Estimating Pan evolutionary history from nucleotide site patterns

Introgression appears increasingly ubiquitous in the evolutionary history of various taxa, including humans. However, accurately estimating introgression is difficult, particularly when 1) there are many parameters, 2) multiple models fit the data well, and 3) parameters are not simultaneously estimated. Here, we use the software Legofit to investigate the evolutionary history of bonobos (Pan paniscus) and chimpanzees (P. troglodytes) using whole genome sequences. This approach 1) ignores within-population variation, reducing the number of parameters requiring estimation, 2) allows for model selection, and 3) simultaneously estimates all parameters. We tabulated site patterns from the autosomes of 71 bonobos and chimpanzees representing all five extant Pan lineages. We then compared previously proposed demographic models and estimated parameters using a deterministic approach. We further considered sex bias in Pan evolutionary history by analyzing the site patterns from the X chromosome. Introgression from bonobos into the ancestor of eastern and central chimpanzees and from western into eastern chimpanzees best explained the autosomal site patterns. This second event was substantial with an estimated 0.21 admixture proportion. Estimates of effective population size and most divergence dates are consistent with previous findings; however, we observe a deeper divergence within chimpanzees at 987 ka. Finally, we identify male-biased reproduction in Pan evolutionary history and suggest that western to eastern chimpanzee introgression was driven by western males mating with eastern females.

Prescriptions For The Control Of A Clonal Invasive Species Using Demographic Models

Until recently, little focus has been given to determine the population dynamics of invasive species and evaluate their genetic variation. Consequently, not much is known of what drives clonal invasive species and their demography. Here we describe the population dynamics of Kalanchoe delagoensis (Crassulaceae), considered invasive to several countries. We quantified the demography of a population in central Mexico using integral projection models (IPM) in a population that reproduced asexually exclusively through plantlets. The effect of clonal recruitment on λ was evaluated by changing plantlet survival and simulating management scenarios that used previous data of watering and seven experimental herbicide treatments. The finite rate of population increase indicated that this Kalanchoe delagoensis population is growing (above one) with significant potential increases that correlated with water availability. The IPM showed that plantlet survival and recruitment were the most critical steps in the cycle for the population and simulations of different management scenarios showed that reducing plantlet survival significantly decreased λ only in two out of the seven herbicides used.

Statistical inference for seed mortality and germination with seed bank experiments

Plant population ecologists regularly study soil seed banks with seed bag burial and seed addition experiments. These experiments contribute crucial data to demographic models, but we lack standard methods to analyze them. Here, we propose statistical models to estimate seed mortality and germination with observations from these experiments. We develop these models following principles of event history analysis, and analyze their identifiability and statistical properties by algebraic methods and simulation. We demonstrate that seed bag burial, but not seed addition experiments, can be used to make inferences about age-dependent mortality and germination. When mortality and germination do not change with seed age, both experiments produce unbiased estimates but seed bag burial experiments are more precise. However, seed mortality and germination estimates may be inaccurate when the statistical model that is fit makes incorrect assumptions about the age-dependence of mortality and germination. The statistical models and simulations that we present can be adopted and modified by plant population ecologists to strengthen inferences about seed mortality and germination in the soil seed bank.

Population genomic structure in Goodman's mouse lemur reveals long-standing separation of Madagascar's Central Highlands and eastern rainforests

Madagascar’s Central Highlands are largely composed of grasslands, interspersed with patches of forest. The pre-human extent of these grasslands is a topic of vigorous debate, with conventional wisdom holding that they are anthropogenic in nature and emerging evidence supporting that grasslands were a component of the pre-human Central Highlands vegetation. Here, we shed light on the temporal dynamics of Madagascar’s vegetative composition by conducting a population genomic investigation of Goodman’s mouse lemur (Microcebus lehilahytsara; Cheirogaleidae). These small-bodied primates occur both in Madagascar’s eastern rainforests and in the Central Highlands, which makes them a valuable indicator species. Population divergences among forest-dwelling mammals can serve as a proxy for habitat fragmentation and patterns of post-divergence gene flow can reveal potential migration corridors consistent with a wooded grassland mosiac. We used RADseq data to infer phylogenetic relationships, population structure, demographic models of post-divergence gene flow, and population size change through time. These analyses offer evidence that open habitats are an ancient component of the Central Highlands, and that wide-spread forest fragmentation occurred naturally during a period of decreased precipitation near the last glacial maximum. Models of gene flow suggest that migration across the Central Highlands has been possible from the Pleistocene through the recent Holocene via riparian corridors. Notably, though our findings support the hypothesis that Central Highland grasslands predate human arrival, we also find evidence for human-mediated population declines. This highlights the extent to which species imminently threatened by human-mediated deforestation may be more vulnerable from paleoclimatic changes.

Neolithic demic diffusion

In 1978, Paolo Menozzi, Alberto Piazza, and Luca Cavalli-Sforza paved the ground for a new multidisciplinary approach to the study of human prehistory, interpreting genetic evidence in the light of archaeological information. By producing synthetic maps of allele frequencies and summarizing them by principal component analysis (PCA), they identified an association between patterns in genetic diversity across Europe and in the Neolithic archaeological record showing the earliest documented dates of farming societies. Based on this observation, they proposed a model of demic diffusion from the Near East. They argued that the observed patterns were the result of population growth due to increased food availability in early farming communities, westward dispersal of early farmers, and relative isolation between dispersing farmers and local hunter-gatherers. These results played a major role in our understanding of the Neolithic transition, but were also criticized on methodological grounds. For instance, it has become increasingly clear that the interpretation of PCA plots is less straightforward than originally thought, and correlations should be corroborated by explicit comparison of alternative demographic models. Despite these valid criticisms, genetic and genomic studies, including those involving ancient DNA, have largely confirmed the crucial role of the Neolithic transition as a process of demographic change in European prehistory, with some qualifications. Today, there is still much to be learned about the details of that complex history, but many researchers regard the European population structure as largely reflecting the genetic consequences of three major migrations: from Africa in Upper Paleolithic times, from the Near East at the beginning of the Neolithic, and from the eastern steppes in the Bronze Age. This deep structure has not been erased, despite many additional processes involving historical migrations, isolation (i.e., drift) and local gene flow, and has been recognized thanks to the pioneering work of Menozzi, Piazza and Cavalli-Sforza. Based on “Menozzi P, Piazza A, Cavalli-Sforza LL Synthetic maps of human gene frequencies in Europeans. Science 1978;201:786-792.”

II December Socio-Political Readings — “How Are You, Russia? The Russian Social State and Civil Society in 2020: The Implementation of National Projects in a Post-Pandemic Reality” (Moscow, December 10, 2020)

The paper presents the results of the II December Socio-Political Readings — “‘How Are You, Russia?’ The Russian Social State and Civil Society in 2020: The Implementation of National Projects in a Post-Pandemic Reality”. The National Research-to-Practice Conference with international participation was held by the Institute of Socio-Political Research and the Institute of Demographic Studies of the Federal Research Sociological Center of the Russian Academy of Sciences in cooperation with the Faculty of Political Science of the Lomonosov Moscow State University and the Sociology Department of the Russian State University for the Humanities. The event was held in December 2020 in face-to-face/remote formats at the Institute of Socio-Political Research — Branch of the Federal Center of Theoretical and Applied Sociology of the Russian Academy of Sciences. The Readings were attended by the leading academics and young researchers of Moscow and regional research institutes and universities, as well as foreign scientists. The papers provided the analysis of current social, socio-political, social and cultural, demographic problems within the focus of academics, politicians, entrepreneurs, and civil society. The scientific discussion provided an opportunity to address and approve the best socio-political, and demographic models and development patterns, considering the revealed COVID pandemic factors.

Genomic evidence of an ancient Inland Temperate Rainforest

The disjunct temperate rainforests of the Pacific Northwest of North America (PNW) are characterized by late-successional dominant tree species western redcedar (Thuja plicata) and western hemlock (Tsuga heterophylla). The demographics of these species, along with the PNW rainforest ecosystem in its entirety, have been heavily impacted by the geological and climatic changes the PNW has experienced over the last 5 million years, including mountain orogeny and repeated Pleistocene glaciations. These environmental events have ultimately shaped the history of these species, with inland segments potentially being extirpated during the Pleistocene glaciation. Here, we collect genomic data for both species across their ranges in order to develop multiple demographic models, each reflecting a different hypothesis on how the ecosystem dominant species may have responded to dramatic climatic change. Results indicate that inland and coastal populations in both species diverged an estimated ~2.5 million years ago and experienced a decrease in population size during glaciation, with a subsequent population expansion. Importantly, we found evidence for gene-flow between coastal and inland populations during the mid-Holocene. It is likely that intermittent migration in these species has prevented allopatric speciation. In conclusion, the combination of genomic data and population demographic inference procedures involving machine learning establish that populations of the ecosystem dominants Thuja plicata and Tsuga heterophylla persisted in refugia located in both the coastal and inland regions, with populations expanding and contracting in response to glacial cycles with occasional gene-flow.

Magic Tolerance Varies Cross-Culturally: Luck and Precognition Beliefs Across the World

Magical thinking is considered a human universal and is evidenced across cultures. However, the extent to which magical thinking is embraced likely varies across cultures, whereby some cultures are more ‘magic tolerant’ than others. We assessed the effect of culture on magical thinking, operationalized as beliefs in luck and precognition, in two large-scale multinational studies (Study 1: k = 16; N = 17,664; Study 2: k = 25; N = 4,024). Over and above the effects of demographic factors, culture was a significant predictor of luck and precognition beliefs in both studies. Indeed, when culture was added to demographic models of beliefs in luck and precognition, the variance accounted for approximately doubled. Beliefs in luck and precognition were highest in Russia and Latvia (Study 1) and South Asia (Study 2), and lowest in Protestant Europe (Studies 1 and 2). Thus, beyond the effects of age, gender, education, and religiosity, culture is a significant factor in explaining variance in people’s beliefs in luck and precognition. These findings suggest that while magical thinking is common across cultures, some cultures may be more magic tolerant than others.

Biochemical and physiological data collection

Physiological and biochemical traits hold great promise for demographic research as potential proxies (biomarkers) of various biotic and environmental variables that determine individual fitness and ultimately demographic rates. Integrating such biomarkers into demographic models can thus provide insights into drivers of population dynamics or increase predictive power of the models by refining estimation of vital rates. Biomarkers also represent promising means to characterise population structure and dynamics on much shorter time-scales compared to classical demographic approaches. Functional traits further emerge as direct targets of conservation efforts directed towards conserving functional diversity. Yet, biomarkers and functional traits remain underutilised in demography and population ecology, indicating that their benefits still await wider recognition. This chapter briefly reviews the most prominent physiological and biochemical traits (e.g. metabolic rates, hormones, oxidative stress markers, telomeres) that may be of interest in animal and plant demographic research, including the methods for collection, storage, and analysis, and the criteria to be met before the trait is validated as a biomarker. Hopefully, this effort will stimulate further integration of physiological and biochemical data into demographic framework.