Domestication of horses fundamentally transformed long-range mobility and warfare1. However, modern domesticated breeds do not descend from the earliest domestic horse lineage associated with archaeological evidence of bridling, milking and corralling2–4 at Botai, Central Asia around 3500 bc3. Other longstanding candidate regions for horse domestication, such as Iberia5 and Anatolia6, have also recently been challenged. Thus, the genetic, geographic and temporal origins of modern domestic horses have remained unknown. Here we pinpoint the Western Eurasian steppes, especially the lower Volga-Don region, as the homeland of modern domestic horses. Furthermore, we map the population changes accompanying domestication from 273 ancient horse genomes. This reveals that modern domestic horses ultimately replaced almost all other local populations as they expanded rapidly across Eurasia from about 2000 bc, synchronously with equestrian material culture, including Sintashta spoke-wheeled chariots. We find that equestrianism involved strong selection for critical locomotor and behavioural adaptations at the GSDMC and ZFPM1 genes. Our results reject the commonly held association7 between horseback riding and the massive expansion of Yamnaya steppe pastoralists into Europe around 3000 bc8,9 driving the spread of Indo-European languages10. This contrasts with the scenario in Asia where Indo-Iranian languages, chariots and horses spread together, following the early second millennium bc Sintashta culture11,12.

Chromosome rearrangements and the way that they impact genetic differentiation and speciation have long raised questions from evolutionary biologists. They are also a major concern for breeders because of their bearing on chromosome recombination. Banana is a major crop that derives from inter(sub)specific hybridizations between various once geographically isolated Musa species and subspecies. We sequenced 155 accessions, including banana cultivars and representatives of Musa diversity, and genotyped-by-sequencing 1059 individuals from 11 progenies. We precisely characterized six large reciprocal translocations and showed that they emerged in different (sub)species of Musa acuminata, the main contributor to currently cultivated bananas. Most diploid and triploid cultivars analyzed were structurally heterozygous for 1 to 4 M. acuminata translocations, highlighting their complex origin. We showed that all translocations induced a recombination reduction of variable intensity and extent depending on the translocations, involving only the breakpoint regions, a chromosome arm, or an entire chromosome. The translocated chromosomes were found preferentially transmitted in many cases. We explore and discuss the possible mechanisms involved in this preferential transmission and its impact on translocation colonization.

BackgroundSalix caprea is a cold-tolerant pioneer species that is ecologically important in Europe and western and central Asia. However, little data is available on its population genetic structure and molecular ecology. We describe the levels of geographic population genetic structure in natural Irish populations of S. caprea and determine the extent of gene flow and sexual reproduction using both chloroplast and nuclear simple sequence repeats (SSRs).ResultsA total of 183 individuals from 21 semi-natural woodlands were collected and genotyped. Gene diversity across populations was high for the chloroplast SSRs (HT = 0.21-0.58) and 79 different haplotypes were discovered, among them 48% were unique to a single individual. Genetic differentiation of populations was found to be between moderate and high (mean GST = 0.38). For the nuclear SSRs, GST was low at 0.07 and observed heterozygosity across populations was high (HO = 0.32-0.51); only 9.8% of the genotypes discovered were present in two or more individuals. For both types of markers, AMOVA showed that most of the variation was within populations. Minor geographic pattern was confirmed by a Bayesian clustering analysis. Gene flow via pollen was found to be approximately 7 times more important than via seeds.ConclusionsThe data are consistent with outbreeding and indicate that there are no significant barriers for gene flow within Ireland over large geographic distances. Both pollen-mediated and seed-mediated gene flow were found to be high, with some of the populations being more than 200 km apart from each other. These findings could simply be due to human intervention through seed trade or accidental transportation of both seeds and pollen. These results are of value to breeders wishing to exploit natural genetic variation and foresters having to choose planting material.

New and comprehensive collections of the perennial rhizomatous reed canary grass (Phalaris arundinacea) were made in NW Europe along north-to-south and east-to-west clines from Denmark, Germany, Ireland, Poland, Sweden and the United Kingdom. Rhizome, seed and leaf samples were taken for analysis and genetic resource conservation. A subsample covering the geographical range was characterized using plastid genome sequencing and SNP discovery generated using a long-read PCR and MiSeq sequencing approach. Samples were also subject to flow cytometry and all found to be tetraploid. New sequences were assembled against a Lolium perenne (perennial ryegrass) reference genome, and an average of approximately 60% of each genome was aligned (81 064 bp). Genetic variation was high among the 48 sequenced genotypes with a total of 1793 SNPs, equating to 23 SNPs per kbp. SNPs were subject to principal coordinate and Structure analyses to detect population genetic groupings and to examine phylogeographical pattern. Results indicate substantial genetic variation and population genetic structuring of this allogamous species at a broad geographical scale in NW Europe with plastid genetic diversity organized more across an east-to-west than a north-to-south cline.

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Self-incompatibility is an important evolutionary feature in angiosperms and has major implications for breeding strategies in horticultural crops. In citrus, when coupled with parthenocarpy, it enables the production of seedless fruits in a mono-varietal orchard. A gametophytic incompatibility system with one S locus was proposed for citrus, but its molecular mechanisms remain the subject of debate. The objective of this work was to locate the S locus by the analyzing segregation distortion in reciprocal crosses of two self-incompatible citrus sharing one self-incompatible allele and to compare this location with previously published models. High density genetic maps of ‘Fortune’ mandarin and ‘Ellendale tangor’ with, respectively, 2164 SNP and 1467 SNP markers, were constructed using genotyping by sequencing data. They are highly syntenic and collinear with the clementine genome. Complete rejection of one allele was only observed in male segregation in the two parents and in only one genomic area, at the beginning of chromosome 7 of the clementine reference genome. Haplotype data in the area surrounding the theoretical S locus were in agreement with previously proposed S genotypes. Overall, our results are in full agreement with the recently proposed gametophytic S-RNase system with the S locus at the beginning of chromosome 7 of the clementine reference genome.

Hydrothermal vents form archipelagos of ephemeral deep‐sea habitats that raise interesting questions about the evolution and dynamics of the associated endemic fauna, constantly subject to extinction‐recolonization processes. These metal‐rich environments are coveted for the mineral resources they harbour, thus raising recent conservation concerns. The evolutionary fate and demographic resilience of hydrothermal species strongly depend on the degree of connectivity among and within their fragmented metapopulations. In the deep sea, however, assessing connectivity is difficult and usually requires indirect genetic approaches. Improved detection of fine‐scale genetic connectivity is now possible based on genome‐wide screening for genetic differentiation. Here, we explored population connectivity in the hydrothermal vent snail Ifremeria nautilei across its species range encompassing five distinct back‐arc basins in the Southwest Pacific. The global analysis, based on 10,570 single nucleotide polymorphism (SNP) markers derived from double digest restriction‐site associated DNA sequencing (ddRAD‐seq), depicted two semi‐isolated and homogeneous genetic clusters. Demogenetic modeling suggests that these two groups began to diverge about 70,000 generations ago, but continue to exhibit weak and slightly asymmetrical gene flow. Furthermore, a careful analysis of outlier loci showed subtle limitations to connectivity between neighbouring basins within both groups. This finding indicates that migration is not strong enough to totally counterbalance drift or local selection, hence questioning the potential for demographic resilience at this latter geographical scale. These results illustrate the potential of large genomic data sets to understand fine‐scale connectivity patterns in hydrothermal vents and the deep sea.

The horse is central to many Indigenous cultures across the American Southwest and the Great Plains. However, when and how horses were first integrated into Indigenous lifeways remain contentious, with extant models derived largely from colonial records. We conducted an interdisciplinary study of an assemblage of historic archaeological horse remains, integrating genomic, isotopic, radiocarbon, and paleopathological evidence. Archaeological and modern North American horses show strong Iberian genetic affinities, with later influx from British sources, but no Viking proximity. Horses rapidly spread from the south into the northern Rockies and central plains by the first half of the 17th century CE, likely through Indigenous exchange networks. They were deeply integrated into Indigenous societies before the arrival of 18th-century European observers, as reflected in herd management, ceremonial practices, and culture.