Estimating time to the most recent common ancestor (TMRCA): comparison and application of eight methods

Abstract

Investigating how an ancestral population diverges to give rise to distinct subpopulations remains a fundamental pursuit in population genetics. There is broad consensus for the 'Out-of-Africa' hypothesis that states that modern humans arose ∼ 200 000 years ago in Africa and spread throughout the continent ∼ 100 000 years ago. This was followed by several waves of major population dispersals across the globe, although the exact nature of the population divergence remains debatable. Existing methods to estimate population divergence time differ in their methodological frameworks and demographic assumptions, and require different types of genetic data as input. These fundamental differences often result in the methods producing inconsistent estimates of the population divergence time, further confounding attempts to robustly uncover the history of human migration, especially when most population genetic studies do not employ multiple methods to estimate the time to the most recent common ancestor (TMRCA). Here, we chose eight popular methods for estimating TMRCA and evaluated their robustness and accuracy in correctly identifying the true TMRCA through a series of simulations that mimicked different evolutionary scenarios. We subsequently applied all eight methods to estimate the population divergence time between Southeast Asian Malays and South Asian Indians using deep whole-genome sequencing data.

Diversity, Transmission, and Cophylogeny of Ledanteviruses (Rhabdoviridae: Ledantevirus) and Nycteribiid Bat Flies Parasitizing Angolan Soft-Furred Fruit Bats in Bundibugyo District, Uganda

“…Therefore, the diversity we have documented may have evolved as viral lineages were transmitted vertically and co-diverged with their bat fly host lineages. Unfortunately, accurate evolutionary rate estimates for ledanteviruses and their bat fly hosts do not currently exist, hindering inferences about the timing of such co-divergence events [50].…”

A practical introduction to sequentially Markovian coalescent methods for estimating demographic history from genomic data

“…Multiple sequentially Markovian coalescent tends to perform better across a range of population divergence scenarios (Zhou & Teo, ) and can be used to provide a more complete picture of how gene flow between populations has changed through time. If we know which samples came from which populations, MSMC can calculate the cross‐coalescence rate between each pair of populations, as well as the coalescence rate within each population (e.g., Fan et al, ; Liang et al, ).…”

The Role of Geomagnetic Field Intensity in Late Quaternary Evolution of Humans and Large Mammals

“…Initially, this conclusion met with considerable resistance, however, increasing numbers of studies, including work on Y‐chromosomes, imply that the Eve hypothesis is substantially correct. There is now broad consensus for the “out‐of‐Africa” hypothesis, whereby modern humans appeared at ∼200 ka in Africa and spread throughout the continent before dispersing across the globe, although the exact chronology and nature of the population divergence remain unclear (Zhou & Teo, ). Dispersal has resulted in the occupation of a wide variety of habitats with selection in response to specific ecological pressures.…”