Past Population Dynamics Research Articles

Retrodiction of forest demography: Backward simulation with reverse matrix models

Abstract Reconstructing past ecological population dynamics and demographic events is crucial for understanding the dynamics of ecological processes, evaluating the impact of environmental changes and making informed conservation decisions. In forest ecosystems, retrodiction (i.e. the backward projection of ecological populations) plays a pivotal role in understanding historical forest carbon levels and the factors that have influenced their variation over time, because forest demography is a major determinant of the amount of carbon stored in forest ecosystems. The persistent lack of quantitative methods has been a significant obstacle in retrodicting forest demography, especially in applications of a broad geographical scale. While there is a wealth of models for predicting future forest conditions, models that can project these conditions backward in time are scarce. This study presents reverse matrix model (RMM), an innovative retrodiction modelling approach grounded in the principles of transition matrix models. RMM is designed to deduce past demographic characteristics of ecological populations using current data, making it one of the first models capable of projecting the fine‐scale dynamics of forest demography into the past. We assessed the retrodictive performance of RMM by fitting it to a dataset of a disturbed tropical rainforest in French Guiana in 2001–2023, then comparing the retrodictions to observations back to 1983 when the disturbance occurred. We further empirically evaluated the viability of retrodiction over a defined duration by inverting the density‐dependent matrix model by Lin et al. (1996), which predicts the dynamics of northern hardwoods in the United States. The case studies demonstrate significant potential for RMM application in various domains of forestry and conservation, including ecosystem management and conservation planning, global change impact assessment and biodiversity monitoring.

Range expansions across landscapes with quenched noise

When biological populations expand into new territory, the evolutionary outcomes can be strongly influenced by genetic drift, the random fluctuations in allele frequencies. Meanwhile, spatial variability in the environment can also significantly influence the competition between subpopulations vying for space. Little is known about the interplay of these intrinsic and extrinsic sources of noise in population dynamics: When does environmental heterogeneity dominate over genetic drift or vice versa, and what distinguishes their population genetics signatures? Here, in the context of neutral evolution, we examine the interplay between a population's intrinsic, demographic noise and an extrinsic, quenched random noise provided by a heterogeneous environment. Using a multispecies Eden model, we simulate a population expanding over a landscape with random variations in local growth rates and measure how this variability affects genealogical tree structure, and thus genetic diversity. We find that, for strong heterogeneity, the genetic makeup of the expansion front is to a great extent predetermined by the set of fastest paths through the environment. The landscape-dependent statistics of these optimal paths then supersede those of the population's intrinsic noise as the main determinant of evolutionary dynamics. Remarkably, the statistics for coalescence of genealogical lineages, derived from those deterministic paths, strongly resemble the statistics emerging from demographic noise alone in uniform landscapes. This cautions interpretations of coalescence statistics and raises new challenges for inferring past population dynamics.

The 'queen of the Andes' (Puya raimondii) is genetically fragile and fragmented: a consequence of long generation time and semelparity?

Understanding how life history shapes genetic diversity is a fundamental issue in evolutionary biology, with important consequences for conservation. However, we still have an incomplete picture of the impact of life history on genome-wide patterns of diversity, especially in long-lived semelparous plants. Puya raimondii is a high-altitude semelparous species from the Andes that flowers at 40-100 years of age. We sequenced the whole genome and estimated the nucleotide diversity of 200 individuals sampled from nine populations. Coalescent-based approaches were then used to infer past population dynamics. Finally, these results were compared with results obtained for the iteroparous species, Puya macrura. The nine populations of P. raimondii were highly divergent, highly inbred, and carried an exceptionally high genetic load. They are genetically depauperate, although, locally in the genome, balancing selection contributed to the maintenance of genetic polymorphism. While both P. raimondii and P. macrura went through a severe bottleneck during the Pleistocene, P. raimondii did not recover from it and continuously declined, while P. macrura managed to bounce back. Our results demonstrate the importance of life history, in particular generation time and reproductive strategy, in affecting population dynamics and genomic variation, and illustrate the genetic fragility of long-lived semelparous plants.

Ornithogenic sedimentary profiles of n-alkanes and PAHs constrain breeding penguin population dynamics at Cape Bird, Ross Island, Antarctica, over the past 1,500 years

Ornithogenic sediment may contain important paleoecological information concerning past bird population dynamics. In this paper, we analyse the distribution of n-alkanes and polycyclic aromatic hydrocarbons (PAHs) in two sedimentary profiles collected from abandoned penguin colonies at Cape Bird, Ross Island, Antarctica. The geochronology of the sediment profiles was determined using 210Pb and AMS 14C dating techniques, and spans the past 1500 years. We observe low levels of n-alkanes (0.93–2.67 μg g−1) and PAHs (20.5–46.8 ng g−1) concentrations dominated by short-chain n-alkanes, low-molecular-weight and alkyl PAHs. Principal Component Analysis (PCA) shows that the PC 1 scores for n-alkanes and PAHs are significantly correlated with the input intensity of penguin guano and penguin bioelements. Using these proxies in combination with Generalized Additive Model (GAM), we reveal that breeding penguin population growth reaches a historical peak during the Medieval Climate Anomaly (MCA) prior to 1550 CE. This growth in population size corresponds to the extent of sea ice cover and the activity of the local atmospheric-ocean circulation. Warming induced by El Niño and the positive phase of the Southern Annular Mode, along with the expansion of ice-free zones and increased oceanic nutrient and food availability, are considered primary factors contributing to the growth of breeding penguin populations. Additionally, variations in sea ice extent and Amundsen Sea Low significantly influence penguin population dynamics. Our study suggests that n-alkanes and PAHs may be valuable organic proxies for reconstructing historical changes in breeding penguin populations, with the local sea ice extent and atmospheric-oceanic circulation exerting a major influence on Antarctic penguin population dynamics.

Y Chromosome Story-Ancient Genetic Data as a Supplementary Tool for the Analysis of Modern Croatian Genetic Pool.

Due to its turbulent demographic history, marked by extensive settlement and gene flow from diverse regions of Eurasia, Southeastern Europe (SEE) has consistently served as a genetic crossroads between East and West and a junction for the migrations that reshaped Europe's population. SEE, including modern Croatian territory, was a crucial passage from the Near East and even more distant regions and human populations in this region, as almost any other European population represents a remarkable genetic mixture. Modern humans have continuously occupied this region since the Upper Paleolithic era, and different (pre)historical events have left a distinctive genetic signature on the historical narrative of this region. Our views of its history have been mostly renewed in the last few decades by extraordinary data obtained from Y-chromosome studies. In recent times, the international research community, bringing together geneticists and archaeologists, has steadily released a growing number of ancient genomes from this region, shedding more light on its complex past population dynamics and shaping the genetic pool in Croatia and this part of Europe.

The rise of baobab trees in Madagascar

The baobab trees (genus Adansonia) have attracted tremendous attention because of their striking shape and distinctive relationships with fauna1. These spectacular trees have also influenced human culture, inspiring innumerable arts, folklore and traditions. Here we sequenced genomes of all eight extant baobab species and argue that Madagascar should be considered the centre of origin for the extant lineages, a key issue in their evolutionary history2,3. Integrated genomic and ecological analyses revealed the reticulate evolution of baobabs, which eventually led to the species diversity seen today. Past population dynamics of Malagasy baobabs may have been influenced by both interspecific competition and the geological history of the island, especially changes in local sea levels. We propose that further attention should be paid to the conservation status of Malagasy baobabs, especially of Adansoniasuarezensis and Adansoniagrandidieri, and that intensive monitoring of populations of Adansoniaza is required, given its propensity for negatively impacting the critically endangered Adansoniaperrieri.

Chromosome-level assembly of the gray fox (Urocyon cinereoargenteus) confirms the basal loss of PRDM9 in Canidae.

Reference genome assemblies have been created from multiple lineages within the Canidae family; however, despite its phylogenetic relevance as a basal genus within the clade, there is currently no reference genome for the gray fox (Urocyon cinereoargenteus). Here, we present a chromosome-level assembly for the gray fox (U. cinereoargenteus), which represents the most contiguous, non-domestic canid reference genome available to date, with 90% of the genome contained in just 34 scaffolds and a contig N50 and scaffold N50 of 59.4 and 72.9 Megabases, respectively. Repeat analyses identified an increased number of simple repeats relative to other canids. Based on mitochondrial DNA, our Vermont sample clusters with other gray fox samples from the northeastern United States and contains slightly lower levels of heterozygosity than gray foxes on the west coast of California. This new assembly lays the groundwork for future studies to describe past and present population dynamics, including the delineation of evolutionarily significant units of management relevance. Importantly, the phylogenetic position of Urocyon allows us to verify the loss of PRDM9 functionality in the basal canid lineage, confirming that pseudogenization occurred at least 10 million years ago.

Demographic responses of oceanic island birds to local and regional ecological disruptions revealed by whole-genome sequencing.

Disentangling the effects of ecological disruptions operating at different spatial and temporal scales in shaping past species' demography is particularly important in the current context of rapid environmental changes driven by both local and regional factors. We argue that volcanic oceanic islands provide useful settings to study the influence of past ecological disruptions operating at local and regional scales on population demographic histories. We investigate potential drivers of past population dynamics for three closely related species of passerine birds from two volcanic oceanic islands, Reunion and Mauritius (Mascarene archipelago), with distinct volcanic history. Using ABC and PSMC inferences from complete genomes, we reconstructed the demographic history of the Reunion Grey White-eye (Zosterops borbonicus (Pennant, 1781)), the Reunion Olive White-eye (Z. olivaceus (Linnaeus, 1766)) and the Mauritius Grey White-eye (Z. mauritianus (Gmelin, 1789)) and searched for possible causes underlying similarities or differences between species living on the same or different islands. Both demographic inferences strongly support ancient and long-term expansions in all species. They also reveal different trajectories between species inhabiting different islands, but consistent demographic trajectories in species or populations from the same island. Species from Reunion appear to have experienced synchronous reductions in population size during the Last Glacial Maximum, a trend not seen in the Mauritian species. Overall, this study suggests that local events may have played a role in shaping population trajectories of these island species. It also highlights the potential of our conceptual framework to disentangle the effects of local and regional drivers on past species' demography and long-term population processes.

Past human expansions shaped the spatial pattern of Neanderthal ancestry.

The worldwide expansion of modern humans (Homo sapiens) started before the extinction of Neanderthals (Homo neanderthalensis). Both species coexisted and interbred, leading to slightly higher introgression in East Asians than in Europeans. This distinct ancestry level has been argued to result from selection, but range expansions of modern humans could provide an alternative explanation. This hypothesis would lead to spatial introgression gradients, increasing with distance from the expansion source. We investigate the presence of Neanderthal introgression gradients after past human expansions by analyzing Eurasian paleogenomes. We show that the out-of-Africa expansion resulted in spatial gradients of Neanderthal ancestry that persisted through time. While keeping the same gradient orientation, the expansion of early Neolithic farmers contributed decisively to reducing the Neanderthal introgression in European populations compared to Asian populations. This is because Neolithic farmers carried less Neanderthal DNA than preceding Paleolithic hunter-gatherers. This study shows that inferences about past human population dynamics can be made from the spatiotemporal variation in archaic introgression.

From the Ground Up: A Multidisciplinary Approach to Past Fertility and Population Narratives

Population dynamics form a crucial component of human narratives in the past. Population responses and adaptations not only tell us about the human past but also offer insights into the present and future. Though an area of substantial interest, it is also one of often limited evidence. As such, traditional techniques from demography and anthropology must be adapted considerably to accommodate the available archaeological and ethnohistoric data and an appropriate inferential framework must be applied. In this article, I propose a ground-up, multidisciplinary approach to the study of past population dynamics. Specifically, I develop an empirically informed path diagram based on modern fertility interactions and sources of past environmental, sociocultural, and biological evidence to guide high-resolution case studies. The proposed approach is dynamic and can evolve in response to data inputs as case studies are undertaken. In application, this approach will create new knowledge of past population processes which can greatly enhance our presently limited knowledge of high-frequency, small-scale demographic fluctuations, as well as contribute to our broader understanding of significant population disturbances and change throughout human history.

Inferring Evolutionary Timescale of Omsk Hemorrhagic Fever Virus.

Until 2020, there were only three original complete genome (CG) nucleotide sequences of Omsk hemorrhagic fever virus (OHFV) in GenBank. For this reason, the evolutionary rate and divergence time assessments reported in the literature were based on the E gene sequences, but notably without temporal signal evaluation, such that their reliability is unclear. As of July 2022, 47 OHFV CG sequences have been published, which enables testing of temporal signal in the data and inferring unbiased and reliable substitution rate and divergence time values. Regression analysis in the TempEst software demonstrated a stronger clocklike behavior in OHFV samples for the complete open reading frame (ORF) data set (R2 = 0.42) than for the E gene data set (R2 = 0.11). Bayesian evaluation of temporal signal indicated very strong evidence, with a log Bayes factor of more than 5, in favor of temporal signal in all data sets. Our results based on the complete ORF sequences showed a more precise OHFV substitution rate (95% highest posterior density (HPD) interval, 9.1 × 10-5-1.8 × 10-4 substitutions per site per year) and tree root height (416-896 years ago) compared with previous assessments. The rate obtained is significantly higher than tick-borne encephalitis virus by at least 3.8-fold. The phylogenetic analysis and past population dynamics reconstruction revealed the declining trend of OHFV genetic diversity, but there was phylogenomic evidence that implicit virus subpopulations evolved locally and underwent an exponential growth phase.

Sedimentary DNA can reveal the past population dynamics of a pelagic copepod

Abstract Copepods play a key trophic role as secondary producers, transferring primary production to higher trophic levels such as fish. Copepod production contributes significantly to successful fish recruitment. Despite their importance, knowledge of copepod dynamics over several decades remains limited due to the lack of long‐term data series with adequate sampling and analysis. However, an understanding of long‐term copepod dynamics is urgently required to strive toward better management for sustainable aquatic ecosystems and fish recruitment. Sedimentary DNA (sedDNA) has been developing as a useful tool for reconstructing past plankton dynamics. This study evaluates whether sedDNA targeting the pelagic copepod, Eodiaptomus japonicus, in Lake Biwa (Japan) can be an effective tool for elucidating its past population dynamics. We applied a quantitative polymerase chain reaction method targeting the mitochondrial cytochrome c oxidase subunit I gene on two sediment cores and compared the detected sedDNA concentrations with the unique long‐term dataset of demographic traits, biomass, specific growth rate, production, subitaneous eggs, and resting eggs of E. japonicus. The sedDNA concentration of E. japonicus recovered from sediment layers correlated significantly with in situ production, biomass, and production of immediately hatching eggs but not with resting eggs or specific growth rate. Our study provides evidence for the effective use of sedDNA as a tracking tool for assessing past copepod production dynamics.

AdaPop: Bayesian inference of dependent population dynamics in coalescent models.

The coalescent is a powerful statistical framework that allows us to infer past population dynamics leveraging the ancestral relationships reconstructed from sampled molecular sequence data. In many biomedical applications, such as in the study of infectious diseases, cell development, and tumorgenesis, several distinct populations share evolutionary history and therefore become dependent. The inference of such dependence is a highly important, yet a challenging problem. With advances in sequencing technologies, we are well positioned to exploit the wealth of high-resolution biological data for tackling this problem. Here, we present adaPop, a probabilistic model to estimate past population dynamics of dependent populations and to quantify their degree of dependence. An essential feature of our approach is the ability to track the time-varying association between the populations while making minimal assumptions on their functional shapes via Markov random field priors. We provide nonparametric estimators, extensions of our base model that integrate multiple data sources, and fast scalable inference algorithms. We test our method using simulated data under various dependent population histories and demonstrate the utility of our model in shedding light on evolutionary histories of different variants of SARS-CoV-2.

Modelling the location of interglacial microrefugia for cold-adapted species

Rhododendron tomentosum is a vascular plant common in northern regions of Europe, Asia and North America. In central Europe, this species is considered a glacial relict. In recent years, systematic floristic mapping of the distribution of this species in the Bohemian Switzerland National Park has revealed that this rare and highly sensitive species is strongly associated with a specific type of habitat. Rhododendron tomentosum adapted to environmental changes throughout the Holocene: soil acidification, repeated fires and negative effect of forestry on species composition. To identify the survival mechanisms of R. tomentosum, suitable sites in well-preserved parts of a sandstone landscape with assumed minimal human influence were selected. Based on data from intensive field sampling and a set of environmental variables for the whole area of the National Park, habitat suitability maps for R. tomentosum were developed. These maps were then combined with the palaeoecological data and used to identify sources of pollen with greater precision and extend the knowledge of the potential distribution of R. tomentosum outside the intensively sampled areas. Palaeoecological data was particularly useful for reconstructing the past population dynamics of R. tomentosum. The results indicate the long-term stability of sites suitable for this species, supported by locally diversified vegetation development in sandstone areas. This research could therefore provide the first direct evidence of the persistence of R. tomentosum micropopulations throughout a large part of the Holocene.

Population dynamics and demographic history of Eurasian collared lemmings

BackgroundAncient DNA studies suggest that Late Pleistocene climatic changes had a significant effect on population dynamics in Arctic species. The Eurasian collared lemming (Dicrostonyx torquatus) is a keystone species in the Arctic ecosystem. Earlier studies have indicated that past climatic fluctuations were important drivers of past population dynamics in this species.ResultsHere, we analysed 59 ancient and 54 modern mitogenomes from across Eurasia, along with one modern nuclear genome. Our results suggest population growth and genetic diversification during the early Late Pleistocene, implying that collared lemmings may have experienced a genetic bottleneck during the warm Eemian interglacial. Furthermore, we find multiple temporally structured mitogenome clades during the Late Pleistocene, consistent with earlier results suggesting a dynamic late glacial population history. Finally, we identify a population in northeastern Siberia that maintained genetic diversity and a constant population size at the end of the Pleistocene, suggesting suitable conditions for collared lemmings in this region during the increasing temperatures associated with the onset of the Holocene.ConclusionsThis study highlights an influence of past warming, in particular the Eemian interglacial, on the evolutionary history of the collared lemming, along with spatiotemporal population structuring throughout the Late Pleistocene.

Long-term demographic trends and spatio-temporal distribution of past human activity in Central Europe: Comparison of archaeological and palaeoecological proxies

Estimating past population dynamics has become a major research topic for archaeology, which uses several proxies for studying past demography. The Czech Republic represents a unique region with abundant digital archaeological and palynological datasets comprising tens of thousands of records covering the whole Holocene. We used these datasets to quantify long-term demographic trends and to delimit past human activity in space and time. Our results, based on large data from both disciplines, are one of the first quantitative results covering the whole Czech Republic. Through summed probability distributions of radiocarbon dates and spatio-temporal modelling of human activity based on archaeological sites, we identified four major demographic events and processes between 10,000 BCE and 1000 CE – the beginning of the Neolithic at 5400 BCE, the Eneolithic/Bronze Age transition in the 3rd millennium BCE, Bronze Age expansion after 1500 BCE, and mediaeval expansion after 500 CE. We identified two settlement cores in the lowlands, with additional inner and outer peripheries with different demographic histories. Our study clearly shows that prehistoric and early historic population dynamics were not a homogenised process and were regionalized according to local environmental and social conditions. The comparison of archaeological results with pollen-based vegetation proxies also showed regional aspects in human-vegetation interactions. Agro-pastoral communities dwelling in the lowlands mostly influenced the openness of the landscape, used for fields and pastures, whereas contemporary communities with a similar economic mode residing in a different region are more visible in pollen records through species and structural changes in woodlands. The agro-pastoral subsistence strategy did not start everywhere with the onset of the Neolithic: in some regions it failed after several centuries, in others, the foraging lifestyle persisted significantly longer, and farming became a major economic strategy much later. Our study shows that archaeological site-based and 14C-based demographic proxies cannot be utilized for all periods and regions due to several limitations. Only the combination of different quantitative and qualitative archaeological proxies for population does reveal important details.

Genomic analysis of a reef-building coral, Acropora digitifera, reveals complex population structure and a migration network in the Nansei Islands, Japan.

Understanding the structure and connectivity of coral populations is fundamental for developing marine conservation policies, especially in patchy environments such as archipelagos. The Nansei Islands, extending more than 1000 km in southwestern Japan, are characterized by high levels of biodiversity and endemism, supported by coral reefs, which make this region ideal for assessing genetic attributes of coral populations. In this study, we conducted population genomic analyses based on genome-wide, single-nucleotide polymorphisms (SNPs) of Acropora digitifera, a common species in the Nansei Islands. By merging newly obtained genome resequencing data with previously published data, we identified more than 4 million genome-wide SNPs in 303 colonies collected at 22 locations, with sequencing coverage ranging from 3.91× to 27.41×. While population structure analyses revealed genetic similarities between the southernmost and northernmost locations, separated by >1000 km, several subpopulations in intermediate locations suggested limited genetic admixture, indicating conflicting migration tendencies in the Nansei Islands. Although migration networks revealed a general tendency of northward migration along the Kuroshio Current, a substantial amount of southward migration was also detected, indicating important contributions of minor ocean currents to coral larval dispersal. Moreover, heterogeneity in the transition of effective population sizes among locations suggests different histories for individual subpopulations. The unexpected complexity of both past and present population dynamics in the Nansei Islands implies that heterogeneity of ocean currents and local environments, past and present, have influenced the population structure of this species, and similar unexpected population complexities may be expected for other marine species with similar reproductive modes.

Robust Phylodynamic Analysis of Genetic Sequencing Data from Structured Populations.

The multi-type birth–death model with sampling is a phylodynamic model which enables the quantification of past population dynamics in structured populations based on phylogenetic trees. The BEAST 2 package bdmm implements an algorithm for numerically computing the probability density of a phylogenetic tree given the population dynamic parameters under this model. In the initial release of bdmm, analyses were computationally limited to trees consisting of up to approximately 250 genetic samples. We implemented important algorithmic changes to bdmm which dramatically increased the number of genetic samples that could be analyzed and which improved the numerical robustness and efficiency of the calculations. Including more samples led to the improved precision of parameter estimates, particularly for structured models with a high number of inferred parameters. Furthermore, we report on several model extensions to bdmm, inspired by properties common to empirical datasets. We applied this improved algorithm to two partly overlapping datasets of the Influenza A virus HA sequences sampled around the world—one with 500 samples and the other with only 175—for comparison. We report and compare the global migration patterns and seasonal dynamics inferred from each dataset. In this way, we show the information that is gained by analyzing the bigger dataset, which became possible with the presented algorithmic changes to bdmm. In summary, bdmm allows for the robust, faster, and more general phylodynamic inference of larger datasets.

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 studies where time–frequency changes of radiocarbon dates have been used as a proxy for inferring past population dynamics. Although its universal and straightforward premise is appealing and undoubtedly offers some unique opportunities for research on long-term comparative demography, practical applications are far from trivial and riddled with issues pertaining to the very nature of the proxy under examination. Here I review the most common criticisms concerning the nature of radiocarbon time–frequency data as a demographic proxy, focusing on key statistical and inferential challenges. I then examine and compare recent methodological advances in the field by grouping them into three approaches: reconstructive, null-hypothesis significance testing, and model fitting. I will then conclude with some general recommendations for applying these techniques in archaeological and paleo-demographic research.

Papua New Guinean Genomes Reveal the Complex Settlement of North Sahul.

The settlement of Sahul, the lost continent of Oceania, remains one of the most ancient and debated human migrations. Modern New Guineans inherited a unique genetic diversity tracing back 50,000 years, and yet there is currently no model reconstructing their past population dynamics. We generated 58 new whole-genome sequences from Papua New Guinea, filling geographical gaps in previous sampling, specifically to address alternative scenarios of the initial migration to Sahul and the settlement of New Guinea. Here, we present the first genomic models for the settlement of northeast Sahul considering one or two migrations from Wallacea. Both models fit our data set, reinforcing the idea that ancestral groups to New Guinean and Indigenous Australians split early, potentially during their migration in Wallacea where the northern route could have been favored. The earliest period of human presence in Sahul was an era of interactions and gene flow between related but already differentiated groups, from whom all modern New Guineans, Bismarck islanders, and Indigenous Australians descend. The settlement of New Guinea was probably initiated from its southeast region, where the oldest archaeological sites have been found. This was followed by two migrations into the south and north lowlands that ultimately reached the west and east highlands. We also identify ancient gene flows between populations in New Guinea, Australia, East Indonesia, and the Bismarck Archipelago, emphasizing the fact that the anthropological landscape during the early period of Sahul settlement was highly dynamic rather than the traditional view of extensive isolation.