AngiospeIn the period between 5,300 and 4,900 calibrated years before present (cal. bp), populations across large parts of Europe underwent a period of demographic decline1,2. However, the cause of this so-called Neolithic decline is still debated. Some argue for an agricultural crisis resulting in the decline3, others for the spread of an early form of plague4. Here we use population-scale ancient genomics to infer ancestry, social structure and pathogen infection in 108 Scandinavian Neolithic individuals from eight megalithic graves and a stone cist. We find that the Neolithic plague was widespread, detected in at least 17% of the sampled population and across large geographical distances. We demonstrate that the disease spread within the Neolithic community in three distinct infection events within a period of around 120 years. Variant graph-based pan-genomics shows that the Neolithic plague genomes retained ancestral genomic variation present in Yersinia pseudotuberculosis, including virulence factors associated with disease outcomes. In addition, we reconstruct four multigeneration pedigrees, the largest of which consists of 38 individuals spanning six generations, showing a patrilineal social organization. Lastly, we document direct genomic evidence for Neolithic female exogamy in a woman buried in a different megalithic tomb than her brothers. Taken together, our findings provide a detailed reconstruction of plague spread within a large patrilineal kinship group and identify multiple plague infections in a population dated to the beginning of the Neolithic decline.

Genetic adaptation refers to changes in a population’s traits that enhance survival in its current environment. As environmental conditions fluctuate, allele frequencies vary, leading to genetic diversity and different phenotypes within the same species. The cooperatively breeding common mole-rats (Cryptomys hottentotus hottentotus) in South Africa serve as an example, as they inhabit areas with varying aridity. By examining mitochondrial genes and a large number of SNP loci, researchers explored the genetic diversity, population structure, and phylogenetic relationships among five mole-rat populations across this gradient. Findings revealed distinct genetic clusters for arid and semi-arid populations compared to mesic ones, with increased genetic diversity and gene flow in arid regions. The study highlighted that environmental isolation, rather than geographical distance, better explains the genetic differences observed. Further research could uncover specific genetic adaptations related to environmental factors, providing insights into how these mole-rats might respond to climate change.

Terrestrial orchids, particularly those in the Orchidinae tribe, are vital both culturally and economically, especially due to their edible tubers used in traditional dishes like ‘salep’. However, overexploitation in the Eastern Mediterranean and Western Asia poses a significant threat to these species, highlighting the need for effective monitoring tools. To address this, a custom bait kit has been developed for the enrichment and sequencing of 205 novel genetic markers specifically designed for phylogenomic research in Orchidinae s.l. Among these, 31 markers are linked to the production of glucomannan, a key polysaccharide in salep. Testing the kit on 73 local taxa yielded high locus recovery across species, outperforming existing alternatives in terms of sequence length. The phylogenetic analysis demonstrated robust support for numerous clades, including some previously unresolved lineages. While challenges remain in resolving hybrid and recently radiated species, further analyses utilizing multiple haplotypes and non-exonic sequences could enhance our understanding of their complex evolutionary history. Overall, the Orchidinae-205 markers represent an advanced resource for studying the evolution, systematics, and trade of terrestrial orchids, surpassing traditional barcoding methods.

Conifers are vital for both ecological and economic reasons, offering valuable insights into land plant evolution. Molecular phylogenetics plays a significant role in studying evolution, but research on conifers using large-scale data from multiple nuclear genes has been limited. Target enrichment sequencing has emerged as a crucial method in phylogenomic studies. However, a specific bait set for conifers is missing. The REMcon probe set targets around 100 single-copy nuclear loci for family- and species-level phylogenetic studies of conifers. High target recovery and read coverage were observed for the REMcon when tested on 69 species, including conifers and other gymnosperm taxa. Phylogenetic analysis based on the DNA sequences generated from REMcon recovered the existing understanding of conifer relationships. The REMcon bait set will be beneficial in generating large-scale nuclear data consistently for any conifer lineage.

Angiosperms are the cornerstone of most terrestrial ecosystems and human livelihoods1,2. A robust understanding of angiosperm evolution is required to explain their rise to ecological dominance. So far, the angiosperm tree of life has been determined primarily by means of analyses of the plastid genome3,4. Many studies have drawn on this foundational work, such as classification and first insights into angiosperm diversification since their Mesozoic origins5,6,7. However, the limited and biased sampling of both taxa and genomes undermines confidence in the tree and its implications. Here, we build the tree of life for almost 8,000 (about 60%) angiosperm genera using a standardized set of 353 nuclear genes8. This 15-fold increase in genus-level sampling relative to comparable nuclear studies9 provides a critical test of earlier results and brings notable change to key groups, especially in rosids, while substantiating many previously predicted relationships. Scaling this tree to time using 200 fossils, we discovered that early angiosperm evolution was characterized by high gene tree conflict and explosive diversification, giving rise to more than 80% of extant angiosperm orders. Steady diversification ensued through the remaining Mesozoic Era until rates resurged in the Cenozoic Era, concurrent with decreasing global temperatures and tightly linked with gene tree conflict. Taken together, our extensive sampling combined with advanced phylogenomic methods shows the deep history and full complexity in the evolution of a megadiverse clade.

An excavation conducted at Harewood Cemetery to identify the unmarked grave of Samuel Washington resulted in the discovery of burials presumably belonging to George Washington’s paternal grandnephews and their mother, Lucy Payne. To confirm their identities this study examined Y-chromosomal, mitochondrial, and autosomal DNA from the burials and a living Washington descendant. The burial’s Y-STR profile was compared to FamilyTreeDNA’s database, which resulted in a one-step difference from the living descendant and an exact match to another Washington. A more complete Y-STR and Y-SNP profile from the descendant was inferred to be the Washington Y profile. Kinship comparisons performed in relation to the descendant, who is a 4th and 5th degree relative of the putative individuals, resulted in >37,000 overlapping autosomal SNPs and strong statistical support with likelihood ratios exceeding one billion. This study highlights the benefits of a multi-marker approach for kinship prediction and DNA-assisted identification of historical remains.

Parchment, the skins of animals prepared for use as writing surfaces, offers a valuable source of genetic information. Many have clearly defined provenance, allowing for the genetic findings to be evaluated in temporal and spatial context. While these documents can yield evidence of the animal sources, the DNA contained within these aged skins is often damaged and fragmented. Previously, genetic studies targeting parchment have used destructive sampling techniques and so the development and validation of non-destructive sampling methods would expand opportunities and facilitate testing of more precious documents, especially those with historical significance. Here we present genetic data obtained by non-destructive sampling of eight parchments spanning the 15th century to the modern day. We define a workflow for enriching the mitochondrial genome (mtGenome), generating next-generation sequencing reads to permit species identification, and providing interpretation guidance. Using sample replication, comparisons to destructively sampled controls, and by establishing authentication criteria, we were able to confidently assign full/near full mtGenome sequences to 56.3% of non-destructively sampled parchments, each with greater than 90% of the mtGenome reference covered. Six of eight parchments passed all four established thresholds with at least one non-destructive sample, highlighting promise for future studies.

The study examines the challenges of genetic analysis in highly incinerated or degraded human skeletal remains, which is critical for identifying victims of mass disasters. Previous research on the effects of thermal degradation on whole-genome single-nucleotide polymorphism (SNP) quality has been limited. This research utilized two DNA extraction techniques to analyze samples from the bones and teeth of 27 fire victims and employed a novel method of enriching for whole-genome SNPs. The sequencing was performed on an Illumina NextSeq 550 platform.

Analysis revealed that the preservation and variability of SNPs were largely influenced by the type of skeletal element and the burn category rather than the extraction technique used. Specifically, long bones, hand and foot bones, and teeth subjected to temperatures below 350°C yielded higher genomic DNA. Conversely, samples exposed to temperatures above 350°C demonstrated a significant decrease in the number of captured SNPs. The findings support the use of a modified Dabney extraction technique for better DNA yield when traditional methods fall short in forensic applications, highlighting the importance of sample selection for maximizing genetic data recovery.

Disease resistance genes in livestock provide health benefits to animals and opportunities for farmers to meet the growing demand for affordable, high-quality protein. Previously, researchers used gene editing to modify the porcine CD163 gene and demonstrated resistance to a harmful virus that causes porcine reproductive and respiratory syndrome (PRRS). To maximize potential benefits, this disease resistance trait needs to be present in commercially relevant breeding populations for multiplication and distribution of pigs. Toward this goal, a first of-its-kind, scaled gene editing program was established to introduce a single modified CD163 allele into four genetically diverse, elite porcine lines. This effort produced healthy pigs that resisted PRRS virus infection as determined by macrophage and animal challenges. This founder population will be used for additional disease and trait testing, multiplication, and commercial distribution upon regulatory approval. Applying CRISPR-Cas to eliminate a viral disease represents a major step toward improving animal health.

Directly observing the chronology and tempo of adaptation in response to ecological change is rarely possible in natural ecosystems. Sedimentary ancient DNA (sedaDNA) has been shown to be a tractable source of genome-scale data of long-dead organisms1,2,3 and to thereby potentially provide an understanding of the evolutionary histories of past populations.4,5 To date, time series of ecosystem biodiversity have been reconstructed from sedaDNA, typically using DNA metabarcoding or shotgun sequence data generated from less than 1 g of sediment.6,7 Here, we maximize sequence coverage by extracting DNA from ∼50× more sediment per sample than the majority of previous studies1,2,3 to achieve genotype resolution. From a time series of Late Pleistocene sediments spanning from a marine to freshwater ecosystem, we compare adaptive genotypes reconstructed from the environmental genomes of three-spined stickleback at key time points of this transition. We find a staggered temporal dynamic in which freshwater alleles at known loci of large effect in marine-freshwater divergence of three-spined stickleback (e.g., EDA)8 were already established during the brackish phase of the formation of the isolation basin. However, marine alleles were still detected across the majority of marine-freshwater divergence-associated loci, even after the complete isolation of the lake from marine ingression. Our retrospective approach to studying adaptation from environmental genomes of three-spined sticklebacks at the end of the last glacial period complements contemporary experimental approaches9,10,11 and highlights the untapped potential for retrospective “evolve and resequence” natural experiments using sedaDNA.