Ancestral Process Research Articles

Tstrait: a quantitative trait simulator for ancestral recombination graphs.

Ancestral recombination graphs (ARGs) encode the ensemble of correlated genealogical trees arising from recombination in a compact and efficient structure and are of fundamental importance in population and statistical genetics. Recent breakthroughs have made it possible to simulate and infer ARGs at biobank scale, and there is now intense interest in using ARG-based methods across a broad range of applications, particularly in genome-wide association studies (GWAS). Sophisticated methods exist to simulate ARGs using population genetics models, but there is currently no software to simulate quantitative traits directly from these ARGs. To apply existing quantitative trait simulators users must export genotype data, losing important information about ancestral processes and producing prohibitively large files when applied to the biobank-scale datasets currently of interest in GWAS. We present tstrait, an open-source Python library to simulate quantitative traits on ARGs, and show how this user-friendly software can quickly simulate phenotypes for biobank-scale datasets on a laptop computer. tstrait is available for download on the Python Package Index. Full documentation with examples and workflow templates is available on https://tskit.dev/tstrait/docs/, and the development version is maintained on GitHub (https://github.com/tskit-dev/tstrait).

The ancestral selection graph for a [formula omitted]-asymmetric Moran model

Motivated by the question of the impact of selective advantage in populations with skewed reproduction mechanisms, we study a Moran model with selection. We assume that there are two types of individuals, where the reproductive success of one type is larger than the other. The higher reproductive success may stem from either more frequent reproduction, or from larger numbers of offspring, and is encoded in a measure Λ for each of the two types. Λ-reproduction here means that a whole fraction of the population is replaced at a reproductive event. Our approach consists of constructing a Λ-asymmetric Moran model in which individuals of the two populations compete, rather than considering a Moran model for each population. Provided the measure are ordered stochastically, we can couple them. This allows us to construct the central object of this paper, the Λ−asymmetric ancestral selection graph, leading to a pathwise duality of the forward in time Λ-asymmetric Moran model with its ancestral process. We apply the ancestral selection graph in order to obtain scaling limits of the forward and backward processes, and note that the frequency process converges to the solution of an SDE with discontinuous paths. Finally, we derive a Griffiths representation for the generator of the SDE and use it to find a semi-explicit formula for the probability of fixation of the less beneficial of the two types.

Bursts of coalescence within population pedigrees whenever big families occur.

We consider a simple diploid population-genetic model with potentially high variability of offspring numbers among individuals. Specifically, against a backdrop of Wright-Fisher reproduction and no selection, there is an additional probability that a big family occurs, meaning that a pair of individuals has a number of offspring on the order of the population size. We study how the pedigree of the population generated under this model affects the ancestral genetic process of a sample of size two at a single autosomal locus without recombination. Our population model is of the type for which multiple-merger coalescent processes have been described. We prove that the conditional distribution of the pairwise coalescence time given the random pedigree converges to a limit law as the population size tends to infinity. This limit law may or may not be the usual exponential distribution of the Kingman coalescent, depending on the frequency of big families. But because it includes the number and times of big families, it differs from the usual multiple-merger coalescent models. The usual multiple-merger coalescent models are seen as describing the ancestral process marginal to, or averaging over, the pedigree. In the limiting ancestral process conditional on the pedigree, the intervals between big families can be modeled using the Kingman coalescent but each big family causes a discrete jump in the probability of coalescence. Analogous results should hold for larger samples and other population models. We illustrate these results with simulations and additional analysis, highlighting their implications for inference and understanding of multilocus data.

On multi-type Cannings models and multi-type exchangeable coalescents

A multi-type neutral Cannings population model with migration and fixed subpopulation sizes is analyzed. Under appropriate conditions, as all subpopulation sizes tend to infinity, the ancestral process, properly time-scaled, converges to a multi-type coalescent sharing the exchangeability and consistency property. The proof gains from coalescent theory for single-type Cannings models and from decompositions of transition probabilities into parts concerning reproduction and migration respectively. The following section deals with a different but closely related multi-type Cannings model with mutation and fixed total population size but stochastically varying subpopulation sizes. The latter model is analyzed forward and backward in time with an emphasis on its behavior as the total population size tends to infinity. Forward in time, multi-type limiting branching processes arise for large population size. Its backward structure and related open problems are briefly discussed.

The salamander blastema within the broader context of metazoan regeneration.

Throughout the animal kingdom regenerative ability varies greatly from species to species, and even tissue to tissue within the same organism. The sheer diversity of structures and mechanisms renders a thorough comparison of molecular processes truly daunting. Are "blastemas" found in organisms as distantly related as planarians and axolotls derived from the same ancestral process, or did they arise convergently and independently? Is a mouse digit tip blastema orthologous to a salamander limb blastema? In other fields, the thorough characterization of a reference model has greatly facilitated these comparisons. For example, the amphibian Spemann-Mangold organizer has served as an amazingly useful comparative template within the field of developmental biology, allowing researchers to draw analogies between distantly related species, and developmental processes which are superficially quite different. The salamander limb blastema may serve as the best starting point for a comparative analysis of regeneration, as it has been characterized by over 200years of research and is supported by a growing arsenal of molecular tools. The anatomical and evolutionary closeness of the salamander and human limb also add value from a translational and therapeutic standpoint. Tracing the evolutionary origins of the salamander blastema, and its relatedness to other regenerative processes throughout the animal kingdom, will both enhance our basic biological understanding of regeneration and inform our selection of regenerative model systems.

Natural Fiano Wines Fermented in Stainless Steel Tanks, Oak Barrels, and Earthenware Amphora

The growing sensitivity toward sustainability is being demonstrated by an increase in sales of natural wines. Natural wines are obtained using exclusively native vines, indigenous yeasts, absence of additives, irregular temperature control during fermentation, and smaller quantities of sulfites even compared to organic wines. In this work, natural wines were obtained from Fiano grape, a historical cultivar of Irpinia (Campania, Italy). The main objective of this study was to compare the chemical and sensory characteristics of natural wines produced using different vessels (10 HL): Test A: stainless steel; Test B: earthenware amphora; Test C: mulberry wood barrel; and Test D: cherry wood barrel without the use of starter yeasts and chemical additives, including sulfites. Our results show a greater concentration of higher alcohols and esters in wines obtained in amphora and wooden barrels. The results of this work reveal that the type of container influences the composition of wine to an important extent. In addition, the Fiano wines obtained have a distinctive sensory profile also due to the ancestral winemaking process used, which did not involve the use of starter yeasts or technological and chemical adjuvants.

Design of a minimal di-nickel hydrogenase peptide.

Ancestral metabolic processes involve the reversible oxidation of molecular hydrogen by hydrogenase. Extant hydrogenase enzymes are complex, comprising hundreds of amino acids and multiple cofactors. We designed a 13-amino acid nickel-binding peptide capable of robustly producing molecular hydrogen from protons under a wide variety of conditions. The peptide forms a di-nickel cluster structurally analogous to a Ni-Fe cluster in [NiFe] hydrogenase and the Ni-Ni cluster in acetyl-CoA synthase, two ancient, extant proteins central to metabolism. These experimental results demonstrate that modern enzymes, despite their enormous complexity, likely evolved from simple peptide precursors on early Earth.

Speeding up Inference of Homologous Recombination in Bacteria

Bacteria reproduce clonally but most species recombine frequently, so that the ancestral process is best captured using an ancestral recombination graph. This graph model is often too complex to be used in an inferential setup, but it can be approximated for example by the ClonalOrigin model. Inference in the ClonalOrigin model is performed via a Reversible-Jump Markov Chain Monte Carlo algorithm, which attempts to jointly explore: the recombination rate, the number of recombination events, the departure and arrival points on the clonal genealogy for each recombination event, and the range of genomic sites affected by each recombination event. However, the Reversible-Jump algorithm often performs poorly due to the complexity of the target distribution since it needs to explore spaces of different dimensions. Recent developments in Bayesian computation methodology have provided ways to improve existing methods and code, but are not well-known outside the statistics community. We show how exploiting one of these new computational methods can lead to faster inference under the ClonalOrigin model.

The molecular evolution of spermatogenesis across mammals

The testis produces gametes through spermatogenesis and evolves rapidly at both the morphological and molecular level in mammals1–6, probably owing to the evolutionary pressure on males to be reproductively successful7. However, the molecular evolution of individual spermatogenic cell types across mammals remains largely uncharacterized. Here we report evolutionary analyses of single-nucleus transcriptome data for testes from 11 species that cover the three main mammalian lineages (eutherians, marsupials and monotremes) and birds (the evolutionary outgroup), and include seven primates. We find that the rapid evolution of the testis was driven by accelerated fixation rates of gene expression changes, amino acid substitutions and new genes in late spermatogenic stages, probably facilitated by reduced pleiotropic constraints, haploid selection and transcriptionally permissive chromatin. We identify temporal expression changes of individual genes across species and conserved expression programs controlling ancestral spermatogenic processes. Genes predominantly expressed in spermatogonia (germ cells fuelling spermatogenesis) and Sertoli (somatic support) cells accumulated on X chromosomes during evolution, presumably owing to male-beneficial selective forces. Further work identified transcriptomal differences between X- and Y-bearing spermatids and uncovered that meiotic sex-chromosome inactivation (MSCI) also occurs in monotremes and hence is common to mammalian sex-chromosome systems. Thus, the mechanism of meiotic silencing of unsynapsed chromatin, which underlies MSCI, is an ancestral mammalian feature. Our study illuminates the molecular evolution of spermatogenesis and associated selective forces, and provides a resource for investigating the biology of the testis across mammals.

Typology of Fermented Porridges and Socio-demographic Characteristics of Respondents in the Northern Part of Benin

Fermentation is an ancestral process and one of the most used economic methods in the preservation and transformation of cereal-based food raw materials. They are essentially rich in carbohydrates, but they can also be a source of micronutrients such as iron and are used in many traditional culinary preparations, in particular fermented porridges. The aim of this study is to identify the variability of fermented cereal-based porridges produced and consumed in northern Benin. Thus, 315 producers and consumers were randomly interviewed in nine localities of northern Benin. First, field surveys were carried out in the traditional areas of porridge production and consumption in the northern region of Benin in order to establish the consumption map of fermented porridges. Secondly, interviews and occasional conversations were used for sample collection as well as occasional interviews (individual survey). During our investigation, eight (koko, bobossou, gbangba, apkan, sagagnega, akloui, bita and fourra) porridge were reported. Corn, millet and sorghum are cereals that are used for proceeding those porridges. The interviewed people are predominantly (35.53%) between 18 and 25 years old of age followed by those aged between 25 and 31 years old (30.82%). Mostly (63.21%) women were interviewed with a sex ratio (M/F = 0.58) and involved in the production of traditional porridge. More than 36% of respondents had at least secondary education, 30.82% are uneducated, 22.64% have primary education and 10.06% had at least university level. A significant association was observed between the cereal used and the type of porridge (p<0.001). It can be seen that the marketing and consumption of different porridges is associated with different communes in northern Benin. The method of preserving these porridges and their processing differs from one producer to another or from one consumer to another. It also differs from one municipality to another.

An anti-inflammatory transcriptional cascade conserved from flies to humans.

Innate immunity is an ancestral process that can induce pro- and anti-inflammatory states. A major challenge is to characterize transcriptional cascades that modulate the response to inflammation. Since the Drosophila glial cells missing (Gcm) transcription factor has an anti-inflammatory role, we explored its regulation and evolutionary conservation. Here, we show that the murine Gcm2 (mGcm2) gene is expressed in a subpopulation of aged microglia (chronic inflammation) and upon lysophosphatidylcholine (LPC)-induced central nervous system (CNS) demyelination (acute inflammation). Moreover, mGcm2 conditional knockout mice show an increased inflammatory phenotype upon aging or LPC injection, and hGCM2 is expressed in active demyelinating lesions of patients with multiple sclerosis. Finally, Drosophila Gcm expression is induced upon aging and acute challenge, and its overexpression decreases the inflammatory phenotype. Altogether, these data indicate that the inducible Gcm cascade is conserved from flies to humans and represents a potential therapeutic target in the control of the inflammatory response.

Robust inference of population size histories from genomic sequencing data.

Unraveling the complex demographic histories of natural populations is a central problem in population genetics. Understanding past demographic events is of general anthropological interest, but is also an important step in establishing accurate null models when identifying adaptive or disease-associated genetic variation. An important class of tools for inferring past population size changes from genomic sequence data are Coalescent Hidden Markov Models (CHMMs). These models make efficient use of the linkage information in population genomic datasets by using the local genealogies relating sampled individuals as latent states that evolve along the chromosome in an HMM framework. Extending these models to large sample sizes is challenging, since the number of possible latent states increases rapidly.Here, we present our method CHIMP (CHMM History-Inference Maximum-Likelihood Procedure), a novel CHMM method for inferring the size history of a population. It can be applied to large samples (hundreds of haplotypes) and only requires unphased genomes as input. The two implementations of CHIMP that we present here use either the height of the genealogical tree (TMRCA) or the total branch length, respectively, as the latent variable at each position in the genome. The requisite transition and emission probabilities are obtained by numerically solving certain systems of differential equations derived from the ancestral process with recombination. The parameters of the population size history are subsequently inferred using an Expectation-Maximization algorithm. In addition, we implement a composite likelihood scheme to allow the method to scale to large sample sizes.We demonstrate the efficiency and accuracy of our method in a variety of benchmark tests using simulated data and present comparisons to other state-of-the-art methods. Specifically, our implementation using TMRCA as the latent variable shows comparable performance and provides accurate estimates of effective population sizes in intermediate and ancient times. Our method is agnostic to the phasing of the data, which makes it a promising alternative in scenarios where high quality data is not available, and has potential applications for pseudo-haploid data.

Lines of descent in the deterministic mutation–selection model with pairwise interaction

We consider the mutation--selection differential equation with pairwise interaction (or, equivalently, the diploid mutation--selection equation) and establish the corresponding ancestral process, which is a random tree and a variant of the ancestral selection graph. The formal relation to the forward model is given via duality. To make the tree tractable, we prune branches upon mutations, thus reducing it to its informative parts. The hierarchies inherent in the tree are encoded systematically via tripod trees with weighted leaves; this leads to the stratified ancestral selection graph. The latter also satisfies a duality relation with the mutation--selection equation. Each of the dualities provides a stochastic representation of the solution of the differential equation. This allows us to connect the equilibria and their bifurcations to the long-term behaviour of the ancestral process. Furthermore, with the help of the stratified ancestral selection graph, we obtain explicit results about the ancestral type distribution in the case of unidirectional mutation.

Simultaneous inference of parental admixture proportions and admixture times from unphased local ancestry calls

Population genetic analyses of local ancestry tracts routinely assume that the ancestral admixture process is identical for both parents of an individual, an assumption that may be invalid when considering recent admixture. Here, we present Parental Admixture Proportion Inference (PAPI), a Bayesian tool for inferring the admixture proportions and admixture times for each parent of a single admixed individual. PAPI analyzes unphased local ancestry tracts and has two components: a binomial model that leverages genome-wide ancestry fractions to infer parental admixture proportions and a hidden Markov model (HMM) that infers admixture times from tract lengths. Crucially, the HMM accounts for unobserved within-ancestry recombination by approximating the pedigree crossover dynamics, enabling inference of parental admixture times. In simulations, we find that PAPI's admixture proportion estimates deviate from the truth by 0.047 on average, outperforming ANCESTOR and PedMix by 46.0% and 57.6%, respectively. Moreover, PAPI's admixture time estimates were strongly correlated with the truth (R=0.76) but have an average downward bias of 1.01 generations that is partly attributable to inaccuracies in local ancestry inference. As an illustration of its utility, we ran PAPI on African American genotypes from the PAGE study (N= 5,786) and found strong evidence of assortative mating by ancestry proportion: couples' ancestry proportions are highly correlated (R= 0.87) and are closer to each other than expected under random mating (p<10-6). We anticipate that PAPI will be useful in studying the population dynamics of admixture and will also be of interest to individuals seeking to learn about their personal genealogies.

Revisiting biocrystallization: purine crystalline inclusions are widespread in eukaryotes.

Despite the widespread occurrence of intracellular crystalline inclusions in unicellular eukaryotes, scant attention has been paid to their composition, functions, and evolutionary origins. Using Raman microscopy, we examined >200 species from all major eukaryotic supergroups. We detected cellular crystalline inclusions in 77% species out of which 80% is composed of purines, such as anhydrous guanine (62%), guanine monohydrate (2%), uric acid (12%) and xanthine (4%). Our findings shifts the paradigm assuming predominance of calcite and oxalates. Purine crystals emerge in microorganisms in all habitats, e.g., in freshwater algae, endosymbionts of reef-building corals, deadly parasites, anaerobes in termite guts, or slime molds. Hence, purine biocrystallization is a general and ancestral eukaryotic process likely present in the last eukaryotic common ancestor (LECA) and here we propose two proteins omnipresent in eukaryotes that are likely in charge of their metabolism: hypoxanthine-guanine phosphoribosyl transferase and equilibrative nucleoside transporter. Purine crystalline inclusions are multifunctional structures representing high-capacity and rapid-turnover reserves of nitrogen and optically active elements, e.g., used in light sensing. Thus, we anticipate our work to be a starting point for further studies spanning from cell biology to global ecology, with potential applications in biotechnologies, bio-optics, or in human medicine.

General selection models: Bernstein duality and minimal ancestral structures

$\Lambda$-Wright--Fisher processes provide a robust framework to describe the type-frequency evolution of an infinite neutral population. We add a polynomial drift to the corresponding stochastic differential equation to incorporate frequency-dependent selection. A decomposition of the drift allows us to approximate the solution of the stochastic differential equation by a sequence of Moran models. The genealogical structure underlying the Moran model leads in the large population limit to a generalisation of the ancestral selection graph of Krone and Neuhauser. Building on this object, we construct a continuous-time Markov chain and relate it to the forward process via a new form of duality, which we call Bernstein duality. We adapt classical methods based on the moment duality to determine the time to absorption and criteria for the accessibility of the boundaries; this extends a recent result by Gonz\'alez Casanova and Span\`o. An intriguing feature of the construction is that the same forward process is compatible with multiple backward models. In this context we introduce suitable notions for minimality among the ancestral processes and characterise the corresponding parameter sets. In this way we recover classic ancestral structures as minimal ones.

Parallel Evolution of Ameloblastic scpp Genes in Bony and Cartilaginous Vertebrates.

In bony vertebrates, skeletal mineralization relies on the secretory calcium-binding phosphoproteins (Scpp) family whose members are acidic extracellular proteins posttranslationally regulated by the Fam20°C kinase. As scpp genes are absent from the elephant shark genome, they are currently thought to be specific to bony fishes (osteichthyans). Here, we report a scpp gene present in elasmobranchs (sharks and rays) that evolved from local tandem duplication of sparc-L 5′ exons and show that both genes experienced recent gene conversion in sharks. The elasmobranch scpp is remarkably similar to the osteichthyan scpp members as they share syntenic and gene structure features, code for a conserved signal peptide, tyrosine-rich and aspartate/glutamate-rich regions, and harbor putative Fam20°C phosphorylation sites. In addition, the catshark scpp is coexpressed with sparc-L and fam20°C in tooth and scale ameloblasts, similarly to some osteichthyan scpp genes. Despite these strong similarities, molecular clock and phylogenetic data demonstrate that the elasmobranch scpp gene originated independently from the osteichthyan scpp gene family. Our study reveals convergent events at the sparc-L locus in the two sister clades of jawed vertebrates, leading to parallel diversification of the skeletal biomineralization toolkit. The molecular evolution of sparc-L and its coexpression with fam20°C in catshark ameloblasts provides a unifying genetic basis that suggests that all convergent scpp duplicates inherited similar features from their sparc-L precursor. This conclusion supports a single origin for the hypermineralized outer odontode layer as produced by an ancestral developmental process performed by Sparc-L, implying the homology of the enamel and enameloid tissues in all vertebrates.

Argan Oil: Chemical Composition, Extraction Process, and Quality Control.

Argan oil is considered a relatively international product exported from Morocco, although different companies in Europe and North America distribute argan oil around the globe. Argan oil is non-refined vegetable oil, of the more well-known “virgin oil” type, is produced from the argan tree [Argania spinosa (L.) Skeels]. The argan tree is deemed to be an important forest species from both social and economic standpoints. Argan oil has rapidly emerged as an important product able to bring more income to the local population. In addition, it also has important environmental implications, owing to its ability to stand against desert progression. Currently, argan oil is mainly produced by women's cooperatives in Morocco using a semi-industrial mechanical extraction process. This allows the production of high-quality argan oil. Depending on the method used to prepare argan kernels, two types of argan oil can be obtained: food or cosmetic grade. Cosmetic argan oil is prepared from unroasted kernels, whereas food argan oil is achieved by cold pressing kernels roasted for a few minutes. Previously, the same food argan oil was prepared exclusively by women according to a laborious ancestral process. Extraction technology has been evolved to obtain high-quality argan oil at a large scale. The extraction process and several accompanying parameters can influence the quality, stability, and purity of argan oil. In view of this, the present review discusses different aspects related to argan oil chemical composition along with its nutritional and cosmetic values. Similarly, it details different processes used to prepare argan oil, as well as its quality control, oxidative stability, and authenticity assessment.

Application of a Markovian ancestral model to the temporal and spatial dynamics of cultural evolution on a population network

Cultural macroevolution concerns a long-term evolutionary process involving transmission of non-genetic or cultural traits between populations as well as birth and death of populations. To understand the spatial dynamics of cultural macroevolution, we present a one-locus model of cultural diffusion in which a cultural trait is transmitted on a network of populations. Borrowing the method of ancestral backward process from population genetics, our model explores the lineage of a trait variant sampled in the present generation to quantify when and where the variant was invented. Mathematical analysis of the model enables us to predict the distribution of cultural age in each population of the network, estimate the frequencies of trait variants originating from given populations, and discuss the time it takes for a trait variant to diffuse between a given pair of populations. We also perform numerical analysis on random scale-free network of populations to investigate the effect of network topology and innovation rate on the age and origin of variants in each population. The result suggests that trait variants are more likely to derive from a population with higher innovation rate. Our numerical analysis also shows that trait variants invented in populations with higher network-centrality values are likely to be maintained at a higher frequency and transmitted to other populations in a shorter time period.

The Ecohydrological Approach in Water Sowing and Harvesting Systems: The Case of the Paltas Catacocha Ecohydrology Demonstration Site, Ecuador

Water sowing and harvesting (WS&H), a term adopted from Latin America, is an ancestral process that involves gathering and infiltration (sowing) of rainwater, surface runoff, and groundwater to recover it (harvesting) later and/or elsewhere. The WS&H systems follow the approaches of integrated water resource management, nature-based solutions and the recovery of ancestral knowledge for water management. In this paper, we present some representative types of WS&H in Latin America, Spain, and Portugal, and then, we focus on the Paltas Catacocha Ecohydrology Demonstration Site in southern Ecuador as a study case. The recovery of such local ecohydrological knowledge in the study case has made enabled the regulation and retention of water in the aquifers through the restoration of artificial wetlands ( cochas ) and stream dams ( tapes or tajamares ). Also, this ancestral way of water management has recently supported and reactivated several biological aspects and human activities. The experience of the Paltas Catacocha site shows that there are more appropriate and sustainable alternatives to gray infrastructure projects for water resources management and denotes the need to study ancestral water and soil management systems.