Biology subjects

Flegontova, O.

Publications and source records attributed to Flegontova, O..

6 recordsLinked to original sources

bioRxiv2026

Sparse sampling and rare-variant depletion distort PCA visualizations of population structure: recovery with objective-guided manifold learning

Principal component analysis (PCA) is routinely used to visualize population structure, yet how sparse sampling and rare-variant depletion affect low-dimensional plots remains poorly understood. Using spatial simulations, we show that these factors interact to distort visualization of genetic landscapes, producing triangular and three-ray patterns, artificial outliers and misleading clines. We develop an objective-guided manifold-learning framework that searches across genotype normalization, PCA representation and dimensionality, distance metrics, and UMAP, densMAP and PHATE parameters. High-dimensional classic PC scores consistently outperform the eigenvectors used in population genetics, but other optimal parameters and ranking objectives depend on data quality, sampling and SNP ascertainment. Across six human and animal datasets, optimized embeddings recover fine-scale structure obscured by PCA and supported by independent genetic evidence. In ancient Eurasia, optimized PHATE resolves Slavic-associated structure corroborated by haplotype-sharing communities, qpAdm, and Y-chromosome lineages. These results call for caution in interpreting PCA plots and establish optimized manifold learning as a hypothesis-generating approach.

genetics↗

bioRxiv2022

On the limits of fitting complex models of population history to genetic data

Our understanding of human population history in deep time has been assisted by fitting "admixture graphs" to data: models that specify the ordering of population splits and mixtures which is the only information needed to capture the patterns of allele frequency correlation among populations. Not needing to specify population size changes, split times, or whether admixture events were sudden or drawn out simplifies the space of models that need to be searched. However, the space of possible admixture graphs relating populations is vast and cannot be sampled fully, and thus most published studies have identified fitting admixture graphs through a manual process driven by prior hypotheses, leaving the vast majority of alternative models unexplored. Here, we develop a method for systematically searching the space of all admixture graphs that can incorporate non-genetic information in the form of topology constraints. We implement this findGraphs tool within a software package, ADMIXTOOLS 2, which is a reimplementation of the ADMIXTOOLS software with new features and large performance gains. We apply this methodology to identify alternative models to admixture graphs that played key roles in eight published studies and find that graphs modeling more than six populations and two or three admixture events are often not unique, with many alternative models fitting nominally or significantly better than the published one. Our results suggest that strong claims about population history from admixture graphs should only be made when all well-fitting and temporally plausible models share common topological features. Our re-evaluation of published data also provides insight into the population histories of humans, dogs, and horses, identifying features that are stable across the models we explored, as well as scenarios of populations relationships that differ in important ways from models that have been highlighted in the literature, that fit the allele frequency correlation data, and that are not obviously wrong.

evolutionary biology↗

bioRxiv2021

Circumpolar peoples and their languages: lexical and genomic data suggest ancient Chukotko-Kamchatkan-Nivkh and Yukaghir-Samoyedic connections

Relationships between universally recognized language families represent a hotly debated topic in historical linguistics, and the same is true for correlation between signals of genetic and linguistic relatedness. We developed a weighted permutation test and applied it on basic vocabularies for 31 pairs of languages and reconstructed proto-languages to show that three groups of circumpolar language families in the Northern Hemisphere show evidence of relationship though borrowing in the basic vocabulary or common descent: [Chukotko-Kamchatkan and Nivkh]; [Yukaghir and Samoyedic]; [Yeniseian, Na-Dene, and Burushaski]. The former two pairs showed the most significant signals of language relationship, and the same pairs demonstrated parallel signals of genetic relationship implying common descent or substantial gene flows. For finding the genetic signals we used genome-wide genetic data for present-day groups and a bootstrapping model comparison approach for admixture graphs or, alternatively, haplotype sharing statistics. Our findings further support some hypotheses on long-distance language relationship put forward based on the linguistic methods but lacking universal acceptance. Significance statementIndigenous people inhabiting polar and sub-polar regions in the Northern Hemisphere speak diverse languages belonging to at least seven language families which are traditionally thought of as unrelated entities. We developed a weighted permutation test and applied it to basic vocabularies of a number of languages and reconstructed proto-languages to show that at least three groups of circumpolar language families show evidence of relationship though either borrowing in the basic vocabulary or common descent: Chukotko-Kamchatkan and Nivkh; Yukaghir and Samoyedic; Yeniseian, Na-Dene, and Burushaski. The former two pairs showed the most significant signals of language relationship, and the same pairs demonstrated parallel signals of genetic relationship implying common descent or substantial gene flows.

genomics↗

bioRxiv2021

Indian genetic heritage in Southeast Asian populations

The great ethnolinguistic diversity found today in mainland Southeast Asia (MSEA) reflects multiple migration waves of people in the past. Deeply divergent East Eurasian hunter-gatherers were the first anatomically modern human population known to migrate to the region. Agriculturalists from South China migrated to the region and admixed with the local hunter-gatherers during the Neolithic period. During the Bronze and Iron Ages, the genetic makeup of people in MSEA changed again, indicating an additional influx of populations from South China. Maritime trading between MSEA and India was established at the latest 300 BCE, and the formation of early states in Southeast Asia during the first millennium CE was strongly influenced by Indian culture, and this cultural influence is still prominent today. Several ancient Indian-influenced states were located in present-day Thailand, and various populations in the country are likely to be descendants of people from those states. To systematically explore Indian genetic heritage in MSEA, we generated genome-wide SNP data (the HumanOrigins array) for 119 present-day individuals belonging to 10 ethnic groups from Thailand and co-analyzed them with published data from MSEA using the PCA, ADMIXTURE, f3-statistics, qpAdm, and qpGraph methods. We found South Asian low-level admixture in various MSEA populations which are probably descendants of people from the ancient Indian-influenced states, but failed to find a South Asian genetic component in present-day hunter-gatherer groups and relatively isolated groups from highlands in Northern Thailand. Our results also support close genetic affinity between Kra-Dai-speaking (also known as Tai-Kadai) and Austronesian-speaking populations, which fits a linguistic hypothesis suggesting cladality of the two language families. Author SummaryMainland Southeast Asia is a region with great ethnolinguistic diversity and complex population history. We studied genetic population history of present-day mainland Southeast Asian populations using genome-wide SNP data (the HumanOrigins array). We generated new data for 10 present-day ethnic groups from Thailand, which we further combined with published data from mainland and island Southeast Asians and worldwide populations. We revealed South Asian genetic admixture in various mainland Southeast Asian ethnic groups which are highly influenced by Indian culture, but failed to find it in groups who remained culturally isolated until recently. Our finding suggests that a massive migration of Indian people in the past was responsible for the spread of Indian culture in mainland Southeast Asia. We also found support for a close genetic affinity between Kra-Dai- and Austronesianspeaking populations, which fits a linguistic hypothesis suggesting cladality of the two language families.

genetics↗

bioRxiv2020

The genomic formation of First American ancestors in East and Northeast Asia

Upward Sun River 1, an individual from a unique burial of the Denali tradition in Alaska (11500 calBP), is considered a type representative of Ancient Beringians who split from other First Americans 22000-18000 calBP in Beringia. Using a new admixture graph model-comparison approach resistant to overfitting, we show that Ancient Beringians do not form the deepest American lineage, but instead harbor ancestry from a lineage more closely related to northern North Americans than to southern North Americans. Ancient Beringians also harbor substantial admixture from a lineage that did not contribute to other Native Americans: Amur River Basin populations represented by a newly reported site in northeastern China. Relying on these results, we propose a new model for the genomic formation of First American ancestors in Asia. One Sentence SummaryAncient Beringians do not form the deepest American lineage, but harbor admixture from Amur River Basin populations.

genetics↗

bioRxiv2017

Paleo-Eskimo genetic legacy across North America

Paleo-Eskimos were the first people to settle vast regions of the American Arctic around 5,000 years ago, and were subsequently joined and largely displaced around 1,000 years ago by ancestors of the present-day Inuit and Yupik. The genetic relationship between Paleo-Eskimos and Native American populations remains uncertain. We analyze ancient and present-day genome-wide data from the Americas and Siberia, including new data from Alaskan Inupiat and West Siberian populations, and the first genome-wide DNA from ancient Aleutian Islanders, ancient northern Athabaskans, and a 4,250-year-old individual of the Chukotkan Ust'-Belaya culture. Employing new methods based on rare allele and haplotype sharing as well as established methods based on allele frequency correlations, we show that Paleo-Eskimo ancestry is widespread among populations who speak Na-Dene and Eskimo-Aleut languages. Using phylogenetic modelling with allele frequency correlations and rare variation, we present a comprehensive model for the complex peopling of North America.

genetics↗