootstrap replicates.

Pairwise relatedness estimates

The interaction between ecology, culture and genome evolution remains poorly understood. Analysing population genomic data from killer whale ecotypes, which we estimate have globally radiated within less than 250,000 years, we show that genetic structuring including the segregation of potentially functional alleles is associated with socially inher...

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...

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...

Global climate change during the Late Pleistocene periodically encroached and then released habitat during the glacial cycles, causing range expansions and contractions in some species. These dynamics have played a major role in geographic radiations, diversification and speciation. We investigate these dynamics in the most widely distributed of ma...

Application of whole‐genome capture ( WGC ) methods to ancient DNA ( aDNA ) promises to increase efficiency of ancient genome sequencing. We compared the performance of two recent WGC methods in enriching human aDNA within Illumina libraries built using both double‐stranded and single‐stranded build protocols. Although both methods effectively enri...

Maize offers an ideal system through which to demonstrate the potential of ancient population genomic techniques for reconstructing the evolution and spread of domesticates. The diffusion of maize from Mexico into the North American Southwest (SW) remains contentious with the available evidence being restricted to morphological studies of ancient m...

Birds are the most species-rich class of tetrapod vertebrates and have wide relevance across many research fields. We explored bird macroevolution using full genomes from 48 avian species representing all major extant clades. The avian genome is principally characterized by its constrained size, which predominantly arose because of lineage-specific...

The application of whole genome capture (WGC) methods to ancient DNA (aDNA) promises to increase the efficiency of ancient genome sequencing. We compared the performance of two recently developed WGC methods in enriching human aDNA within Illumina libraries built using both double-stranded (DSL) and single-stranded (SSL) build protocols. Although b...

Ancient DNA (aDNA) recovered from archaeobotanical remains can provide key insights into many prominent archaeological research questions, including processes of domestication, past subsistence strategies, and human interactions with the environment. However, it is often difficult to isolate aDNA from ancient plant materials, and furthermore, such...

Niche variation owing to individual differences in ecology has been hypothesized to be an early stage of sympatric speciation. Yet to date, no study has tracked niche width over more than a few generations. In this study, we show the presence of isotopic niche variation over millennial timescales and investigate the evolutionary outcomes. Isotopic...

Identifying evolutionary divergent taxonomic units, e.g. species and subspecies, is important for conservation and evolutionary biology. The ‘type D’ killer whale, Orcinus orca, is a rarely observed morphotype with a pelagic, circumpolar subantarctic distribution, making dedicated research and therefore taxonomic study extremely difficult to date....

Transcriptome analysis of polar bears (Ursus maritimus) yielded sequences with highest similarity to the human endogenous retrovirus group HERV-K(HML-2). Further analysis of the polar bear draft genome identified an endogenous betaretrovirus group comprising 26 proviral copies and 231 solo LTRs. Molecular dating indicates the group originated befor...

Background Influenza viruses such as swine-origin influenza A(H1N1) virus (A(H1N1)pdm09) generate genetic diversity due to the high error rate of their RNA polymerase, often resulting in mixed genotype populations (intra-host variants) within a single infection. This variation helps influenza to rapidly respond to selection pressures, such as those...

The characterization of biomolecules from ancient samples can shed otherwise unobtainable insights into the past. Despite the fundamental role of transcriptomal change in evolution, the potential of ancient RNA remains unexploited - perhaps due to dogma associated with the fragility of RNA. We hypothesize that seeds offer a plausible refuge for lon...

Calibration curves for dating of 2 Arizona maize kernels. (TIF)

Fraction of total GS FLX reads mapping to the B73 reference genome for cDNA (4) and DNA (3) libraries. The breakdown of reads mapped with BWA before and after removing sequence duplicates and paralogs is shown. Unmapped reads were then mapped using BLAT to retrieve as many endogenous reads as possible. Estimates of endogenous maize nucleic acid con...

Photo of Arizona kernel, batch 935. (TIF)

Ancient RNA (935130) Fragmentation and Misincorporation Plot. (TIF)

Radiocarbon results BP and analytical data, including stable isotope results. All data is acceptable for a material such as this. ‘Used’ is the material analyzed in pretreatment chemistry, whilst ‘yield’ is the amount remaining after the chemical purification procedures applied. (DOCX)

Functionally annotated exon hits for Arizonan kernel 935130. (DOCX)

Ancient DNA (AZ Shotgun) Fragmentation and Misincorporation Plot. (TIF)

Ancient RNA (935230) Fragmentation and Misincorporation Plot. (TIF)

Functionally annotated exon hits for Arizonan kernel 935230. (DOCX)

Detailed methodology, including nucleic acid extraction method, PCR amplification primer sequences and tests, data analyses and radiocarbon dating. (DOCX)

Fraction of total GAIIx (AZ shotgun) and HiSeq (935130 and 935230) reads mapped to the B73 reference genome. BWA (before and after removing sequence duplicates and paralogs) and BLAT mapping values are shown. (DOCX)

Top 50 exon hits with functional annotation from 935130 cDNA maize read. (DOCX)

Repeat content profiles of HiSeq cDNA and GAIIx DNA sequences using RepeatMasker. (DOCX)

Background The koala (Phascolarctos cinereus) is an arboreal marsupial that was historically widespread across eastern Australia until the end of the 19th century when it suffered a steep population decline. Hunting for the fur trade, habitat conversion, and disease contributed to a precipitous reduction in koala population size during the late 180...

FASTA formatted files of the consensus haplotype sequences for the 73 bp and 112 bp museum koala amplicons.

FASTA formatted files of the consensus haplotype sequences for the 73 bp and 112 bp museum koala amplicons.

One of the main findings derived from the analysis of the Neandertal genome was the evidence for admixture between Neandertals and non-African modern humans. An alternative scenario is that the ancestral population of non-Africans was closer to Neandertals than to Africans because of ancient population substructure. Thus, the study of North African...

Stability of the Neandertal admixture estimates. We present each population's estimate ancestry, the standard error in the estimate, and the Z score for different combinations of Sub-Saharan and non-African populations. O (Out-group), BP (Benchmark population, i.e. population which didn't experience any introgression from Neandertals) and SP (Sourc...

Although endogenous retroviruses are common across vertebrate genomes, the koala retrovirus (KoRV) is the only retrovirus known to be currently invading the germ line of its host. KoRV is believed to have first infected koalas in northern Australia less than two centuries ago. We examined KoRV in 28 koala museum skins collected in the late 19th and...

The genetic background of the European Mesolithic and the extent of population replacement during the Neolithic is poorly understood, both due to the scarcity of human remains from that period and the inherent methodological difficulties of ancient DNA research. However, advances in sequencing technologies are both increasing data yields and provid...

We have recently developed a sequencing method using a second generation sequencing platform. We typed 111 samples for one or two of 10 short tandem repeat loci and discovered a high degree of sequence diversity. Most variation was seen in the D21S11 locus and least variation was found in the D18S51 locus. Our sequencing method gave a better resolu...

We present an Aboriginal Australian genomic sequence obtained from a 100-year-old lock of hair donated by an Aboriginal man from southern Western Australia in the early 20th century. We detect no evidence of European admixture and estimate contamination levels to be below 0.5%. We show that Aboriginal Australians are descendants of an early human d...

Given the major threat of influenza A to human and animal health, and its ability to evolve rapidly through mutation and reassortment, tools that enable its timely characterization are necessary to help monitor its evolution and spread. For this purpose, deep sequencing can be a very valuable tool. This study reports a comprehensive method that ena...

The development of second-generation sequencing technologies has greatly benefitted the field of ancient DNA (aDNA). Its application can be further exploited by the use of targeted capture-enrichment methods to overcome restrictions posed by low endogenous and contaminating DNA in ancient samples. We tested the performance of Agilent's SureSelect a...

Supplementary Results and Methods

The analysis and profiling of short tandem repeat (STR) loci is routinely used in forensic genetics. Current methods to investigate STR loci, including PCR-based standard fragment analyses and capillary electrophoresis, only provide amplicon lengths that are used to estimate the number of STR repeat units. These methods do not allow for the full re...