Statistical inference of prehistoric demography from frequency distributions of radiocarbon dates: a review and a guide for the perplexed

The last decade saw a rapid increase in the number of applications where time-frequency changes of radiocarbon dates have been used as a proxy for inferring past population dynamics. Although its simple and universal premise is appealing and undoubtedly offers some unique opportunities for research on long-term comparative demography, practical applications are far from trivial and riddled by challenges. Here I review: 1) the most common criticisms concerning the nature of radiocarbon time-frequency data as a demographic proxy; 2) the statistical nature of the problem; and 3) three classes of inferential approaches proposed so far in the literature.

A Genetic Perspective on Cetacean Evolution

Studies of cetacean evolution using genetics and other biomolecules have come a long way—from the use of allozymes and short sequences of mitochondrial or nuclear DNA to the assembly of full nuclear genomes and characterization of proteins and lipids. Cetacean research has also advanced from using only contemporary samples to analyzing samples dating back thousands of years, and to retrieving data from indirect environmental sources, including water or sediments. Combined, these studies have profoundly deepened our understanding of the origin of cetaceans; their adaptation and speciation processes; and of the past population change, migration, and admixture events that gave rise to the diversity of cetaceans found today. Expected final online publication date for the Annual Review of Ecology, Evolution, and Systematics, Volume 52 is November 2021. Please see http://www.annualreviews.org/page/journal/pubdates for revised estimates.

Amendment to: populations in environments with a soft carrying capacity are eventually extinct

This sharpens the result in the paper Jagers and Zuyev (J Math Biol 81:845–851, 2020): consider a population changing at discrete (but arbitrary and possibly random) time points, the conditional expected change, given the complete past population history being negative, whenever population size exceeds a carrying capacity. Further assume that there is an $$\epsilon > 0$$ ϵ > 0 such that the conditional probability of a population decrease at the next step, given the past, always exceeds $$\epsilon $$ ϵ if the population is not extinct but smaller than the carrying capacity. Then the population must die out.

Uncertainty in population estimates: a meta-analysis for petrels

Population estimates are commonly generated and used in conservation science. All estimates carry inherent uncertainty, but little attention has been given to when and how this uncertainty limits their use. This requires an understanding of the specific purposes for which population estimates are intended, an assessment of the level of uncertainty each purpose can tolerate, and information on current uncertainty. We conducted a review and meta-analysis for a widespread group of seabirds, the petrels, to better understand how and why population estimates are being used. Globally petrels are highly threatened, and aspects of their ecology make them difficult to survey, introducing high levels of uncertainty into population estimates. We found that by far the most common intended use of population estimates was to inform status and trend assessments, while less common uses were trialling methods to improve estimates, and assessing threat impacts and conservation outcomes. The mean coefficient of variation for published estimates was 0.17 (SD = 0.14), with no evidence that uncertainty has been reduced through time. As a consequence of this high uncertainty, when we simulated declines equivalent to thresholds commonly used to trigger management, only 5% of studies could detect significant differences between population estimates collected 10 years apart for populations declining at a rate of 30% over three generations. Reporting of uncertainty was variable with no dispersion statistics reported with 38% of population estimates and most not reporting key underlying parameters: nest numbers/density and nest occupancy. We also found no correlation between population estimates and either island size, body size or species threat status - potential predictors of uncertainty. Synthesis and applications: Key recommendations for managers are to be mindful of uncertainty in past population estimates if aiming to collect contemporary estimates for comparison, to report uncertainty clearly for new estimates, and to give careful consideration to whether a proposed estimate is likely to achieve the requisite level of certainty for the investment in its generation to be warranted. We recommend a practitioner-based Value of Information assessment to confirm where there is value in reducing uncertainty.

Sum things are not what they seem: Problems with point-wise interpretations and quantitative analyses of proxies based on aggregated radiocarbon dates

Radiocarbon-date assemblages are commonly used as proxies for past human and environmental phenomena. Prominent examples of target phenomena include past population levels and sea level fluctuations. These processes are thought to have affected the amount of organic carbon deposited into the archaeological and/or palaeoenvironmental record. Time-series representing through-time fluctuations in the frequency of radiocarbon samples are, therefore, often used as proxies for such processes. However, there are critical problems with using radiocarbon “dates-as-data” in point-wise comparisons and these problems have gone largely underappreciated. The key problem is that the established proxies are easily misinterpreted. They conflate process variation and chronological uncertainty, which makes them unsuitable for point-wise comparisons aimed at identifying rates of change, comparing variables directly, or estimating parameters in regression models. Here we explore the interpretive and analytical problems in detail in an effort to raise awareness and promote skepticism about the use of the established proxies in point-wise comparisons. We also provide suggestions for future research and point to potential methodological alternatives that may improve the viability of dates-as-data approaches.

The past, present and future of skeletal analysis in palaeodemography

The study of past population dynamics is imperative to our understanding of demographic processes in the context of biology, evolution, environment and sociocultural factors. Retrospective consideration of a population's capacity to resist and adapt to change aims to contribute insights into our past, a point of comparison to the present and predictions for the future. If these aims are to be achieved, the accuracy and precision of palaeodemographic methods are of paramount importance. This article considers the emergence of skeletally based palaeodemographic methods, specifically life tables and demographic proxies, and early controversies and issues. It details the process of methodological development and refinement, and success in addressing many of the historical limitations. The contribution and potential of skeletally based methods are discussed and comparisons and contrasts made with alternative palaeodemographic approaches, and avenues for future research are proposed. Ultimately, it is concluded that skeletal analysis provides unique opportunities to investigate population dynamics with spatial specificity, examine individuals and groups within a population, and integrate demographic and pathological information to evaluate population health in the past. This article is part of the theme issue ‘Cross-disciplinary approaches to prehistoric demography'.

Sacredness to desecration: ‘Languaging’ and ‘othering’ of peoples and places through dumping of domestic waste in Urora, Benin City, Nigeria

This paper examines the dynamics of environmental change of physical spaces and the behaviour of the residents of a formerly close-knit community whose belief systems are contrary to their lifeworld situation as observed in Urora settlement in Benin City, Nigeria. The findings revealed that the satellite images show that the study area was much greener 20 years ago and environmentally attractive compared to the current time. Lack of infrastructure such as waste bins has led to a shift in mindset among the residents to accommodate illegal dumping contrary to attitudes in the past. Population growth and refuse generation and disposal is also a significant challenge. Based on the findings, the paper posits for the realignment and reconsideration of the embodied sacredness of nature with the mode of expression of the past which was pro-environmentally inclined and focussed.

The origin and past demography of murine astrovirus 1 in laboratory mice

Astroviruses are non-enveloped, positive-sense, ssRNA viruses and often associated with gastrointestinal diseases. Murine astrovirus (MuAstV) was first confirmed in a laboratory mouse colony in 2011. Although infected mice do not present significant clinical symptoms, the virus might interfere with research results. A recent surveillance has shown that MuAstV is highly prevalent in laboratory mice. The aims of the present study were to identify and characterize MuAstV strains as well as to investigate the prevalence rate of viral RNA in laboratory mice in Taiwan, and to estimate the origin and past population demography of MuAstVs. Based on molecular surveillance, MuAstV RNA was detected in 45.7 % of laboratory mice (48/105) from seven of nine colonies. Three fully sequenced MuAstV strains, MuAstV TW1, TW2 and TW3, exhibited 89.1−94.4 % and 89.1–90.0 % nucleotide identities with the reference strains MuAstV STL1 and STL2, respectively. Phylogenetic analyses of the partial regions of the RNA-dependent RNA polymerase (RdRp) and capsid protein (CP) genes of 18 Taiwan strains along with other astroviruses revealed that there are three distinct lineages of mouse astrovirus, MuAstV1, MuAstV2 and mouse astrovirus JF755422. The mutation rates of MuAstV1 were 2.6×10−4 and 6.2×10−4 substitutions/site/year for the RdRp and CP regions, respectively. Based on the above molecular clock, the colonization of MuAstV1 in laboratory mice was between 1897 and 1912, in good agreement with the establishment of ‘modern’ laboratory mouse facilities. Since its initial infection, the population size of MuAstV1 has increased 15–60-fold, probably consistent with the increased use of laboratory mice. In conclusion, MuAstV1 has been associated with modern laboratory mice since the beginning, and its influence on research results may require further investigation.

A skyline birth-death process for inferring the population size from a reconstructed tree with occurrences

Phylodynamic models generally aim at jointly inferring phylogenetic relationships, model parameters, and more recently, population size through time for clades of interest, based on molecular sequence data. In the fields of epidemiology and macroevolution these models can be used to estimate, respectively, the past number of infected individuals (prevalence) or the past number of species (paleodiversity) through time. Recent years have seen the development of “total-evidence” analyses, which combine molecular and morphological data from extant and past sampled individuals in a unified Bayesian inference framework. Even sampled individuals characterized only by their sampling time, i.e. lacking morphological and molecular data, which we call occurrences, provide invaluable information to reconstruct past population sizes.Here, we present new methodological developments around the Fossilized Birth-Death Process enabling us to (i) efficiently incorporate occurrence data while remaining computationally tractable and scalable; (ii) consider piecewise-constant birth, death and sampling rates; and (iii) reconstruct past population sizes, with or without knowledge of the underlying tree. We implement our method in the RevBayes software environment, enabling its use along with a large set of models of molecular and morphological evolution, and validate the inference workflow using simulations under a wide range of conditions.We finally illustrate our new implementation using two empirical datasets stemming from the fields of epidemiology and macroevolution. In epidemiology, we apply our model to the Covid-19 outbreak on the Diamond Princess ship. We infer the total prevalence throughout the outbreak, by taking into account jointly the case count record (occurrences) along with viral sequences for a fraction of infected individuals. In macroevolution, we present an empirical case study of cetaceans. We infer the diversity trajectory using molecular and morphological data from extant taxa, morphological data from fossils, as well as numerous fossil occurrences. Our case studies highlight that the advances we present allow us to further bridge the gap between between epidemiology and pathogen genomics, as well as paleontology and molecular phylogenetics.