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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.

In the aquatic microbial food web, scuticociliates are diverse and predominant in almost all kinds of biotopes while extremely confused regarding their taxonomy and systematic relationships within the subclass Scuticociliatia. Here we provide detailed descriptions of two new and one known species, Glauconema sinica sp. nov., Pleuronema parasetigerum sp. nov., and Histiobalantium natans viridis, isolated from a freshwater wetland in northern China, along with their molecular phylogeny based on SSU rRNA gene sequences. Our results show: (1) both molecular and morphological data strongly support that the isolated lineage containing the genera Glauconema, Miamiensis, Paramesanophrys, and Anophryoides should be identified as a new taxon at the family level in the order Philasterida; hence, a new family, Glauconematidae fam. nov., is established. This new family is mainly characterized by the polymorphic life cycle of its members (macrostome and microstome stages); the trophont (or macrostome) has closely spaced membranelles 1-3, whereas in the tomite (or microstome) membranelle 1 is distant from membranelle 2. (2) Phylogenetic analyses using novel data for these species revealed that all three cluster with their congeners, supporting the validity of the genera to which they belong. Molecular information also supports the monophyly of the two main scuticociliate orders Pleuronematida and Philasterida. [ABSTRACT FROM AUTHOR]

Yakutia, Sakha Republic, in the Siberian Far East, represents one of the coldest places on Earth, with winter record temperatures dropping below -70 °C. Nevertheless, Yakutian horses survive all year round in the open air due to striking phenotypic adaptations, including compact body conformations, extremely hairy winter coats, and acute seasonal differences in metabolic activities. The evolutionary origins of Yakutian horses and the genetic basis of their adaptations remain, however, contentious. Here, we present the complete genomes of nine present-day Yakutian horses and two ancient specimens dating from the early 19th century and ∼5,200 y ago. By comparing these genomes with the genomes of two Late Pleistocene, 27 domesticated, and three wild Przewalski's horses, we find that contemporary Yakutian horses do not descend from the native horses that populated the region until the mid-Holocene, but were most likely introduced following the migration of the Yakut people a few centuries ago. Thus, they represent one of the fastest cases of adaptation to the extreme temperatures of the Arctic. We find cis-regulatory mutations to have contributed more than nonsynonymous changes to their adaptation, likely due to the comparatively limited standing variation within gene bodies at the time the population was founded. Genes involved in hair development, body size, and metabolic and hormone signaling pathways represent an essential part of the Yakutian horse adaptive genetic toolkit. Finally, we find evidence for convergent evolution with native human populations and woolly mammoths, suggesting that only a few evolutionary strategies are compatible with survival in extremely cold environments.

The recent discovery that DNA methylation survives in fossil material provides an opportunity for novel molecular approaches in palaeogenomics. Here, we apply to ancient DNA extracts the probe-independent Methylated Binding Domains (MBD)-based enrichment method, which targets DNA molecules containing methylated CpGs. Using remains of a Palaeo-Eskimo Saqqaq individual, woolly mammoths, polar bears and two equine species, we confirm that DNA methylation survives in a variety of tissues, environmental contexts and over a large temporal range (4,000 to over 45,000 years before present). MBD enrichment, however, appears principally biased towards the recovery of CpG-rich and long DNA templates and is limited by the fast post-mortem cytosine deamination rates of methylated epialleles. This method, thus, appears only appropriate for the analysis of ancient methylomes from very well preserved samples, where both DNA fragmentation and deamination have been limited. This work represents an essential step toward the characterization of ancient methylation signatures, which will help understanding the role of epigenetic changes in past environmental and cultural transitions.

Horses, asses, and zebras belong to a single genus, Equus, which emerged 4.0-4.5 Mya. Although the equine fossil record represents a textbook example of evolution, the succession of events that gave rise to the diversity of species existing today remains unclear. Here we present six genomes from each living species of asses and zebras. This completes the set of genomes available for all extant species in the genus, which was hitherto represented only by the horse and the domestic donkey. In addition, we used a museum specimen to characterize the genome of the quagga zebra, which was driven to extinction in the early 1900s. We scan the genomes for lineage-specific adaptations and identify 48 genes that have evolved under positive selection and are involved in olfaction, immune response, development, locomotion, and behavior. Our extensive genome dataset reveals a highly dynamic demographic history with synchronous expansions and collapses on different continents during the last 400 ky after major climatic events. We show that the earliest speciation occurred with gene flow in Northern America, and that the ancestor of present-day asses and zebras dispersed into the Old World 2.1-3.4 Mya. Strikingly, we also find evidence for gene flow involving three contemporary equine species despite chromosomal numbers varying from 16 pairs to 31 pairs. These findings challenge the claim that the accumulation of chromosomal rearrangements drive complete reproductive isolation, and promote equids as a fundamental model for understanding the interplay between chromosomal structure, gene flow, and, ultimately, speciation.

The domestication of the horse ∼ 5.5 kya and the emergence of mounted riding, chariotry, and cavalry dramatically transformed human civilization. However, the genetics underlying horse domestication are difficult to reconstruct, given the near extinction of wild horses. We therefore sequenced two ancient horse genomes from Taymyr, Russia (at 7.4- and 24.3-fold coverage), both predating the earliest archeological evidence of domestication. We compared these genomes with genomes of domesticated horses and the wild Przewalskis horse and found genetic structure within Eurasia in the Late Pleistocene, with the ancient population contributing significantly to the genetic variation of domesticated breeds. We furthermore identified a conservative set of 125 potential domestication targets using four complementary scans for genes that have undergone positive selection. One group of genes is involved in muscular and limb development, articular junctions, and the cardiac system, and may represent physiological adaptations to human utilization. A second group consists of genes with cognitive functions, including social behavior, learning capabilities, fear response, and agreeableness, which may have been key for taming horses. We also found that domestication is associated with inbreeding and an excess of deleterious mutations. This genetic load is in line with the cost of domestication hypothesis also reported for rice, tomatoes, and dogs, and it is generally attributed to the relaxation of purifying selection resulting from the strong demographic bottlenecks accompanying domestication. Our work demonstrates the power of ancient genomes to reconstruct the complex genetic changes that transformed wild animals into their domesticated forms, and the population context in which this process took place.

Ciliated protists are highly differentiated unicellular eukaryotes that possess special sexual processes (conjugation and autogamy) that rely on their unique nuclear dimorphism, i.e., the presence of both a germline micronucleus (MIC) and a somatic macronucleus (MAC) in a single cell. The sexual processes show a high diversity in different ciliates. To better understand the differentiation and evolution of sexual processes in closely related species, we investigated the nuclear events during conjugation in Paramecium jenningsi strain GZ, a poorly studied close relative of the well-known P. aurelia complex. The main results include: (1) the conjugation process takes about 48 h, including three prezygotic divisions (meiosis I, II, and mitosis) and three postzygotic divisions; (2) the MICs are dominated by the "parachute" phase at the prophase of meiosis I; (3) after meiosis II, a variable number of nuclei undergo the third prezygotic division, and the two products near the paroral cone become the genetically identical migratory and stationary pronuclei; (4) the synkaryon divides three times to form the MIC and the MAC anlagen, but only one nuclear product of the first postzygotic division completes the next two divisions; and (5) an extra cell division is required to complete the last step of conjugation, during which two MIC anlagen undergo mitotic division while two MAC anlagen are distributed between the daughter cells without division. The comparison of the nuclear events during conjugation in representatives of the class Oligohymenophorea reveals that usually there are three prezygotic divisions and a variable number of postzygotic divisions. However, the number of selected and differentiated nuclei after each division differs among species. This study provided a new model ciliate for further investigations of nuclear selection and differentiation as well as nuclear morphology during meiosis. [ABSTRACT FROM AUTHOR]