Prehistoric genomes reveal the genetic foundation and cost of horse domestication

Ancient DNA analysis of elite nomadic warrior from Chinge-Tey I funerary commemorative complex in the "Valley of the Kings", Tuva

BACKGROUND

In the Ist millennium BC bearers of the Scythian-type nomadic cultures inhabited the steppes of Eurasia, from Northern China to the Carpathians. According to archaeological data, the origin of nomadic life style and economy can be traced to the eastern part of this steppe "corridor", primarily to the territory of the present-day Republic of Tuva in Russia. Here, in the Turan-Uyuk Basin, also known as the "Valley of the Kings", some of the earliest known Scythian-type archaeological sites called Arzhan-1, Arzhan-2, Chinge-Tey I, Tunnug 1 were studied. Each of them is a large-scale funerary commemorative complex with burials of tribal nomadic leaders, surrounded by graves of supposed members of their families or associates. All these people belonged to the societies which are associated with the earliest nomadic cultures in Asia. Representatives of similar cultures will later be known and described as the Scythians/the Saka in Assyrian, Achaemenid, and Greek sources. Arzhan 2 and Chinge-Tey I elite level sites as well as ordinary pastoralist burials of the early-Scythian period in Tuva are attributed to the Aldy-Bel archaeological culture of the Early Iron Age (8th- 6th century BC). Taking the first step to shed light on the genetic origin of Aldy-Bel elites, we carried out a comparative genome-wide analysis of an elite level person buried in grave 9 at Chinge-Tey I (7th- 6th centuries BC) and two published earlier genomes of individuals, whose burials (graves 14 and 22) accompanied the 'royal couple' (grave 5) at Arzhan-2. This study aims also at checking a hypothesis of genetic kinship between human individuals buried in the large-scale burial complexes of the "Valley of the Kings" and brings up the issue of possible dynastic connections of local elites, buried under different kurgans of the valley.

RESULTS

First, ancient DNA analysis of an elite nomadic warrior from Chinge-Tey I has been carried out, thus a third wide-genome dataset for Aldy-Bel culture- one of the earliest nomadic cultures in Asia, is presented in this study. Second, we undertook a comparative analysis of genome-wide data of three mentioned Aldy-Bel culture representatives and individuals of the other Bronze and Early Iron Age population groups of Asia to estimate their possible genetic connections. Then, kinship analysis was undertaken for these three Aldy-Bel culture individuals. Finally, mitochondrial and Y-chromosome haplogroups of Chinge-Tey princely person were compared to those of other Aldy-Bel culture representatives and to individuals of subsequent Scythian-type Uyuk-Sagly culture in Tuva.

CONCLUSION

(1) Generating the third wide-genome of the enabled us to undertake its comparison with two other genomes of Aldy-Bel culture representatives (Arzhan-2, graves 14 and 22) and with other Bronze and Early Iron Age population groups in Asia to trace the origin and genetic connection of Aldy-Bel population, representing one of the earliest Scythian-type nomadic group. (2) The results obtained show that the princely individual from Chinge-Tey I and two 'king's associates' from Arzhan-2 were genetically close to nomads of simultaneous Tasmola culture in Eastern and Central Kazakhstan and pastoralists buried in the Early Iron Age cemeteries of present-day Xinjiang (first of all, Abusanteer archaeological site). Aldy-Bel culture representatives appeared also close to individuals of the Middle Bronze Age Okunevo culture in the Minusinsk Basin. Besides, Aldy-Bel pastoralists turned out genetically close to nomads of the subsequent Uyuk-Sagly culture in Mongolia (5th - 3rd centuries BC). (3) Ancient DNA kinship analyses, undertaken for three Aldy-Bel culture individuals pointed out to the absence of their tribe kinship. (4) On the other hand, Chinge-Tey warrior's mitochondrial haplogroup G was previously described in two (graves 14 and 5) individuals from Arzhan-2, including a female individual from the "royal" tomb 5. This result provided a possibility of maternal kinship among this so called 'queen' from Arzhan-2 and the princely person from Chinge-Tey I. This possibility supported a hypothesis of their family ties suggested on archaeological materials. Y-chromosome haplogroup Q1b1, revealed for the princely person, was widely distributed among local people of Aldy-Bel and subsequent Uyuk-Sagly cultures.

Unraveling the genetic and physiological potential of donkeys: insights from genomics, proteomics, and metabolomics approaches

Donkeys (Equus asinus) have played a vital role in agriculture, transportation, and companionship, particularly in developing regions where they are indispensable working animals. The domestication of donkeys marked a significant turning point in human history, as they became essential for transportation, agriculture, and trade, especially in arid and semi-arid areas where their resilience and endurance were highly valued. In modern society, donkeys are indispensable due to their diversified applications, including meat, dairy, medicine, and functional bioproducts, supporting economic, cultural, and medical industries. Despite their critical importance, research on donkeys has historically been overshadowed with studies on horses. However, recent advancements in high-throughput sequencing and bioinformatics have significantly deepened our understanding of the molecular landscape of donkey genome, uncovering their unique adaptations, genetic diversity, and potential therapeutic applications. Microsatellite and mitochondrial DNA (mtDNA) markers have proven effective in assessing the genetic diversity of donkeys across various regions of the world. Additionally, significant strides have been made in characterizing differentially abundant genes, proteins, and metabolic profiles in donkey milk, meat, and skin, and in identifying specific genes/proteins/metabolites associated with sperm quality, motility, and reproduction. Advanced genomic technologies, such as genome-wide association studies and the identification of selection signatures, have also been instrumental in delineating genomic regions associated with phenotypic and adaptive traits. This review integrates data from diverse studies, including those on genetic diversity, transcriptomics, whole genome sequencing, protein analysis, and metabolic profiling, to provide a comprehensive overview of donkey biology. It underscores the unique characteristics of donkeys and emphasizes the importance of continued research to improve their genetic management, conservation, and agricultural use, ensuring their ongoing contribution to human societies.

Population Genomics Reveals Elevated Inbreeding and Accumulation of Deleterious Mutations in White Raccoon Dogs

The formation of animal breeds usually begins with a small subsample from their ancestral population. Deleterious mutations accumulate in the population under genetic drift, inbreeding, and artificial selection during the development and maintenance of traits desired by humans. White raccoon dogs are among the most popular breeds of farmed raccoon dogs, but white raccoon dogs are more susceptible to disease and have a lower reproductive ability. However, the accumulation of deleterious mutations in this white breed is largely unknown. By analyzing and comparing whole-genome sequencing data from 20 white raccoon dogs and 38 normal raccoon dogs, we detected an increased occurrence of loss-of-function (LoF) mutations in white raccoon dogs compared with normal raccoon dogs. With the finding of a significantly higher dosage of homozygous missense mutations in the white raccoon dog genome, we detected a greater fitness cost in white raccoon dogs. Although a much higher FROH level for ROH fragments longer than 1 Mb has been reported in white raccoon dogs, we did not detect a genetic signal of genetic purging in white raccoon dogs. This study provides valuable genomic resources and new insights into the accumulation of mutation loads in farmed raccoon dogs.

Modulating vertebrate physiology by genomic fine-tuning of GPCR functions

G protein-coupled receptors (GPCRs) play a crucial role as membrane receptors, facilitating the communication of eukaryotic species with their environment and regulating cellular and organ interactions. Consequently, GPCRs hold immense potential in contributing to adaptation to ecological niches and responding to environmental shifts. Comparative analyses of vertebrate genomes reveal patterns of GPCR gene loss, expansion, and signatures of selection. Integrating these genomic data with insights from functional analyses of gene variants enables the interpretation of genotype-phenotype correlations. This review underscores the involvement of GPCRs in adaptive processes, presenting numerous examples of how alterations in GPCR functionality influence vertebrate physiology or, conversely, how environmental changes impact GPCR functions. The findings demonstrate that modifications in GPCR function contribute to adapting to aquatic, arid, and nocturnal habitats, influencing camouflage strategies, and specializing in particular dietary preferences. Furthermore, the adaptability of GPCR functions provides an effective mechanism in facilitating past, recent, or ongoing adaptations in animal domestication and human evolution and should be considered in therapeutic strategies and drug development.

Telomere-to-telomere sheep genome assembly identifies variants associated with wool fineness

Ongoing efforts to improve sheep reference genome assemblies still leave many gaps and incomplete regions, resulting in a few common failures and errors in genomic studies. Here, we report a 2.85-Gb gap-free telomere-to-telomere genome of a ram (T2T-sheep1.0), including all autosomes and the X and Y chromosomes. This genome adds 220.05 Mb of previously unresolved regions and 754 new genes to the most updated reference assembly ARS-UI_Ramb_v3.0; it contains four types of repeat units (SatI, SatII, SatIII and CenY) in centromeric regions. T2T-sheep1.0 has a base accuracy of more than 99.999%, corrects several structural errors in previous reference assemblies and improves structural variant detection in repetitive sequences. Alignment of whole-genome short-read sequences of global domestic and wild sheep against T2T-sheep1.0 identifies 2,664,979 new single-nucleotide polymorphisms in previously unresolved regions, which improves the population genetic analyses and detection of selective signals for domestication (for example, ABCC4) and wool fineness (for example, FOXQ1).

Evolutionary consequences of domestication on the selective effects of new amino acid changing mutations in canids

The domestication of wild canids led to dogs no longer living in the wild but instead residing alongside humans. Extreme changes in behavior and diet associated with domestication may have led to the relaxation of the selective pressure on traits that may be less important in the domesticated context. Thus, here we hypothesize that strongly deleterious mutations may have become less deleterious in domesticated populations. We test this hypothesis by estimating the distribution of fitness effects (DFE) for new amino acid changing mutations using whole-genome sequence data from 24 gray wolves and 61 breed dogs. We find that the DFE is strikingly similar across canids, with 26-28% of new amino acid changing mutations being neutral/nearly neutral (|s| < 1e-5), and 41-48% under strong purifying selection (|s| > 1e-2). Our results are robust to different model assumptions suggesting that the DFE is stable across short evolutionary timescales, even in the face of putative drastic changes in the selective pressure caused by artificial selection during domestication and breed formation. On par with previous works describing DFE evolution, our data indicate that the DFE of amino acid changing mutations depends more strongly on genome structure and organismal characteristics, and less so on shifting selective pressures or environmental factors. Given the constant DFE and previous data showing that genetic variants that differentiate wolf and dog populations are enriched in regulatory elements, we speculate that domestication may have had a larger impact on regulatory variation than on amino acid changing mutations.

Koban culture genome-wide and archeological data open the bridge between Bronze and Iron Ages in the North Caucasus

The North Caucasus played a key role during the ancient colonization of Eurasia and the formation of its cultural and genetic ancestry. Previous archeogenetic studies described a relative genetic and cultural continuity of ancient Caucasus societies, since the Eneolithic period. The Koban culture, which formed in the Late Bronze Age on the North Caucasian highlands, is considered as a cultural "bridge" between the ancient and modern autochthonous peoples of the Caucasus. Here, we discuss the place of this archeological culture and its representatives in the genetic orbit of Caucasian cultures using genome-wide SNP data from five individuals of the Koban culture and one individual of the early Alanic culture as well as previously published genomic data of ancient and modern North Caucasus individuals. Ancient DNA analysis shows that an ancient individual from Klin-Yar III, who was previously described as male, was in fact a female. Additional studies on well-preserved ancient human specimens are necessary to determine the level of local mobility and kinship between individuals in ancient societies of North Caucasus. Further studies with a larger sample size will allow us gain a deeper understanding of this topic.

Allele-specific transcription factor binding across human brain regions offers mechanistic insight into eQTLs

Transcription factors (TFs) regulate gene expression by facilitating or disrupting the formation of transcription initiation machinery at particular genomic loci. Because TF occupancy is driven in part by recognition of DNA sequence, genetic variation can influence TF-DNA associations and gene regulation. To identify variants that impact TF binding in human brain tissues, we assessed allele-specific binding (ASB) at heterozygous variants for 94 TFs in nine brain regions from two donors. Leveraging graph genomes constructed from phased genomic sequence data, we compared ChIP-seq signals between alleles at heterozygous variants within each brain region and identified thousands of variants exhibiting ASB for at least one TF. ASB reproducibility was measured by comparisons between independent experiments both within and between donors. We found that rare alleles in the general population more frequently led to reduced TF binding, whereas common alleles had an equal likelihood of increasing or decreasing binding. Further, for ASB variants in predicted binding motifs, the favored allele tended to be the one with the stronger expected motif match, but this concordance was not observed within highly occupied sites. We also found that neuron-specific cis-regulatory elements (cCREs), in contrast with oligodendrocyte-specific cCREs, showed depletion of ASB variants. We identified 2670 ASB variants associated with evidence for allele-specific gene expression in the brain from GTEx data and observed increasing eQTL effect direction concordance as ASB significance increases. These results provide a valuable and unique resource for mechanistic analysis of cis-regulatory variation in human brain tissue.

Identification of nonsense variants in the genomes of 15 Murciano-Granadina bucks and analysis of their segregation in parent-offspring trios

Nonsense variants can inactivate gene function by causing the synthesis of truncated proteins or by inducing nonsense mediated decay of messenger RNAs. The occurrence of such variants in the genomes of livestock species is modulated by multiple demographic and selective factors. Even though nonsense variants can have causal effects on embryo lethality, abortions, and disease, their genomic distribution and segregation in domestic goats have not been characterized in depth yet. In this work, we have sequenced the genomes of 15 Murciano-Granadina bucks with an average coverage of 32.92 × ± 1.45 × . Bioinformatic analysis revealed 947 nonsense variants consistently detected with SnpEff and Ensembl-VEP. These variants were especially abundant in the 3'end of the protein-coding regions. Genes related to olfactory perception, ATPase activity coupled to transmembrane movement of substances, defense to virus, hormonal response, and sensory perception of taste were particularly enriched in nonsense variants. Seventeen nonsense variants expected to have harmful effects on fitness were genotyped in parent-offspring trios. We observed that several nonsense variants predicted to be lethal based on mouse knockout data did not have such effect, a finding that could be explained by the existence of multiple mechanisms counteracting lethality. These findings demonstrate that predicting the effects of putative nonsense variants on fitness is extremely challenging. As a matter of fact, such a goal could only be achieved by generating a high quality telomere-to-telomere goat reference genome combined with carefully curated annotation and functional testing of promising candidate variants.

Using high-density SNP data to unravel the origin of the Franches-Montagnes horse breed

BACKGROUND

The Franches-Montagnes (FM) is the last native horse breed of Switzerland, established at the end of the 19th century by cross-breeding local mares with Anglo-Norman stallions. We collected high-density SNP genotype data (Axiom™ 670 K Equine genotyping array) from 522 FM horses, including 44 old-type horses (OF), 514 European Warmblood horses (WB) from Sweden and Switzerland (including a stallion used for cross-breeding in 1990), 136 purebred Arabians (AR), 32 Shagya Arabians (SA), and 64 Thoroughbred (TB) horses, as introgressed WB stallions showed TB origin in their pedigrees. The aim of the study was to ascertain fine-scale population structures of the FM breed, including estimation of individual admixture levels and genomic inbreeding (FROH) by means of Runs of Homozygosity.

RESULTS

To assess fine-scale population structures within the FM breed, we applied a three-step approach, which combined admixture, genetic contribution, and FROH of individuals into a high-resolution network visualization. Based on this approach, we were able to demonstrate that population substructures, as detected by model-based clustering, can be either associated with a different genetic origin or with the progeny of most influential sires. Within the FM breed, admixed horses explained most of the genetic variance of the current breeding population, while OF horses only accounted for a small proportion of the variance. Furthermore, we illustrated that FM horses showed high TB admixture levels and we identified inconsistencies in the origin of FM horses descending from the Arabian stallion Doktryner. With the exception of WB, FM horses were less inbred compared to the other breeds. However, the relatively few but long ROH segments suggested diversity loss in both FM subpopulations. Genes located in FM- and OF-specific ROH islands had known functions involved in conformation and behaviour, two traits that are highly valued by breeders.

CONCLUSIONS

The FM remains the last native Swiss breed, clearly distinguishable from other historically introgressed breeds, but it suffered bottlenecks due to intensive selection of stallions, restrictive mating choices based on arbitrary definitions of pure breeding, and selection of rare coat colours. To preserve the genetic diversity of FM horses, future conservation managements strategies should involve a well-balanced selection of stallions (e.g., by integrating OF stallions in the FM breeding population) and avoid selection for rare coat colours.

An endothelial regulatory module links blood pressure regulation with elite athletic performance

The control of transcription is crucial for homeostasis in mammals. A previous selective sweep analysis of horse racing performance revealed a 19.6 kb candidate regulatory region 50 kb downstream of the Endothelin3 (EDN3) gene. Here, the region was narrowed to a 5.5 kb span of 14 SNVs, with elite and sub-elite haplotypes analyzed for association to racing performance, blood pressure and plasma levels of EDN3 in Coldblooded trotters and Standardbreds. Comparative analysis of human HiCap data identified the span as an enhancer cluster active in endothelial cells, interacting with genes relevant to blood pressure regulation. Coldblooded trotters with the sub-elite haplotype had significantly higher blood pressure compared to horses with the elite performing haplotype during exercise. Alleles within the elite haplotype were part of the standing variation in pre-domestication horses, and have risen in frequency during the era of breed development and selection. These results advance our understanding of the molecular genetics of athletic performance and vascular traits in both horses and humans.

Genome-wide analysis of population structure, effective population size and inbreeding in Iranian and exotic horses

Population structure and genetic diversity are the key parameters to study the breeding history of animals. This research aimed to provide a characterization of the population structure and to compare the effective population size (Ne), LD decay, genetic diversity, and genomic inbreeding in Iranian native Caspian (n = 38), Turkmen (n = 24) and Kurdish (n = 29) breeds and some other exotic horses consisting of Arabian (n = 24), Fell pony (n = 21) and Akhal-Teke (n = 20). A variety of statistical population analysis techniques, such as principal component analysis (PCA), discriminant analysis of principal component (DAPC) and model-based method (STRUCTURE) were employed. The results of the population analysis clearly demonstrated a distinct separation of native and exotic horse breeds and clarified the relationships between studied breeds. The effective population size (Ne) for the last six generations was estimated 54, 49, 37, 35, 27 and 26 for the Caspian, Kurdish, Arabian, Turkmen, Akhal-Teke and Fell pony breeds, respectively. The Caspian breed showed the lowest LD with an average r2 value of 0.079, while the highest was observed in Fell pony (0.148). The highest and lowest average observed heterozygosity were found in the Kurdish breeds (0.346) and Fell pony (0.290) breeds, respectively. The lowest genomic inbreeding coefficient based on run of homozygosity (FROH) and excess of homozygosity (FHOM) was in the Caspian and Kurdish breeds, respectively, while based on genomic relationship matrix) FGRM) and correlation between uniting gametes) FUNI) the lowest genomic inbreeding coefficient was found in the Kurdish breed. The estimation of genomic inbreeding rates in the six breeds revealed that FROH yielded lower estimates compared to the other three methods. Additionally, the Iranian breeds displayed lower levels of inbreeding compared to the exotic breeds. Overall, the findings of this study provide valuable insights for the development of effective breeding management strategies aimed at preserving these horse breeds.

Genomic evidence for domestication selection in three hatchery populations of Chinook salmon, Oncorhynchus tshawytscha

Fish hatcheries are widely used to enhance fisheries and supplement declining wild populations. However, substantial evidence suggests that hatchery fish are subject to differential selection pressures compared to their wild counterparts. Domestication selection, or adaptation to the hatchery environment, poses a risk to wild populations if traits specific to success in the hatchery environment have a genetic component and there is subsequent introgression between hatchery and wild fish. Few studies have investigated domestication selection in hatcheries on a genomic level, and even fewer have done so in parallel across multiple hatchery-wild population pairs. In this study, we used low-coverage whole-genome sequencing to investigate signals of domestication selection in three separate hatchery populations of Chinook salmon, Oncorhynchus tshawytscha, after approximately seven generations of divergence from their corresponding wild progenitor populations. We sequenced 192 individuals from populations across Southeast Alaska and estimated genotype likelihoods at over six million loci. We discovered a total of 14 outlier peaks displaying high genetic differentiation (F ST) between hatchery-wild pairs, although no peaks were shared across the three comparisons. Peaks were small (53 kb on average) and often displayed elevated absolute genetic divergence (D xy) and linkage disequilibrium, suggesting some level of domestication selection has occurred. Our study provides evidence that domestication selection can lead to genetic differences between hatchery and wild populations in only a few generations. Additionally, our data suggest that population-specific adaptation to hatchery environments likely occurs through different genetic pathways, even for populations with similar standing genetic variation. These results highlight the need to collect paired genotype-phenotype data to understand how domestication may be affecting fitness and to identify potential management practices that may mitigate genetic risks despite multiple pathways of domestication.

The genomic landscape of mammal domestication might be orchestrated by selected transcription factors regulating brain and craniofacial development

Domestication transforms once wild animals into tamed animals that can be then exploited by humans. The process entails modifications in the body, cognition, and behavior that are essentially driven by differences in gene expression patterns. Although genetic and epigenetic mechanisms were shown to underlie such differences, less is known about the role exerted by trans-regulatory molecules, notably transcription factors (TFs) in domestication. In this paper, we conducted extensive in silico analyses aimed to clarify the TF landscape of mammal domestication. We first searched the literature, so as to establish a large list of genes selected with domestication in mammals. From this list, we selected genes experimentally demonstrated to exhibit TF functions. We also considered TFs displaying a statistically significant number of targets among the entire list of (domestication) selected genes. This workflow allowed us to identify 5 candidate TFs (SOX2, KLF4, MITF, NR3C1, NR3C2) that were further assessed in terms of biochemical and functional properties. We found that such TFs-of-interest related to mammal domestication are all significantly involved in the development of the brain and the craniofacial region, as well as the immune response and lipid metabolism. A ranking strategy, essentially based on a survey of protein-protein interactions datasets, allowed us to identify SOX2 as the main candidate TF involved in domestication-associated evolutionary changes. These findings should help to clarify the molecular mechanics of domestication and are of interest for future studies aimed to understand the behavioral and cognitive changes associated to domestication.

Single nucleotide polymorphisms (SNPs) and indels identified from whole-genome re-sequencing of four Chinese donkey breeds

This paper represents the fundamental report of the survey of genome-wide changes of four Chinese indigenous donkey breeds, Dezhou (DZ), Guangling (GL), North China (NC), and Shandong Little donkey (SDL), and the findings will prove usefully for identification of biomarkers that perhaps predict or characterize the growth and coat color patterns. Three genomic regions in CYP3A12, TUBGCP5, and GSTA1 genes, were identified as putative selective sweeps in all researched donkey populations. The loci of candidate genes that may have contributed to the phenotypes in body size (ACSL4, MSI2, ADRA1B, and CDKL5) and coat color patterns (KITLG and TBX3) in donkey populations would be found in underlying strong selection signatures when compared between large and small donkey types, and between different coat colors. The results of the phylogenetic analysis, FST, and principal component analysis (PCA) supported that each population cannot clearly deviate from each other, showing no obvious population structure. We can conclude from the population history that the formation processes between DZS and NC, GL, and SDL are completely different. The genetic variants discovered here provide a rich resource to help identify potential genomic markers and their associated molecular mechanisms that impact economically important traits for Chinese donkey breeding programs.

Allele biased transcription factor binding across human brain regions gives mechanistic insight into eQTLs

Transcription Factors (TFs) influence gene expression by facilitating or disrupting the formation of transcription initiation machinery at particular genomic loci. Because genomic localization of TFs is in part driven by TF recognition of DNA sequence, variation in TF binding sites can disrupt TF-DNA associations and affect gene regulation. To identify variants that impact TF binding in human brain tissues, we quantified allele bias for 93 TFs analyzed with ChIP-seq experiments of multiple structural brain regions from two donors. Using graph genomes constructed from phased genomic sequence data, we compared ChIP-seq signal between alleles at heterozygous variants within each tissue sample from each donor. Comparison of results from different brain regions within donors and the same regions between donors provided measures of allele bias reproducibility. We identified thousands of DNA variants that show reproducible bias in ChIP-seq for at least one TF. We found that alleles that are rarer in the general population were more likely than common alleles to exhibit large biases, and more frequently led to reduced TF binding. Combining ChIP-seq with RNA-seq, we identified TF-allele interaction biases with RNA bias in a phased allele linked to 6,709 eQTL variants identified in GTEx data, 3,309 of which were found in neural contexts. Our results provide insights into the effects of both common and rare variation on gene regulation in the brain. These findings can facilitate mechanistic understanding of cis-regulatory variation associated with biological traits, including disease.

Genetic variation and domestication of horses revealed by 10 chromosome-level genomes and whole-genome resequencing

Understanding the genetic variations of the horse (Equus caballus) genome will improve breeding conservation and welfare. However, genetic variations in long segments, such as structural variants (SVs), remain understudied. We de novo assembled 10 chromosome-level three-dimensional horse genomes, each representing a distinct breed, and analysed horse SVs using a multi-assembly approach. Our findings suggest that SVs with the accumulation of mammalian-wide interspersed repeats related to long interspersed nuclear elements might be a horse-specific mechanism to modulate genome-wide gene regulatory networks. We found that olfactory receptors were commonly loss and accumulated deleterious mutations, but no purge of deleterious mutations occurred during horse domestication. We examined the potential effects of SVs on the spatial structure of chromatin via topologically associating domains (TADs). Breed-specific TADs were significantly enriched by breed-specific SVs. We identified 4199 unique breakpoint-resolved novel insertions across all chromosomes that account for 2.84 Mb sequences missing from the reference genome. Several novel insertions might have potential functional consequences, as 519 appeared to reside within 449 gene bodies. These genes are primarily involved in pathogen recognition, innate immune responses and drug metabolism. Moreover, 37 diverse horses were resequenced. Combining this with public data, we analysed 97 horses through a comparative population genomics approach to identify the genetic basis underlying breed characteristics using Thoroughbreds as a case study. We provide new scientific evidence for horse domestication, an understanding of the genetic mechanism underlying the phenotypic evolution of horses, and a comprehensive genetic variation resource for further genetic studies of horses.

Characterization of the Caudal Ventral Tubercle in the Sixth Cervical Vertebra in Modern Equus ferus caballus

This study examined the anomalous variations of the ventral process of C6 in modern E. ferus caballus. The aim was to provide an incremental grading protocol measuring the absence of the caudal ventral tubercle (CVT) in this ventral process. The findings revealed the most prevalent absent CVT (aCVT) was left unilateral (n = 35), with bilateral (n = 29) and right unilateral (n = 12). Grading was determined in equal increments of absence 1/4, 2/4, 3/4, with 4/4 representing a complete aCVT in 56/76, with a significance of p = 0.0013. This also applied to bilateral specimens. In those C6 osseous specimens displaying a 4/4 grade aCVT, 41/56 had a partial absence of the caudal aspect of the cranial ventral tubercle (CrVT). Here, grading absent CrVTs (aCrVT) followed similarly to aCVTs, though 4/4 was not observed. The significance between 4/4 grade aCVTs and the presentation of an aCrVT was left p = 0.00001 and right p = 0.00018. In bilateral specimens, C6 morphologically resembled C5, implying a homeotic transformation that limited the attachment sites for the cranial and thoracal longus colli muscle. This potentially diminishes function and caudal cervical stability. Therefore, it is recommended that further studies examine the morphological extent of this equine complex vertebral malformation (ECVM) as well as its interrelationships and genetic code/blueprint.

Imputed genomes of historical horses provide insights into modern breeding

Historical genomes can provide important insights into recent genomic changes in horses, especially the development of modern breeds. In this study, we characterized 8.7 million genomic variants from a panel of 430 horses from 73 breeds, including newly sequenced genomes from 20 Clydesdales and 10 Shire horses. We used this modern genomic variation to impute the genomes of four historically important horses, consisting of publicly available genomes from 2 Przewalski's horses, 1 Thoroughbred, and a newly sequenced Clydesdale. Using these historical genomes, we identified modern horses with higher genetic similarity to those in the past and unveiled increased inbreeding in recent times. We genotyped variants associated with appearance and behavior to uncover previously unknown characteristics of these important historical horses. Overall, we provide insights into the history of Thoroughbred and Clydesdale breeds and highlight genomic changes in the endangered Przewalski's horse following a century of captive breeding.

High-Resolution Genotyping of Expressed Equine MHC Reveals a Highly Complex MHC Structure

The Major Histocompatibility Complex (MHC) genes play a key role in a number of biological processes, most notably in immunological responses. The MHCI and MHCII genes incorporate a complex set of highly polymorphic and polygenic series of genes, which, due to the technical limitations of previously available technologies, have only been partially characterized in non-model but economically important species such as the horse. The advent of high-throughput sequencing platforms has provided new opportunities to develop methods to generate high-resolution sequencing data on a large scale and apply them to the analysis of complex gene sets such as the MHC. In this study, we developed and applied a MiSeq-based approach for the combined analysis of the expressed MHCI and MHCII repertoires in cohorts of Thoroughbred, Icelandic, and Norwegian Fjord Horses. The approach enabled us to generate comprehensive MHCI/II data for all of the individuals (n = 168) included in the study, identifying 152 and 117 novel MHCI and MHCII sequences, respectively. There was limited overlap in MHCI and MHCII haplotypes between the Thoroughbred and the Icelandic/Norwegian Fjord horses, showcasing the variation in MHC repertoire between genetically divergent breeds, and it can be inferred that there is much more MHC diversity in the global horse population. This study provided novel insights into the structure of the expressed equine MHC repertoire and highlighted unique features of the MHC in horses.

Shared reproductive disruption, not neural crest or tameness, explains the domestication syndrome

Altered neural crest cell (NCC) behaviour is an increasingly cited explanation for the domestication syndrome in animals. However, recent authors have questioned this explanation, while others cast doubt on whether domestication syndrome even exists. Here, we review published literature concerning this syndrome and the NCC hypothesis, together with recent critiques of both. We synthesize these contributions and propose a novel interpretation, arguing shared trait changes under ancient domestication resulted primarily from shared disruption of wild reproductive regimes. We detail four primary selective pathways for 'reproductive disruption' under domestication and contrast these succinct and demonstrable mechanisms with cryptic genetic associations posited by the NCC hypothesis. In support of our perspective, we illustrate numerous important ways in which NCCs contribute to vertebrate reproductive phenotypes, and argue it is not surprising that features derived from these cells would be coincidentally altered under major selective regime changes, as occur in domestication. We then illustrate several pertinent examples of Darwin's 'unconscious selection' in action, and compare applied selection and phenotypic responses in each case. Lastly, we explore the ramifications of reproductive disruption for wider evolutionary discourse, including links to wild 'self-domestication' and 'island effect', and discuss outstanding questions.

Deleterious Variation in Natural Populations and Implications for Conservation Genetics

Deleterious mutations decrease reproductive fitness and are ubiquitous in genomes. Given that many organisms face ongoing threats of extinction, there is interest in elucidating the impact of deleterious variation on extinction risk and optimizing management strategies accounting for such mutations. Quantifying deleterious variation and understanding the effects of population history on deleterious variation are complex endeavors because we do not know the strength of selection acting on each mutation. Further, the effect of demographic history on deleterious mutations depends on the strength of selection against the mutation and the degree of dominance. Here we clarify how deleterious variation can be quantified and studied in natural populations. We then discuss how different demographic factors, such as small population size, nonequilibrium population size changes, inbreeding, and gene flow, affect deleterious variation. Lastly, we provide guidance on studying deleterious variation in nonmodel populations of conservation concern.

MetaDamage tool: Examining post-mortem damage in sedaDNA on a metagenomic scale

The use of metagenomic datasets to support ancient sedimentary DNA (sedaDNA) for paleoecological reconstruction has been demonstrated to be a powerful tool to understand multi-organism responses to climatic shifts and events. Authentication remains integral to the ancient DNA discipline, and this extends to sedaDNA analysis. Furthermore, distinguishing authentic sedaDNA from contamination or modern material also allows for a better understanding of broader questions in sedaDNA research, such as formation processes, source and catchment, and post-depositional processes. Existing tools for the detection of damage signals are designed for single-taxon input, require a priori organism specification, and require a significant number of input sequences to establish a signal. It is therefore often difficult to identify an established cytosine deamination rate consistent with ancient DNA across a sediment sample. In this study, we present MetaDamage, a tool that examines cytosine deamination on a metagenomic (all organisms) scale for multiple previously undetermined taxa and can produce a damage profile based on a few hundred reads. We outline the development and testing of the MetaDamage tool using both authentic sedaDNA sequences and simulated data to demonstrate the resolution in which MetaDamage can identify deamination levels consistent with the presence of ancient DNA. The MetaDamage tool offers a method for the initial assessment of the presence of sedaDNA and a better understanding of key questions of preservation for paleoecological reconstruction.

Common protein-coding variants influence the racing phenotype in galloping racehorse breeds

Selection for system-wide morphological, physiological, and metabolic adaptations has led to extreme athletic phenotypes among geographically diverse horse breeds. Here, we identify genes contributing to exercise adaptation in racehorses by applying genomics approaches for racing performance, an end-point athletic phenotype. Using an integrative genomics strategy to first combine population genomics results with skeletal muscle exercise and training transcriptomic data, followed by whole-genome resequencing of Asian horses, we identify protein-coding variants in genes of interest in galloping racehorse breeds (Arabian, Mongolian and Thoroughbred). A core set of genes, G6PC2, HDAC9, KTN1, MYLK2, NTM, SLC16A1 and SYNDIG1, with central roles in muscle, metabolism, and neurobiology, are key drivers of the racing phenotype. Although racing potential is a multifactorial trait, the genomic architecture shaping the common athletic phenotype in horse populations bred for racing provides evidence for the influence of protein-coding variants in fundamental exercise-relevant genes. Variation in these genes may therefore be exploited for genetic improvement of horse populations towards specific types of racing.

Developmental instability in domesticated mammals

Measures of fluctuating asymmetry (FA) have been adopted widely as an estimate of developmental instability. Arising from various sources of stress, developmental instability is associated with an organism's capacity to maintain fitness. The process of domestication has been framed as an environmental stress with human-specified parameters, suggesting that FA may manifest to a larger degree among domesticates compared to their wild relatives. This study used three-dimensional geometric morphometric landmark data to (a) quantify the amount of FA in the cranium of six domestic mammal species and their wild relatives and, (b) provide novel assessment of the commonalities and differences across domestic/wild pairs concerning the extent to which random variation arising from the developmental system assimilates into within-population variation. The majority of domestic mammals showed greater disparity for asymmetric shape, however, only two forms (Pig, Dog) showed significantly higher disparity as well as a higher degree of asymmetry compared to their wild counterparts (Wild Boar, Wolf). Contra to predictions, most domestic and wild forms did not show a statistically significant correspondence between symmetric shape variation and FA, however, a moderate correlation value was recorded for most pairs (r-partial least squares >0.5). Within pairs, domestic and wild forms showed similar correlation magnitudes for the relationship between the asymmetric and symmetric components. In domesticates, new variation may therefore retain a general, conserved pattern in the gross structuring of the cranium, whilst also being a source for response to selection on specific features.

Analysis of ancient and modern horse genomes reveals the critical impact of lncRNA-mediated epigenetic regulation on horse domestication

Background: The domestication of horses has played critical roles in human civilizations. The excavation of ancient horse DNA provides crucial data for studying horse domestication. Studies of horse domestication can shed light on the general mechanisms of animal domestication.

Objective: We wish to explore the gene transcription regulation by long noncoding RNAs (lncRNAs) that influence horse domestication.

Methods: First, we assembled the ancient DNA sequences of multiple horses at different times and the genomes of horses, donkeys, and Przewalski horses. Second, we extracted sequences of lncRNA genes shared in ancient horses and sequences of lncRNA genes and the promoter regions of domestication-critical genes shared in modern horses, modern donkeys, and Przewalski horses to form two sample groups. Third, we used the LongTarget program to predict potential regulatory interactions between these lncRNAs and these domestication-critical genes and analyzed the differences between the regulation in ancient/modern horses and between horses/donkeys/Przewalski horses. Fourth, we performed functional enrichment analyses of genes that exhibit differences in epigenetic regulation.

Results: First, genes associated with neural crest development and domestication syndrome are important targets of lncRNAs. Second, compared with undomesticated Przewalski horses, more lncRNAs participate in the epigenetic regulation in modern horses and donkeys, suggesting that domestication is linked to more epigenetic regulatory changes. Third, lncRNAs’ potential target genes in modern horses are mainly involved in two functional areas: 1) the nervous system, behavior, and cognition, and 2) muscle, body size, cardiac function, and metabolism.

Conclusion: Domestication is linked to substantial epigenetic regulatory changes. Genes associated with neural crest development and domestication syndrome underwent noticeable lncRNA-mediated epigenetic regulation changes during horse domestication.

The genomic history and global expansion of domestic donkeys

Donkeys transformed human history as essential beasts of burden for long-distance movement, especially across semi-arid and upland environments. They remain insufficiently studied despite globally expanding and providing key support to low- to middle-income communities. To elucidate their domestication history, we constructed a comprehensive genome panel of 207 modern and 31 ancient donkeys, as well as 15 wild equids. We found a strong phylogeographic structure in modern donkeys that supports a single domestication in Africa ~5000 BCE, followed by further expansions in this continent and Eurasia and ultimately returning to Africa. We uncover a previously unknown genetic lineage in the Levant ~200 BCE, which contributed increasing ancestry toward Asia. Donkey management involved inbreeding and the production of giant bloodlines at a time when mules were essential to the Roman economy and military.

Detection of common copy number of variation underlying selection pressure in Middle Eastern horse breeds using whole-genome sequence data

Dareshouri, Arabian, and Akhal-Teke are three Middle Eastern horse breeds that have been selected for endurance and adaptation to harsh climates. Deciphering the genetic characteristics of these horses by tracing selection footprints and copy number of variations will be helpful in improving our understanding of equine breeds' development and adaptation. For this purpose, we sequenced the whole-genome of four Dareshouri horses using Illumina Hiseq panels and compared them with publicly available whole-genome sequences of Arabian (n=3) and Akhal-Teke (n=3) horses . Three tests of FLK, hapFLK, and pooled heterozygosity were applied using a sliding window (window size=100kb, step size=50kb) approach to detect putative selection signals. Copy number variation analysis was applied to investigate copy number of variants (CNVs), and the results were used to suggest selection signatures involving CNVs. Whole-genome sequencing demonstrated 8,837,950 single nucleotide polymorphisms (SNPs) in autosomal chromosomes. We suggested 58 genes and three quantitative trait loci (QTLs), including some related to horse gait, insect bite hypersensitivity, and withers height, based on selective signals detected by adjusted p-value of Mahalanobis distance based on the rank-based P-values (Md-rank-P) method. We proposed 12 genomic regions under selection pressure involving CNVs which were previously reported to be associated with metabolism energy (SLC5A8), champagne dilution in horses (SLC36A1), and synthesis of polyunsaturated fatty acids (FAT2). Only 10 Middle Eastern horses were tested in this study; therefore, the conclusions are speculative. Our findings are useful to better understanding the evolution and adaptation of Middle Eastern horse breeds.

Radiocarbon and genomic evidence for the survival of Equus Sussemionus until the late Holocene

The exceptionally rich fossil record available for the equid family has provided textbook examples of macroevolutionary changes. Horses, asses, and zebras represent three extant subgenera of Equus lineage, while the Sussemionus subgenus is another remarkable Equus lineage ranging from North America to Ethiopia in the Pleistocene. We sequenced 26 archaeological specimens from Northern China in the Holocene that could be assigned morphologically and genetically to Equus ovodovi, a species representative of Sussemionus. We present the first high-quality complete genome of the Sussemionus lineage, which was sequenced to 13.4× depth of coverage. Radiocarbon dating demonstrates that this lineage survived until ~3500 years ago, despite continued demographic collapse during the Last Glacial Maximum and the great human expansion in East Asia. We also confirmed the Equus phylogenetic tree and found that Sussemionus diverged from the ancestor of non-caballine equids ~2.3–2.7 million years ago and possibly remained affected by secondary gene flow post-divergence. We found that the small genetic diversity, rather than enhanced inbreeding, limited the species’ chances of survival. Our work adds to the growing literature illustrating how ancient DNA can inform on extinction dynamics and the long-term resilience of species surviving in cryptic population pockets.

Genetic load: genomic estimates and applications in non-model animals

Genetic variation, which is generated by mutation, recombination and gene flow, can reduce the mean fitness of a population, both now and in the future. This 'genetic load' has been estimated in a wide range of animal taxa using various approaches. Advances in genome sequencing and computational techniques now enable us to estimate the genetic load in populations and individuals without direct fitness estimates. Here, we review the classic and contemporary literature of genetic load. We describe approaches to quantify the genetic load in whole-genome sequence data based on evolutionary conservation and annotations. We show that splitting the load into its two components - the realized load (or expressed load) and the masked load (or inbreeding load) - can improve our understanding of the population genetics of deleterious mutations.

Signatures of selection underpinning rapid coral adaptation to the world's warmest reefs

Coral populations in the world’s warmest reefs, the Persian/Arabian Gulf (PAG), represent an ideal model system to understand the evolutionary response of coral populations to past and present environmental change and to identify genomic loci that contribute to elevated thermal tolerance. Here, we use population genomics of the brain coral Platygyra daedalea to show that corals in the PAG represent a distinct subpopulation that was established during the Holocene marine transgression, and identify selective sweeps in their genomes associated with thermal adaptation. We demonstrate the presence of positive and disruptive selection and provide evidence for selection of differentially methylated haplotypes. While demographic analyses suggest limited potential for genetic rescue of neighboring Indian Ocean reefs, the presence of putative targets of selection in corals outside of the PAG offers hope that loci associated with thermal tolerance may be present in the standing genetic variation.

Genetic diversity and selection in Puerto Rican horses

Since the first Spanish settlers brought horses to America centuries ago, several local varieties and breeds have been established in the New World. These were generally a consequence of the admixture of the different breeds arriving from Europe. In some instances, local horses have been selectively bred for specific traits, such as appearance, endurance, strength, and gait. We looked at the genetics of two breeds, the Puerto Rican Non-Purebred (PRNPB) (also known as the "Criollo") horses and the Puerto Rican Paso Fino (PRPF), from the Caribbean Island of Puerto Rico. While it is reasonable to assume that there was a historic connection between the two, the genetic link between them has never been established. In our study, we started by looking at the genetic ancestry and diversity of current Puerto Rican horse populations using a 668 bp fragment of the mitochondrial DNA D-loop (HVR1) in 200 horses from 27 locations on the island. We then genotyped all 200 horses in our sample for the "gait-keeper" DMRT3 mutant allele previously associated with the paso gait especially cherished in this island breed. We also genotyped a subset of 24 samples with the Illumina Neogen Equine Community genome-wide array (65,000 SNPs). This data was further combined with the publicly available PRPF genomes from other studies. Our analysis show an undeniable genetic connection between the two varieties in Puerto Rico, consistent with the hypothesis that PRNPB horses represent the descendants of the original genetic pool, a mix of horses imported from the Iberian Peninsula and elsewhere in Europe. Some of the original founders of PRNRB population must have carried the "gait-keeper" DMRT3 allele upon arrival to the island. From this admixture, the desired traits were selected by the local people over the span of centuries. We propose that the frequency of the mutant "gait-keeper" allele originally increased in the local horses due to the selection for the smooth ride and other characters, long before the PRPF breed was established. To support this hypothesis, we demonstrate that PRNPB horses, and not the purebred PRPF, carry a signature of selection in the genomic region containing the DMRT3 locus to this day. The lack of the detectable signature of selection associated with the DMRT3 in the PRPF would be expected if this native breed was originally derived from the genetic pool of PRNPB horses established earlier and most of the founders already had the mutant allele. Consequently, selection specific to PRPF later focused on allels in other genes (including CHRM5, CYP2E1, MYH7, SRSF1, PAM, PRN and others) that have not been previously associated with the prized paso gait phenotype in Puerto Rico or anywhere else.

Sequence Variant in the TRIM39-RPP21 Gene Readthrough is Shared Across a Cohort of Arabian Foals Diagnosed with Juvenile Idiopathic Epilepsy

Juvenile idiopathic epilepsy (JIE) is a self-limiting neurological disorder with a suspected genetic predisposition affecting young Arabian foals of the Egyptian lineage. The condition is characterized by tonic-clonic seizures with intermittent post-ictal blindness, in which most incidents are sporadic and unrecognized. This study aimed to identify genetic components shared across a local cohort of Arabian foals diagnosed with JIE via a combined whole genome and targeted resequencing approach: Initial whole genome comparisons between a small cohort of nine diagnosed foals (cases) and 27 controls from other horse breeds identified variants uniquely shared amongst the case cohort. Further validation via targeted resequencing of these variants, that pertain to non-intergenic regions, on additional eleven case individuals revealed a single 19bp deletion coupled with a triple-C insertion (Δ19InsCCC) within the TRIM39-RPP21 gene readthrough that was uniquely shared across all case individuals, and absent from three additional Arabian controls. Furthermore, we have confirmed recent findings refuting potential linkage between JIE and other inherited diseases in the Arabian lineage, and refuted the potential linkage between JIE and genes predisposing a similar disorder in human newborns. This is the first study to report a genetic variant to be shared in a sub-population cohort of Arabian foals diagnosed with JIE. Further evaluation of the sensitivity and specificity of the Δ19InsCCC allele within additional cohorts of the Arabian horse is warranted in order to validate its credibility as a marker for JIE, and to ascertain whether it has been introduced into other horse breeds by Arabian ancestry.

Museum Genomics

Natural history collections are invaluable repositories of biological information that provide an unrivaled record of Earth's biodiversity. Museum genomics-genomics research using traditional museum and cryogenic collections and the infrastructure supporting these investigations-has particularly enhanced research in ecology and evolutionary biology, the study of extinct organisms, and the impact of anthropogenic activity on biodiversity. However, leveraging genomics in biological collections has exposed challenges, such as digitizing, integrating, and sharing collections data; updating practices to ensure broadly optimal data extraction from existing and new collections; and modernizing collections practices, infrastructure, and policies to ensure fair, sustainable, and genomically manifold uses of museum collections by increasingly diverse stakeholders. Museum genomics collections are poised to address these challenges and, with increasingly sensitive genomics approaches, will catalyze a future era of reproducibility, innovation, and insight made possible through integrating museum and genome sciences.

Role of genes related to performance and reproduction of Thoroughbreds in training and breeding - A review

Thoroughbreds have been selected for speed and stamina since the 1700s. This selection resulted in structural and functional system-wide adaptations that enhanced physiological characteristics for outstanding speed of 61-71 kph (38-44 mph) between 1,000 and 3,200 m (5 furlongs - 2 miles). At present, horseracing is still an economically important industrial sector, therefore intensive research is underway to explore genes that allow the utilisation of genetic abilities and are significant in breeding and training. This study aims to provide an overview of genetic research and its applicability related to Thoroughbreds.

Deleterious protein-coding variants in diverse cattle breeds of the world

The domestication of wild animals has resulted in a reduction in effective population sizes, which can affect the deleterious mutation load of domesticated breeds. In addition, artificial selection contributes to the accumulation of deleterious mutations because of an increased rate of inbreeding among domesticated animals. Since founder population sizes and artificial selection differ between cattle breeds, their deleterious mutation load can vary. We investigated this question by using whole-genome data from 432 animals belonging to 54 worldwide cattle breeds. Our analysis revealed a negative correlation between genomic heterozygosity and nonsynonymous-to-silent diversity ratio, which suggests a higher proportion of single nucleotide variants (SNVs) affecting proteins in low-diversity breeds. Our results also showed that low-diversity breeds had a larger number of high-frequency (derived allele frequency (DAF) > 0.51) deleterious SNVs than high-diversity breeds. An opposite trend was observed for the low-frequency (DAF ≤ 0.51) deleterious SNVs. Overall, the number of high-frequency deleterious SNVs was larger in the genomes of taurine cattle breeds than of indicine breeds, whereas the number of low-frequency deleterious SNVs was larger in the genomes of indicine cattle than in those of taurine cattle. Furthermore, we observed significant variation in the counts of deleterious SNVs within taurine breeds. The variations in deleterious mutation load between taurine and indicine breeds could be attributed to the population sizes of the wild progenitors before domestication, whereas the variations observed within taurine breeds could be due to differences in inbreeding level, strength of artificial selection, and/or founding population size. Our findings imply that the incidence of genetic diseases can vary between cattle breeds.

Ancient Faunal History Revealed by Interdisciplinary Biomolecular Approaches

Starting four decades ago, studies have examined the ecology and evolutionary dynamics of populations and species using short mitochondrial DNA fragments and stable isotopes. Through technological and analytical advances, the methods and biomolecules at our disposal have increased significantly to now include lipids, whole genomes, proteomes, and even epigenomes. At an unprecedented resolution, the study of ancient biomolecules has made it possible for us to disentangle the complex processes that shaped the ancient faunal diversity across millennia, with the potential to aid in implicating probable causes of species extinction and how humans impacted the genetics and ecology of wild and domestic species. However, even now, few studies explore interdisciplinary biomolecular approaches to reveal ancient faunal diversity dynamics in relation to environmental and anthropogenic impact. This review will approach how biomolecules have been implemented in a broad variety of topics and species, from the extinct Pleistocene megafauna to ancient wild and domestic stocks, as well as how their future use has the potential to offer an enhanced understanding of drivers of past faunal diversity on Earth.

Suggested Absence of Horizontal Transfer of Retrotransposons between Humans and Domestic Mammal Species

Transposable element sequences are usually vertically inherited but have also spread across taxa via horizontal transfer. Previous investigations of ancient horizontal transfer of transposons have compared consensus sequences, but this method resists detection of recent single or low copy number transfer events. The relationship between humans and domesticated animals represents an opportunity for potential horizontal transfer due to the consistent shared proximity and exposure to parasitic insects, which have been identified as plausible transfer vectors. The relatively short period of extended human-animal contact (tens of thousands of years or less) makes horizontal transfer of transposons between them unlikely. However, the availability of high-quality reference genomes allows individual element comparisons to detect low copy number events. Using pairwise all-versus-all megablast searches of the complete suite of retrotransposons of thirteen domestic animals against human, we searched a total of 27,949,823 individual TEs. Based on manual comparisons of stringently filtered BLAST search results for evidence of vertical inheritance, no plausible instances of HTT were identified. These results indicate that significant recent HTT between humans and domesticated animals has not occurred despite the close proximity, either due to the short timescale, inhospitable recipient genomes, a failure of vector activity, or other factors.

Modularity patterns in mammalian domestication: Assessing developmental hypotheses for diversification

The neural crest hypothesis posits that selection for tameness resulted in mild alterations to neural crest cells during embryonic development, which directly or indirectly caused the appearance of traits associated with the "domestication syndrome" (DS). Although representing an appealing unitary explanation for the generation of domestic phenotypes, support for this hypothesis from morphological data and for the validity of the DS remains a topic of debate. This study used the frameworks of morphological integration and modularity to assess patterns that concern the embryonic origin of the skull and issues around the neural crest hypothesis. Geometric morphometric landmarks were used to quantify cranial trait interactions between six pairs of wild and domestic mammals, comprising representatives that express between five and 17 of the traits included in the DS, and examples from each of the pathways by which animals entered into relationships with humans. We predicted the presence of neural crest vs mesoderm modular structure to the cranium, and that elements in the neural crest module would show lower magnitudes of integration and higher disparity in domestic forms compared to wild forms. Our findings support modular structuring based on tissue origin (neural crest, mesoderm) modules, along with low module integration magnitudes for neural crest cell derived cranial elements, suggesting differential capacity for evolutionary response among those elements. Covariation between the neural crest and mesoderm modules accounted for major components of shape variation for most domestic/wild pairs. Contra to our predictions, however, we find domesticates share similar integration magnitudes to their wild progenitors, indicating that higher disparity in domesticates is not associated with magnitude changes to integration among either neural crest or mesoderm derived elements. Differences in integration magnitude among neural crest and mesoderm elements across species suggest that developmental evolution preserves a framework that promotes flexibility under the selection regimes of domestication.

Recent selection of candidate genes for mammal domestication in Europeans and language change in Europe: a hypothesis

BACKGROUND AND AIM

Human evolution resulted from changes in our biology, behaviour, and culture. One source of these changes has been hypothesised to be our self-domestication (that is, the development in humans of features commonly found in domesticated strains of mammals, seemingly as a result of selection for reduced aggression). Signals of domestication, notably brain size reduction, have increased in recent times.

METHODS

In this paper, we compare whole-genome data between the Late Neolithic/Bronze Age individuals and modern Europeans.

RESULTS

We show that genes associated with mammal domestication and with neural crest development and function are significantly differently enriched in nonsynonymous single nucleotide polymorphisms between these two groups.

CONCLUSION

We hypothesise that these changes might account for the increased features of self-domestication in modern humans and, ultimately, for subtle recent changes in human cognition and behaviour, including language.

From the Eurasian Steppes to the Roman Circuses: A Review of Early Development of Horse Breeding and Management

Simple Summary

Horses were domesticated later than any other major livestock species. Their role in shaping ancient civilizations cannot be overestimated. As a primary means of transportation, an essential asset in warfare, and later one of the key elements of circus entertainment, horses quickly became luxurious goods. Vast amounts of money were invested in the horse industry resulted resulting in the rapid development of horse breeding and husbandry. This review examines paleogenetic, archeological, and classical studies on managing horses in antiquity. Many ancient approaches and practices in horse management are still relevant today and some of them, now abandoned, are worth re-examination.

Abstract

The domestication of the horse began about 5500 years ago in the Eurasian steppes. In the following millennia horses spread across the ancient world, and their role in transportation and warfare affected every ancient culture. Ownership of horses became an indicator of wealth and social status. The importance of horses led to a growing interest in their breeding and management. Many phenotypic traits, such as height, behavior, and speed potential, have been proven to be a subject of selection; however, the details of ancient breeding practices remain mostly unknown. From the fourth millennium BP, through the Iron Age, many literature sources thoroughly describe horse training systems, as well as various aspects of husbandry, many of which are still in use today. The striking resemblance of ancient and modern equine practices leaves us wondering how much was accomplished through four thousand years of horse breeding.

Large-scale genomic analysis reveals the genetic cost of chicken domestication

BACKGROUND

Species domestication is generally characterized by the exploitation of high-impact mutations through processes that involve complex shifting demographics of domesticated species. These include not only inbreeding and artificial selection that may lead to the emergence of evolutionary bottlenecks, but also post-divergence gene flow and introgression. Although domestication potentially affects the occurrence of both desired and undesired mutations, the way wild relatives of domesticated species evolve and how expensive the genetic cost underlying domestication is remain poorly understood. Here, we investigated the demographic history and genetic load of chicken domestication.

RESULTS

We analyzed a dataset comprising over 800 whole genomes from both indigenous chickens and wild jungle fowls. We show that despite having a higher genetic diversity than their wild counterparts (average π, 0.00326 vs. 0.00316), the red jungle fowls, the present-day domestic chickens experienced a dramatic population size decline during their early domestication. Our analyses suggest that the concomitant bottleneck induced 2.95% more deleterious mutations across chicken genomes compared with red jungle fowls, supporting the "cost of domestication" hypothesis. Particularly, we find that 62.4% of deleterious SNPs in domestic chickens are maintained in heterozygous states and masked as recessive alleles, challenging the power of modern breeding programs to effectively eliminate these genetic loads. Finally, we suggest that positive selection decreases the incidence but increases the frequency of deleterious SNPs in domestic chicken genomes.

CONCLUSION

This study reveals a new landscape of demographic history and genomic changes associated with chicken domestication and provides insight into the evolutionary genomic profiles of domesticated animals managed under modern human selection.

Genomics of Adaptations in Ungulates

Ungulates are a group of hoofed animals that have long interacted with humans as essential sources of food, labor, clothing, and transportation. These consist of domesticated, feral, and wild species raised in a wide range of habitats and biomes. Given the diverse and extreme environments inhabited by ungulates, unique adaptive traits are fundamental for fitness. The documentation of genes that underlie their genomic signatures of selection is crucial in this regard. The increasing availability of advanced sequencing technologies has seen the rapid growth of ungulate genomic resources, which offers an exceptional opportunity to understand their adaptive evolution. Here, we summarize the current knowledge on evolutionary genetic signatures underlying the adaptations of ungulates to different habitats.

An overview of current population genomics methods for the analysis of whole-genome resequencing data in eukaryotes

Characterizing the population history of a species and identifying loci underlying local adaptation is crucial in functional ecology, evolutionary biology, conservation and agronomy. The constant improvement of high-throughput sequencing techniques has facilitated the production of whole genome data in a wide range of species. Population genomics now provides tools to better integrate selection into a historical framework, and take into account selection when reconstructing demographic history. However, this improvement has come with a profusion of analytical tools that can confuse and discourage users. Such confusion limits the amount of information effectively retrieved from complex genomic data sets, and impairs the diffusion of the most recent analytical tools into fields such as conservation biology. It may also lead to redundancy among methods. To address these isssues, we propose an overview of more than 100 state-of-the-art methods that can deal with whole genome data. We summarize the strategies they use to infer demographic history and selection, and discuss some of their limitations. A website listing these methods is available at www.methodspopgen.com.

Ancient horse genomes reveal the timing and extent of dispersals across the Bering Land Bridge

The Bering Land Bridge (BLB) last connected Eurasia and North America during the Late Pleistocene. Although the BLB would have enabled transfers of terrestrial biota in both directions, it also acted as an ecological filter whose permeability varied considerably over time. Here we explore the possible impacts of this ecological corridor on genetic diversity within, and connectivity among, populations of a once wide-ranging group, the caballine horses (Equus spp.). Using a panel of 187 mitochondrial and eight nuclear genomes recovered from present-day and extinct caballine horses sampled across the Holarctic, we found that Eurasian horse populations initially diverged from those in North America, their ancestral continent, around 1.0-0.8 million years ago. Subsequent to this split our mitochondrial DNA analysis identified two bidirectional long-range dispersals across the BLB ~875-625 and ~200-50 thousand years ago, during the Middle and Late Pleistocene. Whole genome analysis indicated low levels of gene flow between North American and Eurasian horse populations, which probably occurred as a result of these inferred dispersals. Nonetheless, mitochondrial and nuclear diversity of caballine horse populations retained strong phylogeographical structuring. Our results suggest that barriers to gene flow, currently unidentified but possibly related to habitat distribution across Beringia or ongoing evolutionary divergence, played an important role in shaping the early genetic history of caballine horses, including the ancestors of living horses within Equus ferus.

Steller's sea cow genome suggests this species began going extinct before the arrival of Paleolithic humans

Anthropogenic activity is the top factor directly related to the extinction of several animal species. The last Steller's sea cow (Hydrodamalis gigas) population on the Commander Islands (Russia) was wiped out in the second half of the 18^th century due to sailors and fur traders hunting it for the meat and fat. However, new data suggests that the extinction process of this species began much earlier. Here, we present a nuclear de novo assembled genome of H. gigas with a 25.4× depth coverage. Our results demonstrate that the heterozygosity of the last population of this animal is low and comparable to the last woolly mammoth population that inhabited Wrangel Island 4000 years ago. Besides, as a matter of consideration, our findings also demonstrate that the extinction of this marine mammal starts along the North Pacific coastal line much earlier than the first Paleolithic humans arrived in the Bering sea region.