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PubMed2026

Ancient Mongolian aurochs and cattle genomes reveal population shifts associated with the expansion of herding.

Humans hunted aurochs (Bos primigenius) for millennia in Mongolia prior to the introduction of domestic cattle sometime after ca. 5,000 years ago. Here, we present genomic data from Mongolian aurochs and domestic cattle at key points in Mongolia's prehistory to understand changes in population history associated with the adoption of domestic taurine cattle (B. taurus). We compare these low-coverage genomes with other cattle genomes worldwide and make comparisons about the nature of bovine populations before and after the adoption of domestic cattle. Individuals dating to before the introduction of taurine cattle have shared ancestry with North Asian aurochs, and individuals dating after the introduction of taurine cattle are related to other ancient East Asian cattle from archaeological sites such as Shimao in the Ordos region. We identify unique connections between ancient Mongolian aurochs and cattle and modern cattle breeds from Central China and Tibet.

Bos primigenius↗
PubMed2026

Beyond species trees: pervasive gene flow limits phylogenomic resolution in the diversification of Juniperus from the Qinghai-Tibet Plateau.

Understanding how lineages diversify despite persistent ancestral polymorphism and recurrent gene flow remains a central challenge in evolutionary biology. Juniperus distributed across the Qinghai-Tibet Plateau provide an ideal system for addressing this question because repeated geological uplift and climatic oscillations have likely promoted cycles of lineage divergence, range shifts, and secondary contact. Here, we combined approximately 1.08 million genome-wide SNPs from 164 individuals representing thirteen Juniperus lineages with phylogenomic datasets comprising 3,381 nuclear single-copy genes and nearly complete plastomes. We detected extensive phylogenomic discordance and cytonuclear incongruence across genomic datasets. Topology weighting, coalescent simulations, quartet-based tests, and analyses of gene flow and reticulation collectively support the interpretation that these patterns were shaped by the combined effects of prolonged incomplete lineage sorting and gene flow during lineage diversification. Ecological niche analyses further provide a spatial and climatic context in which environmentally similar lineages may have had greater opportunities for secondary contact during historical range shifts. Collectively, our results reveal that the evolutionary history of Qinghai-Tibet Plateau Juniperus is characterized by reticulate diversification rather than strictly bifurcating evolution, and demonstrate how genome-wide discordance can provide biological insights into the evolutionary processes underlying lineage diversification.

Gene Flow↗
PubMed2026

Diploids derived from polyploids: genetic characteristics of four novel interspecific Sorghum populations.

Polyploidy has repeatedly shaped grass evolution, yet direct observations of how polyploid-derived chromosomes behave when returned to diploidy remain rare. Interspecific crosses between diploid Sorghum bicolor and tetraploid hybrids derived from Sorghum halepense generate mixed-ploidy progeny, providing an opportunity to examine chromosome transmission during the early stages of diploidization. Using genome-wide SNP markers, we characterized chromosomal inheritance patterns in 2 diploid and 2 tetraploid families derived from these crosses. Genotype-dosage profiles alone distinguished diploids from tetraploids with complete accuracy, reflecting strong ploidy-dependent differences in dosage-class distributions. Although diploid progeny retained much of the halepense-derived genomic background, several genomic intervals exhibited extended, nonrandom runs of S. bicolor homozygosity that remained polymorphic in corresponding tetraploid populations. These patterns, together with recurrent segregation distortion across independent families, suggest that the transition from tetraploidy to diploidy can expose allelic combinations that differ in transmission or viability. Analyses of flowering time further indicated that diploid and tetraploid derivatives possess distinct genomic architectures, with major association peaks occurring in different chromosomal regions across ploidy levels. Collectively, these results indicate that early diploidization involves nonrandom retention and loss of parental haplotypes shaped by both selective and structural constraints. The diploid extractions characterized here provide a rare empirical system for investigating the early stages of diploidization and a practical framework for studying and eventually mobilizing polyploid-derived variation for sorghum germplasm development. However, broader integration into elite breeding programs will require additional evaluation of cross-fertility, meiotic behavior, and chromosomal stability across diverse breeding backgrounds.

Sorghum↗
PubMed2026

Evolving conservation: The role of unconventional approaches to restore contemporary vertebrate populations and genomic biodiversity.

Conservation biology and restoration ecology are two essential yet distinct disciplines that address the growing challenge of biodiversity loss. Traditionally, these fields have relied on ecological principles and management practices aimed at protecting or reestablishing natural systems. The crisis is no longer just ecological; it is evolutionary and genomic. The accelerating pace of environmental change has outstripped the capacity of conventional approaches, creating a pressing need for innovative solutions. Biotechnology offers potentially transformative tools that can enhance the effectiveness and precision of both conservation and restoration efforts, especially for species where conventional conservation approaches have proved insufficient. Techniques such as genetic rescue, synthetic biology, and gene editing are increasingly being explored to address critical challenges, such as invasive species control, genetic diversity loss, and habitat fragmentation, to both invigorate endangered species and restore historical biodiversity. Despite its promise, the integration of biotechnology into conservation and restoration has raised ethical, ecological, and regulatory concerns. These include ecological unpredictability and public resistance to genetic interventions in wild populations. This perspective examines the current landscape of biotechnological applications in conservation and restoration, highlighting successful case studies, ongoing controversies, and optimism for additional progress. We argue that thoughtful, transparent integration of biotechnology that is grounded in ecological knowledge and stakeholder engagement can reconcile the goals of conservation and restoration. As ecosystems face mounting pressures, biotech-enabled strategies may prove essential for fostering resilience and ensuring long-term ecological sustainability.

Conservation of Natural Resources↗
PubMed2025

Inference of Gene Flow between Species from Genomic Data When the Mode, Direction, and Lineages are Misspecified.

Thanks to genomic data, interspecific gene flow is increasingly recognized as a major evolutionary force that shapes biodiversity. Two models have been developed in the multispecies coalescent (MSC) framework to infer gene flow from genomic data, assuming either constant-rate continuous migration (MSC-M) or discrete introgression/hybridization (MSC-I). The extreme simplicity of these models raises concerns about their usefulness as they represent misspecified models when applied to real data. Here, we study inference of gene flow under the MSC-M model, considering mis-assignment of gene flow onto incorrect parental or daughter lineages, misspecification of the direction of gene flow, and misspecification of the mode of gene flow. Mis-assignment of gene flow to an incorrect lineage causes large biases in the estimated rates. The Bayesian test has high power for inferring both recent and ancient gene flow, between either sister lineages or nonsister lineages, although misspecification of the direction of gene flow may make it hard to distinguish early divergence with gene flow from recent complete isolation. Misspecification of the mode of gene flow (MSC-I versus MSC-M) has small local effects, and gene flow is detected with high power despite the misspecification. We analyze a genomic dataset from the purple cone spruce (Picea spp., Pinaceae), which putatively arose through homoploid hybrid speciation, to demonstrate practical implications of our theoretical analyses. Overall, we find that the extremely idealized models of gene flow (in particular the discrete MSC-I model) are very effective for extracting information about species divergence and gene flow from genomic data.

Gene Flow↗