Ancient DNA Research Articles

Ancient Rapanui genomes reveal resilience and pre-European contact with the Americas

Rapa Nui (also known as Easter Island) is one of the most isolated inhabited places in the world. It has captured the imagination of many owing to its archaeological record, which includes iconic megalithic statues called moai1. Two prominent contentions have arisen from the extensive study of Rapa Nui. First, the history of the Rapanui has been presented as a warning tale of resource overexploitation that would have culminated in a major population collapse—the ‘ecocide’ theory2–4. Second, the possibility of trans-Pacific voyages to the Americas pre-dating European contact is still debated5–7. Here, to address these questions, we reconstructed the genomic history of the Rapanui on the basis of 15 ancient Rapanui individuals that we radiocarbon dated (1670–1950 ce) and whole-genome sequenced (0.4–25.6×). We find that these individuals are Polynesian in origin and most closely related to present-day Rapanui, a finding that will contribute to repatriation efforts. Through effective population size reconstructions and extensive population genetics simulations, we reject a scenario involving a severe population bottleneck during the 1600s, as proposed by the ecocide theory. Furthermore, the ancient and present-day Rapanui carry similar proportions of Native American admixture (about 10%). Using a Bayesian approach integrating genetic and radiocarbon dates, we estimate that this admixture event occurred about 1250–1430 ce.

SVA Regulation of Transposable Element Clustered Transcription within the Major Histocompatibility Complex Genomic Class II Region of the Parkinson's Progression Markers Initiative.

SINE-VNTR-Alu (SVA) retrotransposons can regulate expression quantitative trait loci (eQTL) of coding and noncoding genes including transposable elements (TEs) distributed throughout the human genome. Previously, we reported that expressed SVAs and human leucocyte antigen (HLA) class II genotypes on chromosome 6 were associated significantly with Parkinson's disease (PD). Here, our aim was to follow-up our previous study and evaluate the SVA associations and their regulatory effects on the transcription of TEs within the HLA class II genomic region. We reanalyzed the transcriptome data of peripheral blood cells from the Parkinson's Progression Markers Initiative (PPMI) for 1530 subjects for TE and gene RNAs with publicly available computing packages. Four structurally polymorphic SVAs regulate the transcription of 20 distinct clusters of 235 TE loci represented by LINES (37%), SINES (28%), LTR/ERVs (23%), and ancient transposon DNA elements (12%) that are located in close proximity to HLA genes. The transcribed TEs were mostly short length, with an average size of 389 nucleotides. The numbers, types and profiles of positive and negative regulation of TE transcription varied markedly between the four regulatory SVAs. The expressed SVA and TE RNAs in blood cells appear to be enhancer-like elements that are coordinated differentially in the regulation of HLA class II genes. Future work on the mechanisms underlying their regulation and potential impact is essential for elucidating their roles in normal cellular processes and disease pathogenesis.

Investigating population continuity and ghost admixture among ancient genomes

Ancient DNA (aDNA) can prove a valuable resource when investigating the evolutionary relationships between ancient and modern populations. Performing demographic inference using datasets that include aDNA samples however, requires statistical methods that explicitly account for the differences in drift expected among a temporally distributed sample. Such drift due to temporal structure can be challenging to discriminate from admixture from an unsampled, or “ghost", population, which can give rise to very similar summary statistics and confound methods commonly used in population genetics. Sequence data from ancient individuals also have unique characteristics, including short fragments, increased sequencing-error rates, and often limited genome-coverage that poses further challenges. Here we present a novel and conceptually simple approach for assessing questions of population continuity among a temporally distributed sample. We note that conditional on heterozygote sites in an individual genome at a particular point in time, the mean proportion of derived variants at those sites in other individuals has different expectations forwards in time and backwards in time. The difference in these processes enables us to construct a statistic that can detect population continuity in a temporal sample of genomes. We show that the statistic is sensitive to historical admixture events from unsampled populations. Simulations are used to evaluate the power of this approach. We investigate a set of ancient genomes from Early Neolithic Scandinavia to assess levels of population continuity to an earlier Mesolithic individual.

The Genomic and Cultural Diversity of the Inka Qhapaq Hucha Ceremony in Chile and Argentina.

The South American archaeological record has ample evidence of the socio-cultural dynamism of human populations in the past. This has also been supported through the analysis of ancient genomes, by showing evidence of gene flow across the region. While the extent of these signals is yet to be tested, the growing number of ancient genomes allows for more fine-scaled hypotheses to be evaluated. In this study, we assessed the genetic diversity of individuals associated with the Inka ritual, Qhapaq hucha. As part of this ceremony, one or more individuals were buried with Inka and local-style offerings on mountain summits along the Andes, leaving a very distinctive record. Using paleogenomic tools, we analyzed three individuals: two newly generated genomes from El Plomo Mountain (Chile) and El Toro Mountain (Argentina), and a previously published genome from Argentina (Aconcagua Mountain). Our results reveal a complex demographic scenario with each of the individuals showing different genetic affinities. Furthermore, while two individuals showed genetic similarities with present-day and ancient populations from the southern region of the Inka empire, the third individual may have undertaken long-distance movement. The genetic diversity we observed between individuals from similar cultural contexts supports the highly diverse strategies Inka implemented while incorporating new territories. More broadly, this research contributes to our growing understanding of the population dynamics in the Andes by discussing the implications and temporality of population movements in the region.

Ancient Genome of Broomcorn Millet from Northwest China in Seventh Century CE: Shedding New Light to Its Origin and Dispersal Patterns

Broomcorn millet (Panicum miliaceum) is among the earliest domesticated staple crops in the world’s agricultural history and facilitated the development of several early agrarian cultures, particularly those originating in northern China. However, the propagation route of broomcorn millet in China from the Middle Ages to the present remains unclear. The aim of this study is to explore the genetic affinity between ancient and modern millet samples, trace the genetic origins and diffusion pathways of broomcorn millet, and provide insights into its domestication and spread. To achieve this, we sequence ancient DNA from broomcorn millet remains excavated from the Chashan Village cemetery (AD 691) in Gansu Province, China. Phylogenetic and population genetic analyses, integrating ancient and modern millet genomes, reveal a close genetic relationship between ancient millet and contemporary millet from Ningxia Province (445 km away from Chashan Village), suggesting a potential origin for the Chashan millet. This finding aligns with the tomb’s epitaph, which documents the reburial of the tomb’s owner, who was originally buried in Ningxia, and provides important archaeological evidence for understanding the interaction between geopolitical dynamics and the natural environment in northwest China during the late seventh century. Furthermore, outgroup-f3 and D statistics evidence suggests substantial genetic interactions between ancient millet and modern varieties from the Loess Plateau, Huang-Huai-Hai Plain, and Northeast Plain, indicating the dispersal route of broomcorn millet, along with human migration routes, from the northwest to northern China and ultimately to the northeast region, starting from the Middle Ages onward. This study enhances our understanding of millet’s genetic history, offers a novel perspective on burial archaeology, and provides valuable insights into the origins, domestication, and diffusion of broomcorn millet.

A novel method to assess the integrity of frozen archival DNA samples: Alpha‐diversity ratios of short‐ and long‐read 16S rRNA gene sequences

Abstract Archival DNA samples collected and analysed for a range of research and applied questions have accumulated in the laboratories of universities, government agencies and commercial service providers for decades. These DNA archives represent a valuable, yet largely un‐tapped repository of genomic information. With lowering costs of, and increasing access to, high‐throughput sequencing, we predict an increase in retrospective research to explore the wealth of information that resides in these archival samples. However, for this to occur, we need confidence in the integrity of the DNA samples, often stored under suboptimal conditions and their fitness of purpose for downstream genomic analysis. Here, we borrow from a well‐established concept in ancient DNA to evaluate sample integrity, defined as loss of information content in recovered amplicons, of frozen DNA samples and based on the ratio of ⍺‐diversity of short‐ and long‐read 16S rRNA gene sequences. The 16S rRNA variable region of 87 stored DNA samples, extracted from soil, collected from western and southern agricultural regions of Australia between 2001 and 2021 were sequenced using both PacBio full length reads (V1–V9, 1.5 kbp) and Illumina short‐reads (V3–V4, 200–450 bp). When ⍺‐diversity ratios were calculated between the long and short reads to assess DNA degradation, the ratio of ⍺‐diversity did not decrease in older samples versus younger samples. We suggest this as a novel method to confirm integrity of DNA before embarking on large‐scale diversity profiling projects using archival DNA.

Evaluation of genotype imputation using Glimpse tools on low coverage ancient DNA.

Ancient DNA provides a unique frame for directly studying human population genetics in time and space. Still, since most of the ancient genomic data is low coverage, analysis is confronted with a low number of SNPs, genotype uncertainties, and reference-bias. Here, we for the first time benchmark the two distinct versions of Glimpse tools on 120 ancient human genomes from Eurasia including those largely from previously under-evaluated regions and compare the performance of genotype imputation with de facto analysis approaches for low coverage genomic data analysis. We further investigate the impact of two distinct reference panels on imputation accuracy for low coverage genomic data. We compute accuracy statistics and perform PCA and f4-statistics to explore the behaviour of genotype imputation on low coverage data regarding (i)two versions of Glimpse, (ii)two reference panels, (iii)four post-imputation filters and coverages, as well as (iv)data type and geographical origin of the samples on the analyses. Our results reveal that even for 0.1X coverage ancient human genomes, genotype imputation using Glimpse-v2 is suitable. Additionally, using the 1000 Genomes merged with Human Genome Diversity Panel improves the accuracy of imputation for the rare variants with low MAF, which might be important not only for ancient genomics but also for modern human genomic studies based on low coverage data and for haplotype-based analysis. Most importantly, we reveal that genotype imputation of low coverage ancient human genomes reduces the genetic affinity of the samples towards human reference genome. Through solving one of the most challenging biases in data analysis, so-called reference bias, genotype imputation using Glimpse v2 is promising for low coverage ancient human genomic data analysis and for rare-variant-based and haplotype-based analysis.

FamilyTreeDNA Group Project Administrator Stockholm, Sweden

Abstract. Several scholars have in the past hypothesized a northward movement of Hunnic contingents which ultimately reached Scandinavia on the basis of archaeological and philological evidence, an event which should be detectable in both ancient and modern DNA if true. Here I report that when analyzing a combination of ancient and modern DNA samples from across Eurasia one can detect a westward movement from the Altai-Sayan region to Europe which ultimately reached southern Sweden, and also accurately date this migration event to the 4th and 5th centuries CE with the help of carbon-14 dating and estimated TMRCAs of certain Y-DNA lineages. It is possible to identify these individuals and groups as Huns by analyzing their Y-chromosomal and autosomal DNA in combination with burial context. The significance and implications of this become clear when looking at the philological evidence which suggests that the Huns had a formative and lasting impact on the development of the peoples, cultures and beliefs of Scandinavia Keywords: Attila, Huns, Scythians, Y-DNA, Xiongnu

The ancient mitochondrial genome of a Siberian roe deer (Capreolus pygargus) from Jartai Pass Site in Xinjiang, China, and its phylogenetic relationships

The ancient mitochondrial genome of a Siberian roe deer (Capreolus pygargus) coded as NJ26S from Jartai Pass Site was obtained by high throughput sequencing. The damage pattern demonstrated the authenticity and reliability of the ancient DNA data. The length of the mitogenome was 16,357 bp, which contained 13 protein-coding genes, two rRNA genes, 22 tRNA genes, and one control region. The total base composition of the mitochondrial genome is 28.17% A, 25.01% T, 11.89% G, 19.72% C, and 15.21% missing data with an AT composition of 53.18%. A maximum-likelihood phylogenetic tree was recovered including other roe deer sequences under the TIM2 + I + G4 model. This study presents molecular evidence indicating the presence of Capreolus pygargus in the Xinjiang Uygur Autonomous Region in China more than 3,000 years ago.

Deep estimation of the intensity and timing of natural selection from ancient genomes.

Leveraging past allele frequencies has proven to be key for identifying the impact of natural selection across time. However, this approach suffers from imprecise estimations of the intensity (s) and timing (T) of selection, particularly when ancient samples are scarce in specific epochs. Here, we aimed to bypass the computation of allele frequencies across arbitrarily defined past epochs and refine the estimations of selection parameters by implementing convolutional neural networks (CNNs) algorithms that directly use ancient genotypes sampled across time. Using computer simulations, we first show that genotype-based CNNs consistently outperform an approximate Bayesian computation (ABC) approach based on past allele frequency trajectories, regardless of the selection model assumed and the number of available ancient genotypes. When applying this method to empirical data from modern and ancient Europeans, we replicated the reported increased number of selection events in post-Neolithic Europe, independently of the continental subregion studied. Furthermore, we substantially refined the ABC-based estimations of s and T for a set of positively and negatively selected variants, including iconic cases of positive selection and experimentally validated disease-risk variants. Our CNN predictions support a history of recent positive and negative selection targeting variants associated with host defence against pathogens, aligning with previous work that highlights the significant impact of infectious diseases, such as tuberculosis, in Europe. These findings collectively demonstrate that detecting the footprints of natural selection on ancient genomes is crucial for unravelling the history of severe human diseases.

Propagating Terroir Revival in the Negev: How the Wine Industry Can Amplify Its Resilience to Climate Adversity through a Deeper Understanding of Historic Dryland Viticulture

Based on an examination of the outlooks and practices held by past and present Negev desert viticulturists vis-à-vis their environs, the article offers insights into how the wine sector can bolster its response to current climate adversity. The discussion fuses bio-archaeological research on the evolution of ancient grape cultivars (Vitis vinifera) in the Negev with an extensive ethnographic inquiry into the ongoing wine revival in arid southern Israel. Ancient DNA analysis of relic grape material led to the identification of an historical Negev viticulture lineage. The findings provide a temporal framework for contextualizing tphe interrelated anthropological data obtained on contemporary dryland viticulturalists and wine makers in Israel. Since the climate in the Negev has remained relatively stable over the last several millennia, it makes for an apt point of comparison via which to gauge the outlooks held by both historical and modern viticulturalists towards the local landscape. We suggest enacting two evidence-based adjustments to counter ecological instabilities: the holistic revival and applied renewal of historical cultivars, and the attendant agronomic routines that sustained their growth in the past. A more nuanced understanding of the unique terroir arid viticulturalists are operating in, together with the learned incorporation of the hardy genetic traits of age-old cultivars, will benefit wine growers to attune their responses to the array of challenges wrought by climate change on the wine industry. It is therefore our hope that the research methodologies and heritage-oriented horticultural perspectives we present in this paper will prove beneficial to broader wine growing regions (pax-Mediterranean and beyond) who are fortunate to likewise possess their own rich viticultural histories and lineages.

Gut-Brain Axis: Role of Microbiome, Metabolomics, Hormones, and Stress in Mental Health Disorders.

The influence of gut microbiome, metabolites, omics, hormones, and stress on general and mental health is increasingly being recognized. Ancient cultures recognized the importance of diet and gut health on the overall health of an individual. Western science and modern scientific methods are beginning to unravel the foundations and mechanisms behind some of the ancient beliefs and customs. The gut microbiome, an organ itself, is now thought to influence almost all other organs, ranging from the brain to the reproductive systems. Gut microbiome, metabolites, hormones, and biological sex also influence a myriad of health conditions that range from mental health disorders, obesity, gastrointestinal disorders, and cardiovascular diseases to reproductive health. Here, we review the history and current understanding of the gut-brain axis bidirectional talk in various mental health disorders with special emphasis on anxiety and depressive disorders, whose prevalence has increased by over 50% in the past three decades with COVID-19 pandemic being the biggest risk factor in the last few years. The vagal nerve is an important contributor to this bidirectional talk, but other pathways also contribute, and most remain understudied. Probiotics containing Lactobacillus and Bifidobacterium species seem to have the most impact on improvement in mental health symptoms, but the challenge appears to be maintaining sustained levels, especially since neither Lactobacillus nor Bifidobacterium can permanently colonize the gut. Ancient endogenous retroviral DNA in the human genome is also linked to several psychiatric disorders, including depression. These discoveries reveal the complex and intricately intertwined nature of gut health with mental health disorders.

Decoding the Baltic Sea’s past and present: A simple molecular index for ecosystem assessment

Marginal sea ecosystems, such as the Baltic Sea, are severely affected by anthropogenic pressures, such as climate warming, pollution, and eutrophication, which increased in the course of the past century. Biodiversity monitoring data and assessment of environmental status in such systems have typically been carried out only for the past few decades, if at all, and knowledge on pre-impact stability and good ecological status is limited. An extension of monitoring time series can potentially be achieved through analyses of paleoecological records, e.g. for phytoplankton, which form the base of the food web and are highly susceptible to environmental changes. Within the phytoplankton community, dinoflagellates and diatoms play a significant role as primary producers, and their relative dominance in the spring bloom, calculated as Dia/Dino index, is used as an indicator for the environmental status of the Baltic Sea. To extend time series on the dominance patterns and include non-fossilized dinoflagellates, we here establish a simple droplet digital PCR (ddPCR) reaction on ancient DNA from sediment cores that decodes phytoplankton dynamics. We focus on two common spring bloom species, the diatom Skeletonema marinoi and the dinoflagellate Apocalathium malmogiense, for which we evaluate a DNA based dominance index. It performs very well in comparison to DNA metabarcoding and modern monitoring and can elucidate past species dominance across the past century and across millennia in different basins of the Baltic. For the past century, we see a dominance shift already starting before the mid-20th century in two of the Baltic Sea basins, thus substantially predating current monitoring programs. Shifts are only partly coeval among the cores and the index shows different degrees of stability. This pattern is confirmed across millennia, where a long-term stable relationship between the diatom and the dinoflagellate is observed in the Eastern Gotland Basin, while data from the Gulf of Finland bear testimony to a much more unstable relationship. This confirms that good ecological status based on the dominance pattern of diatoms and dinoflagellates must be established locally and exemplifies how sediment core DNA can be employed to extend monitoring data.

Sex estimation using long bones in the largest burial site of the Copper Age: Linear discriminant analysis and random forest

Sex estimation of the individuals in a sample is fundamental for any bioarchaeological study to define a particular demographic assemblage or to classify isolated remains. Long bones are an excellent alternative for sex estimation when the most dimorphic anatomical parts are not preserved or are highly altered. Here we propose a set of discriminant functions and classification models to estimate the sex of prehistoric individuals using linear discriminant analysis and machine learning approaches. Different osteometric variables were taken from the humeri, ulnae, radii, femurs and tibias of a sample of 109 articulated skeletons buried in the collective tomb of Camino del Molino (Region of Murcia, SE-Spain), dated to the 3rd millennium BC. Sex was estimated based on standard anthropological methods and ancient DNA analysis of a control sample. Fifty-two discriminant functions with prediction thresholds higher than 0.8 on the ROC curve were obtained using independent (22) and combined variables (30). The best LDA models for sex prediction were those based on proximal epiphyseal widths or their combination with other variables, reaching values close to 0.98 on the ROC curve. The random forest-based model obtained an accuracy of 0.94 and confirmed the importance of epiphyseal widths in sex classification. This analysis is more comprehensive than univariate LDA, as it allows for ranking the importance of bones in sex discrimination and considers correlations between long bones rather than treating them as independent observations. In contrast, applying LDA to each bone makes it easier to predict the sex of other coeval collections that do not have such a complete sample. This work aims to overcome the scarcity of methods that can be applied to sex estimation of the large volume of isolated remains from Camino del Molino and for other Mediterranean skeletal series from the Late Prehistory with high biological affinity and that share similar environmental conditions.

Genomes of the Caribbean reef-building corals Colpophyllia natans, Dendrogyra cylindrus, and Siderastrea siderea.

Corals populations worldwide are declining rapidly due to elevated ocean temperatures and other human impacts. The Caribbean harbors a high number of threatened, endangered, and critically endangered coral species compared to reefs of the larger Indo-Pacific. The reef corals of the Caribbean are also long diverged from their Pacific counterparts and may have evolved different survival strategies. Most genomic resources have been developed for Pacific coral species which may impede our ability to study the changes in genetic composition of Caribbean reef communities in response to global change. To help fill the gap in genomic resources, we used PacBio HiFi sequencing to generate the first genome assemblies for three Caribbean, reef-building corals, Colpophyllia natans, Dendrogyra cylindrus, and Siderastrea siderea. We also explore the genomic novelties that shape scleractinian genomes. Notably, we find abundant gene duplications of all classes (e.g., tandem and segmental), especially in S. siderea. This species has one of the largest genomes of any scleractinian coral (822Mb) which seems to be driven by repetitive content and gene family expansion and diversification. As the genome size of S. siderea was double the size expected of stony corals, we also evaluated the possibility of an ancient whole genome duplication using Ks tests and found no evidence of such an event in the species. By presenting these genome assemblies, we hope to develop a better understanding of coral evolution as a whole and to enable researchers to further investigate the population genetics and diversity of these three species.

Maximizing efficiency in sedimentary ancient DNA analysis: a novel extract pooling approach

In the last few decades, the field of ancient DNA has taken a new direction towards using sedimentary ancient DNA (sedaDNA) for studying human and mammalian population dynamics as well as past ecosystems. However, the screening of numerous sediment samples from archaeological sites remains a time-consuming and costly endeavor, particularly when targeting hominin DNA. Here, we present a novel high-throughput method that facilitates the fast and efficient analysis of sediment samples by applying a pooled testing approach. This method combines multiple extracts, enabling early parallelization of laboratory procedures and effective aDNA screening. Pooled samples with detectable aDNA signals undergo detailed analysis, while empty pools are discarded. We have successfully applied our method to multiple sediment samples from Middle and Upper Paleolithic sites in Europe, Asia, and Africa. Notably, our results reveal that an aDNA signal remains discernible even when pooled with four negative samples. We also demonstrate that the DNA yield of double-stranded libraries increases significantly when reducing the extract input, potentially mitigating the effects of inhibition. By embracing this innovative approach, researchers can analyze large numbers of sediment samples for aDNA preservation, achieving significant cost reductions of up to 70% and reducing hands-on laboratory time to one-fifth.

Genomic dynamics of the Lower Yellow River Valley since the Early Neolithic

The Yellow River Delta played a vital role in the development of the Neolithic civilization of China. However, the population history of this region from the Neolithic transitions to the present remains poorly understood due to the lack of ancient human genomes. This especially holds for key Neolithic transitions and tumultuous turnovers of dynastic history. Here, we report genome-wide data from 69 individuals dating to 5,410-1,345 years before present (BP) at 0.008 to 2.49× coverages, along with 325 present-day individuals collected from 16 cities across Shandong. During the Middle to Late Dawenkou period, we observed a significant influx of ancestry from Neolithic Yellow River farmers in central China and some southern Chinese ancestry that mixed with local hunter-gatherers in Shandong. The genetic heritage of the Shandong Longshan people was found to be most closely linked to the Dawenkou culture. During the Shang to Zhou Dynasties, there was evidence of genetic admixture of local Longshan populations with migrants from the Central Plain. After the Qin to Han Dynasties, the genetic composition of the region began to resemble that of modern Shandong populations. Our genetic findings suggest that the middle Yellow River Basin farmers played a role in shaping the genetic affinity of neighboring populations in northern China during the Middle to Late Neolithic period. Additionally, our findings indicate that the genetic diversity in the Shandong region during the Zhou Dynasty may be linked with their complex ethnicities.

READv2: advanced and user-friendly detection of biological relatedness in archaeogenomics

The advent of genome-wide ancient DNA analysis has revolutionized our understanding of prehistoric societies. However, studying biological relatedness in these groups requires tailored approaches due to the challenges of analyzing ancient DNA. READv2, an optimized Python3 implementation of the most widely used tool for this purpose, addresses these challenges while surpassing its predecessor in speed and accuracy. For sufficient amounts of data, it can classify up to third-degree relatedness and differentiate between the two types of first-degree relatedness, full siblings and parent-offspring. READv2 enables user-friendly, efficient, and nuanced analysis of biological relatedness, facilitating a deeper understanding of past social structures.

The role of deep hybridization in fern speciation: Examples from the Thelypteridaceae.

Hybridization is recognized as an important mechanism in fern speciation, with many allopolyploids known among congeners, as well as evidence of ancient genome duplications. Several contemporary instances of deep (intergeneric) hybridization have been noted, invariably resulting in sterile progeny. We chose the christelloid lineage of the family Thelypteridaceae, recognized for its high frequency of both intra- and intergeneric hybrids, to investigate recent hybrid speciation between deeply diverged lineages. We also seek to understand the ecological and evolutionary outcomes of resulting lineages across the landscape. By phasing captured reads within a phylogenomic data set of GoFlag 408 nuclear loci using HybPhaser, we investigated candidate hybrids to identify parental lineages. We estimated divergence ages by inferring a dated phylogeny using fossil calibrations with treePL. We investigated ecological niche conservatism between one confirmed intergeneric allotetraploid and its diploid progenitors using the centroid, overlap, unfilling, and expansion (COUE) framework. We provide evidence for at least six instances of intergeneric hybrid speciation within the christelloid clade and estimate up to 45 million years of divergence between progenitors. The niche quantification analysis showed moderate niche overlap between an allopolyploid species and its progenitors, with significant divergence from the niche of one progenitor and conservatism to the other. The examples provided here highlight the overlooked role that allopolyploidization following intergeneric hybridization may play in fern diversification and range and niche expansions. Applying this approach to other fern taxa may reveal a similar pattern of deep hybridization resulting in highly successful novel lineages.

A microfossil-based object biogeography of a set of stocks from the Rijksmuseum in Amsterdam

In 2019 the Rijksmuseum in Amsterdam acquired a set of oak stocks about which little was known. Radiocarbon wiggle-matching revealed that the tree used to make the stocks was likely felled around 1800 C.E., while ancient DNA indicated the tree's growing zone to be Central Europe. The question remained where and how these stocks were used. To answer these questions, traces of former use at the surface of the stocks were studied and sediment from cracks and holes in the stocks was analyzed for pollen, fungal spores, diatoms and other algae, phytoliths, and insects. The biogeographical information of the recorded taxa shows that the stocks had been used in the western Iberian Peninsula. Although the sediments could have entered in various ways and at various moments, a dungeon seems the most likely context in which these stocks have been used.