Brief Population Bottlenecks Are Beyond The Genetic Streetlight

Inferring human demographic history from extant genomes is an important goal of population genetics. To date, the sensitivity of coalescence-based methods in detecting population bottlenecks has not been well characterized. In this study, we find that brief bottlenecks, of just a few generations, are undetectable by current methods. A new approach to population inference, Lineage Time Inference (LiTI), uses data-derived windows to demarcate the limits of the genetic data. We find that a sharp population bottleneck at the time of the Youngest Toba Eruption, and also at more ancient timepoints in the human lineage, would be outside the genetic streetlight.

More Rule than Exception: Parallel Evidence of Ancient Migrations in Grammars and Genomes of Finno-Ugric Speakers

To reconstruct aspects of human demographic history, linguistics and genetics complement each other, reciprocally suggesting testable hypotheses on population relationships and interactions. Relying on a linguistic comparative method based on syntactic data, here we focus on the non-straightforward relation of genes and languages among Finno-Ugric (FU) speakers, in comparison to their Indo-European (IE) and Altaic (AL) neighbors. Syntactic analysis, in agreement with the indications of more traditional linguistic levels, supports at least three distinct clusters, corresponding to these three Eurasian families; yet, the outliers of the FU group show linguistic convergence with their geographical neighbors. By analyzing genome-wide data in both ancient and contemporary populations, we uncovered remarkably matching patterns, with north-western FU speakers linguistically and genetically closer in parallel degrees to their IE-speaking neighbors, and eastern FU speakers to AL speakers. Therefore, our analysis indicates that plausible cross-family linguistic interference effects were accompanied, and possibly caused, by recognizable demographic processes. In particular, based on the comparison of modern and ancient genomes, our study identified the Pontic-Caspian steppes as the possible origin of the demographic processes that led to the expansion of FU languages into Europe.

More rule than exception: Parallel evidence of ancient migrations in grammars and genomes of Finno-Ugric speakers

To reconstruct aspects of human demographic history, linguistics and genetics complement each other, reciprocally suggesting testable hypotheses on population relationships and interactions. Relying on a linguistic comparative method exclusively based on syntactic data, here we focus on the complex relation of genes and languages among Finno-Ugric (FU) speakers, in comparison to their Indo-European (IE) and Altaic (AL) neighbors. Syntactic analysis supports three distinct clusters corresponding to these three Eurasian families; yet, the outliers of the FU group show linguistic convergence with their geographical neighbors. By analyzing genome-wide data in both ancient and contemporary populations, we uncovered remarkably matching patterns, with north-western FU speakers linguistically and genetically closer in parallel degrees to their IE-speaking neighbors, and eastern FU speakers to AL-speakers. Therefore, our study indicates plausible secondary convergence in the syntax of languages of different families, providing evidence that such interference effects were accompanied, and possibly caused, by recognizable processes at the population level. In particular, based on the comparison of modern and ancient genomes, our analysis identified the Pontic-Caspian steppes as the possible origin of the demographic processes that led to the expansion of the FU into Europe.

Ancient DNA helps trace the peopling of the world

Many of us are fascinated by narratives regarding the origin and evolution of our species. Who are we? How did we people the world? Answers to these simple questions remain elusive even though researchers have been quite successful in describing past human morphology and culture using evidence from anthropology, archaeology, history, sociology and linguistics. However, when they address human migrations, archaeologists are somewhat restricted to surviving artifactual evidence and limited to descriptions of culture expansions, which may have occurred by the movement of either ideas or people. The advent of genomics, by which one can sequence whole or part of an individual's DNA, provided a powerful means to dig into past human demographic history. Notably, the coalescent theory posits that individuals in a population share genetic variants that originated from a common ancestor. This powerful theory is the basis for a number of bioanalytical innovations that utilize genetic data to reconstruct human movements around the world.

Importance of human demographic history knowledge in genetic studies involving multi-ethnic cohorts

Paucity of data from African populations due to under-representation in human genetic studies has impeded detailed understanding of the heritable human genome variation. This is despite the fact that Africa has sizeable genetic, cultural and linguistic diversity. There are renewed efforts to understand health problems relevant to African populations using more comprehensive datasets, and by improving expertise in health-related genomics among African scientists. We emphasise that careful consideration of the sampled populations from national and within-continental cohorts in large multi-ethnic genetic research efforts is required to maximise the prospects of identifying and fine-mapping novel risk variants in indigenous populations. We caution that human demographic history should be taken into consideration in such prospective genetic-association studies.

Importance of human demographic history knowledge in genetic studies involving multi-ethnic cohorts

Paucity of data from African populations due to under-representation in human genetic studies has impeded detailed understanding of the heritable human genome variation. This is despite the fact that Africa has sizeable genetic, cultural and linguistic diversity. There are renewed efforts to understand health problems relevant to African populations using more comprehensive datasets, and by improving expertise in health-related genomics among African scientists. We emphasise that careful consideration of the sampled populations from national and within-continental cohorts in large multi-ethnic genetic research efforts is required to maximise the prospects of identifying and fine-mapping novel risk variants in indigenous populations. We caution that human demographic history should be taken into consideration in such prospective genetic-association studies.

H3Africa: crucial importance of knowledge on human demographic history in strategies for data exploitation – an analysis of the Luhya in Webuye, Kenya population from the 1000 Genomes Project

Paucity of data from African populations has restricted understanding of the heritable human genome variation. Although under-represented in human genetic studies, Africa has sizeable genetic, cultural and linguistic diversity. The Human Heredity and Health in Africa (H3Africa) initiative is aimed at understanding health problems relevant to African populations, and titling the scales of data deficit and lacking expertise in health-related genomics among African scientists. We emphasise that careful consideration of the sampled populations in the H3Africa projects is required to maximise the prospects of identifying and fine-mapping novel risk variants in indigenous populations. H3Africa which considers national and within-continental cohorts must have well thought out documented protocols that carefully consider human demographic history.