家养动物的起源与驯化研究进展

动物的驯化是新石器时代农业革命的主要内容之一, 导致了人类生活方式从狩猎向畜牧的转变。开展家养动物起源与驯化的研究, 不仅有助于了解人类社会的发展史和人工选择下动物的进化过程, 而且有助于开展家养动物的良种选育和遗传多样性保护, 因此该研究领域受到了人们的长期关注。近年来, 随着更多考古证据的发现与分子遗传学的发展, 人们对于家养动物的起源与驯化有了更深入的认识。本文对家养动物起源与驯化研究中一些基本问题的研究方法和进展进行了综述。文章第一部分介绍了家养动物的野生祖先、起源地、起源时间、建群者大小和扩散路线等问题; 第二部分则涉及家养动物驯化的条件、过程、性状改变及其遗传机制等方面。最后指出了家养动物起源与驯化研究中依然存在的问题, 并对未来研究发展的趋势进行了讨论。     

The origin of the 'Mycoplasma mycoides cluster' coincides with domestication of ruminants

The 'Mycoplasma mycoides cluster' comprises the ruminant pathogens Mycoplasma mycoides subsp. mycoides the causative agent of contagious bovine pleuropneumonia (CBPP), Mycoplasma capricolum subsp. capripneumoniae the agent of contagious caprine pleuropneumonia (CCPP), Mycoplasma capricolum subsp. capricolum, Mycoplasma leachii and Mycoplasma mycoides subsp. capri. CBPP and CCPP are major livestock diseases and impact the agricultural sector especially in developing countries through reduced food-supply and international trade restrictions. In addition, these diseases are a threat to disease-free countries. We used a multilocus sequence typing (MLST) approach to gain insights into the demographic history of and phylogenetic relationships among the members of the 'M. mycoides cluster'. We collected partial sequences from seven housekeeping genes representing a total of 3,816 base pairs from 118 strains within this cluster, and five strains isolated from wild Caprinae. Strikingly, the origin of the 'M. mycoides cluster' dates to about 10,000 years ago, suggesting that the establishment and spread of the cluster coincided with livestock domestication. In addition, we show that hybridization and recombination may be important factors in the evolutionary history of the cluster.     

家养动物驯化起源的研究方法与进展

驯化动物伴随了人类上万年的进化历程。在驯化过程中, 家养动物表型和行为特征发生巨大改变, 并与人类生产生活的进步相适应。研究动物驯化问题对于了解遗传多样性及适应性进化, 解析复杂性状的遗传机制等具有重要的意义, 成为生物学领域的重点研究内容之一。本文专注于动物驯化的初始阶段, 首先介绍了驯化起源的时间与地点、驯化途径和驱动因、驯化后的扩散和品种选育; 其次从驯化对象的角度着重介绍了考古学、分子和群体遗传学两方面的家养动物驯化起源的研究策略、优势与不足, 以及未来的发展方向; 最后, 我们综合多方面的证据, 介绍了在中国驯化的家猪(Sus domesticus)和家鸡(Gallus gallus domesticus)以及其他主要家养动物考古和分子水平上驯化起源的研究进展。本文整合多种证据为家养动物驯化起源的研究提供了相对完整的视角和新的思路。     

Mining the pig genome to investigate the domestication process

Pig domestication began around 9000 YBP in the Fertile Crescent and Far East, involving marked morphological and genetic changes that occurred in a relatively short window of time. Identifying the alleles that drove the behavioural and physiological transformation of wild boars into pigs through artificial selection constitutes a formidable challenge that can only be faced from an interdisciplinary perspective. Indeed, although basic facts regarding the demography of pig domestication and dispersal have been uncovered, the biological substrate of these processes remains enigmatic. Considerable hope has been placed on new approaches, based on next-generation sequencing, which allow whole-genome variation to be analyzed at the population level. In this review, we provide an outline of the current knowledge on pig domestication by considering both archaeological and genetic data. Moreover, we discuss several potential scenarios of genome evolution under the complex mixture of demography and selection forces at play during domestication. Finally, we highlight several technical and methodological approaches that may represent significant advances in resolving the conundrum of livestock domestication.     

Ontogeny of domestic dogs and the developmental foundations of carnivoran domestication

Whereas hundreds of breeds of domestic dogs are known, only several dozen domestic cat breeds are currently recognized, and the ferret is not classified into specific breeds. We studied pre- and postnatal patterns of development and growth in the domesticated forms of these three carnivoran species. We present the most comprehensive staging system for domestic dog embryos to date and define qualitative characters for phylogenetic comparisons. For postnatal development, we present analyses of new and literature measurements of cranial and limb proportions. We analyze changes in the progress of growth among different domestic dog and domestic cat breeds. All three domesticated forms drastically differ in the relative timing of prenatal development. This is correlated with ontogenetic plasticity at birth, which enables artificial selection to act. For postnatal development, we detected a greater shape variance in domestic dog ontogeny when compared to that of the domestic cat. We conclude that ontogenetic preconditions as well as body size constrain the species’ capability for artificial selection in domestic dogs and cats. However, we speculate that the human requirements for functional performance of their domesticates might render some developmental biases substantially. Although ferrets would be preferable for artificial selection given their plastic embryonic development, they have been of less interest for domestication due to their small body size - by which they were already well adapted for hunting in burrows - and due to the fact that other relevant tasks were already assumed by domestic cats and dogs since earlier phases of human cultural evolution.     

Cacao domestication I: the origin of the cacao cultivated by the Mayas

Criollo cacao (Theobroma cacao ssp. cacao) was cultivated by the Mayas over 1500 years ago. It has been suggested that Criollo cacao originated in Central America and that it evolved independently from the cacao populations in the Amazon basin. Cacao populations from the Amazon basin are included in the second morphogeographic group: Forastero, and assigned to T. cacao ssp. sphaerocarpum. To gain further insight into the origin and genetic basis of Criollo cacao from Central America, RFLP and microsatellite analyses were performed on a sample that avoided mixing pure Criollo individuals with individuals classified as Criollo but which might have been introgressed with Forastero genes. We distinguished these two types of individuals as Ancient and Modern Criollo. In contrast to previous studies, Ancient Criollo individuals formerly classified as 'wild', were found to form a closely related group together with Ancient Criollo individuals from South America. The Ancient Criollo trees were also closer to Colombian-Ecuadorian Forastero individuals than these Colombian-Ecuadorian trees were to other South American Forastero individuals. RFLP and microsatellite analyses revealed a high level of homozygosity and significantly low genetic diversity within the Ancient Criollo group. The results suggest that the Ancient Criollo individuals represent the original Criollo group. The results also implies that this group does not represent a separate subspecies and that it probably originated from a few individuals in South America that may have been spread by man within Central America.     

Mitochondrial DNA variation in cattle of South China: origin and introgression

Ten restriction endonucleases were used to investigate the mitochondrial DNA restriction fragment length polymorphism (mtDNA RFLP) of 11 native cattle breeds and one cultivated cattle breed in South China. Twenty-three restriction morphs were detected, which can be sorted into five haplotypes. A phylogenetic tree of the haplotypes was constructed by using the 'upgMa' method. Our study showed that haplotype I and II are identical to the zebu (Bos indicus) and taurine (Bos taurus) haplotypes, respectively. Zebu and taurine were the two major origins of cattle populations in South China, and the zebu probably had more influence on the native cattle population than taurine did. Haplotype III is identical to haplotype I of yak (Bos grunniens), which was only detected in the Diqing cattle breed. Haplotype IV was detected for the first time. This haplotype, found only in Dehong cattle, might be from an independent domestication event, probably from another Bos indicus population. Divergence of haplotypes I and IV occurred about 268,000-535,000 years ago, much earlier than the 10,000-year history of cattle husbandry. Our results also suggest a secondary introgession of mtDNA from yak to Diqing cattle.     

Mitochondrial DNA analysis shows a Near Eastern Neolithic origin for domestic cattle and no indication of domestication of European aurochs

The extinct aurochs (Bos primigenius primigenius) was a large type of cattle that ranged over almost the whole Eurasian continent. The aurochs is the wild progenitor of modern cattle, but it is unclear whether European aurochs contributed to this process. To provide new insights into the demographic history of aurochs and domestic cattle, we have generated high-confidence mitochondrial DNA sequences from 59 archaeological skeletal finds, which were attributed to wild European cattle populations based on their chronological date and/or morphology. All pre-Neolithic aurochs belonged to the previously designated P haplogroup, indicating that this represents the Late Glacial Central European signature. We also report one new and highly divergent haplotype in a Neolithic aurochs sample from Germany, which points to greater variability during the Pleistocene. Furthermore, the Neolithic and Bronze Age samples that were classified with confidence as European aurochs using morphological criteria all carry P haplotype mitochondrial DNA, suggesting continuity of Late Glacial and Early Holocene aurochs populations in Europe. Bayesian analysis indicates that recent population growth gives a significantly better fit to our data than a constant-sized population, an observation consistent with a postglacial expansion scenario, possibly from a single European refugial population. Previous work has shown that most ancient and modern European domestic cattle carry haplotypes previously designated T. This, in combination with our new finding of a T haplotype in a very Early Neolithic site in Syria, lends persuasive support to a scenario whereby gracile Near Eastern domestic populations, carrying predominantly T haplotypes, replaced P haplotype-carrying robust autochthonous aurochs populations in Europe, from the Early Neolithic onward. During the period of coexistence, it appears that domestic cattle were kept separate from wild aurochs and introgression was extremely rare.     

Genetic analyses reveal independent domestication origins of Eurasian reindeer

Although there is little doubt that the domestication of mammals was instrumental for the modernization of human societies, even basic features of the path towards domestication remain largely unresolved for many species. Reindeer are considered to be in the early phase of domestication with wild and domestic herds still coexisting widely across Eurasia. This provides a unique model system for understanding how the early domestication process may have taken place. We analysed mitochondrial sequences and nuclear microsatellites in domestic and wild herds throughout Eurasia to address the origin of reindeer herding and domestication history. Our data demonstrate independent origins of domestic reindeer in Russia and Fennoscandia. This implies that the Saami people of Fennoscandia domesticated their own reindeer independently of the indigenous cultures in western Russia. We also found that augmentation of local reindeer herds by crossing with wild animals has been common. However, some wild reindeer populations have not contributed to the domestic gene pool, suggesting variation in domestication potential among populations. These differences may explain why geographically isolated indigenous groups have been able to make the technological shift from mobile hunting to large-scale reindeer pastoralism independently.     

The behavioral endocrinology of domestication: A comparison between the domestic guinea pig (Cavia aperea f. porcellus) and its wild ancestor, the cavy (Cavia aperea)

In this study spontaneous behavior and endocrine parameters were compared between the domestic guinea pig (Cavia aperea f. porcellus) and its wild ancestor, the cavy (Cavia aperea), to elucidate the process of domestication in this species. In 120 h of observation time the behavior of five groups of wild and seven groups of domestic guinea pigs, each consisting of one adult male and two adult females, was analyzed quantitatively. To assess the activities of the pituitary-adrenocortical (PAC), the pituitary-gonadal (PG), and the sympathetic-adrenomedullary (SAM) systems, serum cortisol, testosterone, epinephrine, and norepinephrine concentrations, as well as adrenal tyrosine hydroxylase activities, were determined in males of both forms. The following significant differences between wild cavies and domestic guinea pigs were found: the domesticated animals displayed less aggressive but more sociopositive and more male courtship behavior than their wild ancestors. In addition, they were distinctly less attentive to their physical environment than the wild cavies. The basal activity of the SAM system, as well as the reactivity of the SAM and the PAC systems, was distinctly reduced in the domesticated animals. In contrast, the basal activity of the PAC system did not differ between both forms. The activity of the PG system was significantly higher in males of the domestic guinea pig than in male wild cavies. Thus, in guinea pigs the process of domestication has led to typical behavioral traits-reduced aggressiveness, increased social tolerance-which have also been found in comparisons between wild and domestic forms of other species. The decreased reactivity of the organism's stress axes can be regarded as a physiological mechanism which helps domesticated animals to adjust to man-made housing conditions.     

The local origin of the Tibetan pig and additional insights into the origin of Asian pigs

Background

The domestic pig currently indigenous to the Tibetan highlands is supposed to have been introduced during a continuous period of colonization by the ancestors of modern Tibetans. However, there is no direct genetic evidence of either the local origin or exotic migration of the Tibetan pig.

Methods and Findings

We analyzed mtDNA hypervariable segment I (HVI) variation of 218 individuals from seven Tibetan pig populations and 1,737 reported mtDNA sequences from domestic pigs and wild boars across Asia. The Bayesian consensus tree revealed a main haplogroup M and twelve minor haplogroups, which suggested a large number of small scale in situ domestication episodes. In particular, haplogroups D1 and D6 represented two highly divergent lineages in the Tibetan highlands and Island Southeastern Asia, respectively. Network analysis of haplogroup M further revealed one main subhaplogroup M1 and two minor subhaplogroups M2 and M3. Intriguingly, M2 was mainly distributed in Southeastern Asia, suggesting for a local origin. Similar with haplogroup D6, M3 was mainly restricted in Island Southeastern Asia. This pattern suggested that Island Southeastern Asia, but not Southeastern Asia, might be the center of domestication of the so-called Pacific clade (M3 and D6 here) described in previous studies. Diversity gradient analysis of major subhaplogroup M1 suggested three local origins in Southeastern Asia, the middle and downstream regions of the Yangtze River, and the Tibetan highlands, respectively.

Conclusions

We identified two new origin centers for domestic pigs in the Tibetan highlands and in the Island Southeastern Asian region.     

On the origin and domestication history of Barley (Hordeum vulgare)

Remains of barley (Hordeum vulgare) grains found at archaeological sites in the Fertile Crescent indicate that about 10,000 years ago the crop was domesticated there from its wild relative Hordeum spontaneum. The domestication history of barley is revisited based on the assumptions that DNA markers effectively measure genetic distances and that wild populations are genetically different and they have not undergone significant change since domestication. The monophyletic nature of barley domestication is demonstrated based on allelic frequencies at 400 AFLP polymorphic loci studied in 317 wild and 57 cultivated lines. The wild populations from Israel-Jordan are molecularly more similar than are any others to the cultivated gene pool. The results provided support for the hypothesis that the Israel-Jordan area is the region in which barley was brought into culture. Moreover, the diagnostic allele I of the homeobox gene BKn-3, rarely but almost exclusively found in Israel H. spontaneum, is pervasive in western landraces and modern cultivated varieties. In landraces from the Himalayas and India, the BKn-3 allele IIIa prevails, indicating that an allelic substitution has taken place during the migration of barley from the Near East to South Asia. Thus, the Himalayas can be considered a region of domesticated barley diversification.     

走出中国：酿酒酵母的起源、驯养与演化

酿酒酵母(Saccharomyces cerevisiae)被广泛应用于酒类酿造和食品发酵等行业,其被人类利用的历史已有近万年。酿酒酵母也是遗传学、分子生物学、基因组学和合成生物学等研究中常用的模式生物。近年来研究者对其自然和驯养种群进行了全球范围的生态学、群体遗传学和群体基因组学等方面的研究,更新了对其生态分布、遗传多样性、自然进化和驯养史以及进化动力等方面的认知。发现酿酒酵母在原始森林等自然环境中普遍存在,并可能偏好阔叶树树干、腐木和周围土壤等生境。中国酿酒酵母的遗传多样性显著高于世界其他地区,该物种最古老的谱系也仅发现于中国,说明中国可能是该物种的起源地。生态适应是塑造该物种群体结构的主要力量,导致其野生和驯养群体之间的明显分化。驯养群体又分化为固态发酵和液态发酵两大类群,每个类群内又形成不同的驯养谱系。该物种野生群体的遗传多样性远高于其驯养群体,而野生群体遗传多样性的形成主要由中性突变引起。中国野生和驯养群体在麦芽糖利用能力、基因组杂合性、子囊孢子形成率和孢子活力等方面表现出显著差异,表明这2个群体采取不同的生活策略来适应其不同的生活环境。驯养群体通过群体或谱系特异性基因拷贝数...     

A Hu sheep genome with the first ovine Y chromosome reveal introgression history after sheep domestication

The Y chromosome plays key roles in male fertility and reflects the evolutionary history of paternal lineages. Here, we present a de novo genome assembly of the Hu sheep with the first draft assembly of ovine Y chromosome(o MSY), using nanopore sequencing and Hi-C technologies. The o MSY that we generated spans 10.6 Mb from which 775 Y-SNPs were identified by applying a large panel of whole genome sequences from worldwide sheep and wild Iranian mouflons. Three major paternal lineages(HY1a, HY1b and HY2) were defined across domestic sheep, of which HY2 was newly detected. Surprisingly, HY2 forms a monophyletic clade with the Iranian mouflons and is highly divergent from both HY1a and HY1b. Demographic analysis of Y chromosomes, mitochondrial and nuclear genomes confirmed that HY2 and the maternal counterpart of lineage C represented a distinct wild mouflon population in Iran that diverge from the direct ancestor of domestic sheep, the wild mouflons in Southeastern Anatolia. Our results suggest that wild Iranian mouflons had introgressed into domestic sheep and thereby introduced this Iranian mouflon specific lineage carrying HY2 to both East Asian and Africa sheep populations.     

Sex-linked erythrocyte antigens of the domestic pig

It has been demonstrated that the domestic pig has a blood group systems whose haplotypes (complex alleles) are formed by at least three closely linked loci that are located, like the MIC2 locus of human blood group systems, in the homologous region of sex chromosomes.     

Sacrifice as the ideal hunt: a cosmological explanation for the origin of reindeer domestication

The Siberian Northeast shows striking parallels between the cosmologies of hunters and reindeer herders. What may this tell us about the transformation from hunting to pastoralism? This article argues for a structural identity between hunting and sacrifice, and for the domestication of the reindeer as the result of hunters' efforts to use sacrifice to control the accidental variables of the hunt. Hunters can practise their ethos of ‘trust’ with prey only through highly controlled ritual enactments. We describe two: the famous bear festival of the Amur Gulf region and the consecrated reindeer of the Eveny. Both express the same overall logic by which sacrifice functions as an ideal hunt. The animal is involved in a relation not of domination but of trust, while also undergoing a process of taming. We therefore suggest that the reindeer's domestication may be based not only on ecological or economic adaptations, but also on cosmology.     

Sex-linked erythrocyte antigens of the domestic pig

It has been demonstrated that the domestic pig has a blood group systems whose haplotypes (complex alleles) are formed by at least three closely linked loci that are located, like the MIC2 locus of human blood group systems, in the homologous region of sex chromosomes.     

Comparative map between the domestic pig and dog

Cross-species chromosome painting with probes derived from flow-sorted dog and human chromosomes was used to construct a high-resolution comparative map for the pig. In total 98 conserved autosomal segments between pig and dog were detected by probes specific for the 38 autosomes and X Chromosome of the dog. Further integration of our results with the published human--dog and cat--dog comparative maps, and with data from comparative gene mapping, increases the resolution of the current pig--human comparative map. It allows for the conserved syntenies detected in the pig, human, and cat to be aligned against the putative ancestral karyotype of eutherian mammals and for the history of karyotype evolution of the pig lineage to be reconstructed. Fifteen fusions, 17 fissions, and 23 inversions are required to convert the ancestral mammalian karyotype into the extant karyotype of the pig.