Bricks and Roof Tiles of Alanya Castle: Evaluation of Animal Footprints from an Ichnoarchaeological Perspective

After the domestication of goats around 10,000 years before the present (BP), humans transported goats far beyond the range of their wild ancestor, the bezoar goat. This brought domestic goats into contact with many wild goat species such as ibex and markhor, enabling introgression between domestic and wild goats. To investigate this, while shedding light on the taxonomic status of wild and domestic goats, we analysed genome-wide SNP data of 613 specimens from 14 taxonomic units, including Capra hircus, C. pyrenaica, C. ibex (from Switzerland, Austria, Germany and Slovenia), C. aegagrus aegagrus, C. a. cretica, C. h. dorcas, C. caucasica caucasica, C. c. severtzovi, C. c. cylindricornis, C. falconeri, C. sibirica sibirica, C. s. alaiana and C. nubiana, as well as Oreamnos americanus (mountain goat) as an outgroup. To trace gene flow between domestic and wild goats, we integrated genotype data of local goat breeds from the Alps as well as from countries such as Spain, Greece, Türkiye, Egypt, Sudan, Iran, Russia (Caucasus and Altai) and Pakistan. Our phylogenetic analyses displayed a clear separation between bezoar-type and ibex-type clades with wild goats from the Greek islands of Crete and Youra clustered within domestic goats, confirming their feral origin. Our analyses also revealed gene flow between the lineages of Caucasian tur and domestic goats that most likely occurred before or during early domestication. Within the clade of domestic goats, analyses inferred gene flow between African and Iberian goats. The detected events of introgression were consistent with previous reports and offered interesting insights into the historical relationships among domestic and wild goats.

Domestic goats (Capra hircus) are globally represented by over 300 breeds, making them a useful model for investigating patterns of morphological change related to domestication. However, they have been little studied, likely due to their poor representation in museum collections and the difficulty in obtaining truly wild goat (Capra aegagrus, the bezoar) samples. Similar studies on other species reveal that domestication correlates with craniofacial alterations in domestics, which are non-uniform and often species-specific. Here, we use three-dimensional geometric morphometric methods (3DGMM) to describe and quantify cranial shape variation in wild (n = 21) versus domestic (n = 54) goats. We find that mean cranial shapes differ significantly between wild and domestic goats as well as between certain breeds. The detected differences are lower in magnitude than those reported for other domestic groups, possibly explained by the fewer directions of artificial selection in goat breeding, and their low global genetic diversity compared to other livestock. We also find tooth-row length reduction in the domestics, suggestive of rostral shortening—a prediction of the “domestication syndrome” (DS). The goat model thus expands the array—and combinations of—morphological changes observed under domestication, notably detecting alterations to the calvarium form which could be related to the ~ 15% brain size reduction previously reported for domestic compared to wild goats. The global success of domestic goats is due more to their ability to survive in a variety of harsh environments than to systematized human management. Nonetheless, their domestication has resulted in a clear disruption from the wild cranial form, suggesting that even low-intensity selection can lead to significant morphological changes under domestication.

Parasites are transferred between domestic and wild animals, when host animals come in contact with each other, particularly while grazing the same pastures, or when using same water bodies for drinking. Chances of parasite transmission and adaptation are high when hosts are genetically related. Afghan urial (Ovis vignei blanfordi), Suleiman markhor (Capra falconeri jerdoni) and Chiltan wild goat (C. aegagrus chialtanensis) are wild kin of domestic sheep and goats, sharing numerous parasitic diseases with each other. The present study was conducted in 2014–2015, to determine parasitic infections of Suleiman markhor and Afghan urial of Torghar Game Reserve, and the endemic wild goat of Chiltan National Park. For comparison, parasites of domestic small ruminants of these areas were also studied. A total of 11 species of helminth and 20 species of protozoa were recorded. Highly prevalent helminth among wild ruminants were Trichuris spp., Nematodirus spp., Protostrongylus rufescens and Moniezia benedeni, while highly prevalent Eimeria were E. arloingi and E. ninakohlyakimovae in caprines and E. ovinoidalis in urial. Chiltan wild goats were also found infected with Entamoeba spp. A short tabulated review of the helminth and protozoan parasites of wild sheep and goats of Pakistan, India, Iran and Turkey has been presented.

BackgroundThe species Capra hircus encompasses numerous breeds that exhibit a high level of phenotypic and genetic variability, resulting from environmental adaptation and artificial selection for meat, milk, and fiber production. Today, the global domestic goat population is steadily increasing, primarily due to their ability to adapt to harsh environments. Their worldwide distribution offers the opportunity to study how different environmental conditions and farming systems have shaped the goat genome. In this work, 194 whole-genome sequencing data sets from wild, feral, and domestic goats have been used to detect Runs of Homozygosity (ROH) and study Extended Haplotype Homozygosity (EHH) to identify the so-called 'Signatures of Selection' that uniquely characterize each goat population.ResultsCommon signals of selection have been identified in CCSER1 and ADAMTSL3, two genes associated with body development, which were under selection in feral and wild goats, and in Angora and Boer breeds, respectively. Similarly, both feral and cashmere breeds exhibited selection signals in PCDH15, a gene linked to environmental adaptation. Selection in wild and feral goats was primarily observed at loci related to environmental adaptation and immune response. Moreover, selection signals related to productive traits such as milk and meat production were still detectable in feral populations. The Angora goat genome showed selective pressure mainly targeting efficient reproduction and body development, with relatively low pressure related to environmental adaptation. The four cashmere breeds studied displayed selection signals predominantly in genes involved in environmental adaptation, immune response, and hair follicle biology. Several signatures of selection related to environmental adaptation were also observed in both meat- and milk-producing goats, as well as in genes associated with reproduction, milk, and meat production.ConclusionThese findings suggest that, despite long-term domestication, natural and environmental selection have shaped the goat genome more than artificial selection. Identifying genes linked to adaptation and fitness is vital for future livestock production amid climate change. Our study highlights genetic loci related to environmental adaptation and disease resistance, offering a foundation for targeted breeding and conservation strategies to enhance resilience and sustainability in goat populations.Supplementary InformationThe online version contains supplementary material available at 10.1186/s12864-025-12133-4.

In Iraq generally and Kurdistan region especially, goats are an important resource for meat and milk production. It is well known that growth hormone (GH) is involved in a variety of biological activities in livestock animals, including reproduction, growth, lactation, metabolism etc. The goal of this research was to reveal the polymorphism of GH gene in different Capra hircus breeds (native, Shami, Meriz and Kamori goat) and in wild mountain goat (Capra aegagrus) via PCR-RFLP technique and direct seqencing. GH1 (exon 2 and 3) and GH2 (exon 4) polymorphisms on the GH gene were investigated. In all breeds, GH1-Hae III/RFLP revealed only two genotypes (homozygous AA and heterozygous AB), with absent genotype BB. The genotype frequency was 0.886 for the AB genotype and 0.114 for the AA genotype; the allelic frequency was 0.558 for the A allele and 0.442 for the B allele. The average of observed heterozygosity was 0.882 and observed homozygosity was 0.118, indicating that the GH1 was polymorphic. The sequence data of GH1 gene of Meriz and wild goats revealed a SNP at the position 58 (C to T) of the wild goat that has led to a change in amino acid proline to serine. GH2 digestion by Hae III, on the other hand, was monomorphic with the CC homozygous genotype. The results of PCR-RFLP and SNP experiments from this investigation were evaluated as very useful in genotype analysis of local goat breeds/populations. Thus, DNA polymorphisms in the growth hormone gene could be used as reliable genetic markers in breeding programmes in this region.

Routes of migration and exchange are important factors in the debate about how the Neolithic transition spread into Europe. Studying the genetic diversity of livestock can help in tracing back some of these past events. Notably, domestic goat (Capra hircus) did not have any wild progenitors (Capra aegagrus) in Europe before their arrival from the Near East. Studies of mitochondrial DNA have shown that the diversity in European domesticated goats is a subset of that in the wild, underlining the ancestral relationship between both populations. Additionally, an ancient DNA study on Neolithic goat remains has indicated that a high level of genetic diversity was already present early in the Neolithic in northwestern Mediterranean sites. We used coalescent simulations and approximate Bayesian computation, conditioned on patterns of modern and ancient mitochondrial DNA diversity in domesticated and wild goats, to test a series of simplified models of the goat domestication process. Specifically, we ask if domestic goats descend from populations that were distinct prior to domestication. Although the models we present require further analyses, preliminary results indicate that wild and domestic goats are more likely to descend from a single ancestral wild population that was managed 11,500 years before present, and that serial founding events characterise the spread of Capra hircus into Europe.

Browsing preference of feral goats (Capra hircus L.) in a Mediterranean mountain scrubland

Identification of selection signatures may provide a better understanding of domestication process and candidate genes contributing to this process. In this study, two populations of domestic and wild goats from Iran were analyzed to identify selection signatures. RSB, iHS, and XP-EHH statistics were used in order to identify robust selection signatures in the goat genome. Genotype data of domestic and wild goats from the NextGen project was used. The data was related to 18 Capra aegagrus (wild goat) and 20 Capra hircus (domestic goat) from Iran. The iHS method indicated 675 and 441 selection signatures in C. aegagrus and C. hircus, respectively. RSB and XP-EHH methods showed about 370 and 447 selection signatures in C. aegagrus and C. hircus, respectively. These selection signatures were mainly associated with milk production, fleece trait, mammary epithelial cells, reproduction, and immune system.

Comparative study of trophic behaviour and herd structure in wild and feral goats living in a Mediterranean island: Management implications

The aim of this study was to investigate the intron 2 of leptin gene polymorphism in wild, native and exotic goat breeds in Iran using PCR-RFLP. Blood samples were collected from 14 wild and domestic goat breeds including (Cashmere Abadeh, Torki-Ghashghaei, Naeini, Robati, Nadoushani, Adani, Shahrbabaki, Birjandi, China goat, Sannen, Pakistani, Raeini cashmere, Najdi and Wild goat) and then the genomic DNA was extracted. A 422bp fragment from intron 2 of the leptin gene was amplified. PCR products were digested by Sau3AI restriction enzyme and were separated and visualized on the agarose gel. Three genotypes including MM, Mm and mm with genotype frequency of 94%, 1% and 5%, respectively, were observed in the studied populations. The number of observed alleles, number of the effective alleles, Nei’s Index and Shanon’s Index were 2, 1.10, 0.09 and 0.19, respectively. The studied populations were not found to be in a Hardy-Weinberg equilibrium. Our investigation demonstrated that MM genotype and M allele had a very high frequency (0.94 and 0.95, respectively) in Iranian goats. Hence, it can be concluded that this finding can provide basis for selection when considering evolution and differentiation among breeds, however further studies should be carried out on a larger population of different domestic and wild breeds to verify the final conclusions.

「紅磚」是完成建築的主要元素之一，而當我們看著運用紅磚的建築時，我們可以看到許多不同的表現方式，而這其實都透露不同的美學或價值觀。淡水地區因為區位和紅磚對居民之意義等因素，使得各文化層時期都留下過紅磚使用的痕跡，紅磚進而變成淡水地區的特色之一，是故淡水地區紅磚建造之建築具有一定程度的研究價值。 對紅磚而言，其經歷了兩個重要的步驟，即是「原料→紅磚」、「紅磚→建造建築」，而這兩階段的連續完整歷程也正是本文所謂的「建築構成」。本文在第一階段探討紅磚這材料的本質；而在第二階段以材料、構造、構築等理論為主要切入角度，也因此發現，紅磚具有「構造特質」、「裝飾特質」和「意象化」三大部分特質。而也藉著上述研究，將本論文架構分為「紅磚之製成與取得」、「紅磚之建造過程思考」、「『紅磚』之意象化歷程」三大主軸。 在「紅磚之製成與取得」部分，透過紅磚於淡水地區的取得和運用，了解到淡水地區紅磚的運用與在地所生活的「人」有很大的關係；而對紅磚製造生採過程之了解，也進一步知曉紅磚自身所呈現出來的外觀原因。 在「紅磚之建造過程思考」部分，則是套用紅磚材料本質與「構造特質」、「裝飾特質」來觀察紅磚建築。而我們發現，淡水地區紅磚建築基本上是以材料本質與「構造特質」為最基本需求，然後藉以從中再發展出「裝飾特質」。而透過本研究觀察，各時代紅磚展現的差異，最主要的關鍵即是在不同時代文化的影響，以及業主和匠師之間的互動關係。 在「『紅磚』之意象化歷程」部分，本論文思索的是紅磚的「意象化」原因和過程。在本研究中發現，因著時代的變遷，紅磚因不敵新式材料衝擊而漸不使用，而之後的使用者為了尋求過去的記憶，往往會藉由其他材料來創造出「仿紅磚」的建築，而「仿紅磚」建築雖賦予人紅磚的感受，但紅磚卻從來沒有在這建築物之中出現，因而紅磚於此種建築物之中僅剩「意象」存在。

The immune systems are fundamentally vital for evolution and survival of species; as such, selection patterns in innate immune loci are of special interest in molecular evolutionary research. The interferon regulatory factor (IRF) gene family control many different aspects of the innate and adaptive immune responses in vertebrates. Among these, IRF3 is known to take active part in very many biological processes. We assembled and evaluated 1356 base pairs of the IRF3 gene coding region in domesticated goats from Africa (Nigeria, Ethiopia and South Africa) and Asia (Iran and China) and the wild goat (Capra aegagrus). Five segregating sites with θ value of 0.0009 for this gene demonstrated a low diversity across the goats’ populations. Fu and Li tests were significantly positive but Tajima’s D test was significantly negative, suggesting its deviation from neutrality. Neighbor joining tree of IRF3 gene in domesticated goats, wild goat and sheep showed that all domesticated goats have a closer relationship than with the wild goat and sheep. Maximum likelihood tree of the gene showed that different domesticated goats share a common ancestor and suggest single origin. Four unique haplotypes were observed across all the sequences, of which, one was particularly common to African goats (MOCH-K14-0425, Poitou and WAD). In assessing the evolution mode of the gene, we found that the codon model dN/dS ratio for all goats was greater than one. Phylogenetic Analysis by Maximum Likelihood (PAML) gave a ω0 (dN/dS) value of 0.067 with LnL value of -6900.3 for the first Model (M1) while ω2 = 1.667 in model M2 with LnL value of -6900.3 with positive selection inferred in 3 codon sites. Mechanistic empirical combination (MEC) model for evaluating adaptive selection pressure on particular codons also confirmed adaptive selection pressure in three codons (207, 358 and 408) in IRF3 gene. Positive diversifying selection inferred with recent evolutionary changes in domesticated goat IRF3 led us to conclude that the gene evolution may have been influenced by domestication processes in goats.

The leading hypothesis on the ancestor of domestic goats (Capra hircus) is that it is the wild goat called the bezoar or pasang (Capra aegagrus). To verify this hypothesis, we sequenced and compared the cytochrome b gene of mitochondrial DNA from six domestic goats and bezoar. A further sequence for the markhor was taken from the database. In total we detected 51 nucleotide substitutions among the domestic goats, bezoar and markhor. However, only one specific nucleotide substitution was found between the domestic goats and the bezoar. On the other hand, 43 nucleotide substitutions were specific for the markhor. This result suggested a close relationship between the domestic goats and the bezoar. A neighbor-joining and parsimony phylogenetic tree constructed using the sequences showed that the domestic goats and the bezoar belong to the same cluster, while the markhor showed a distinct cluster separate from that of the domestic/bezoar cluster. This result was confirmed by trees based on the sequence of the mitochondrial displacement loop regions. These results suggest that the strongest candidate for a matriarchal ancestor of domestic goats is the bezoar.

This article describes the complete sequences of the mitochondrial DNA displacement loop (D-loop) region and cytochrome b gene from domestic goats in Laos (Laos native) and wild goat "markhor" (C. falconeri). The wild goat "bezoar" (Capra aegagrus) has been considered to be the strongest candidate for the ancestor of the domestic goats (C. hircus); however, there is not sufficient molecular data to verify the hypothesis at present. In phylogenetic analyses, two wild goats, the markhor and the ibex (C. ibex), appeared as an outgroup, while the bezoar was located in a cluster of domestic goats. Mitochondrial haplotypes of Laos natives revealed two distinct major clusters: one was the same as the bezoar, the second, unique to Laos natives. The topology and calibrated levels of sequence divergence suggests that these clusters might represent at least two different subspecies of ancestral bezoars.

BackgroundDomestic goats (Capra hircus) have been selected to play an essential role in agricultural production systems, since being domesticated from their wild progenitor, bezoar (Capra aegagrus). A detailed understanding of the genetic consequences imparted by the domestication process remains a key goal of evolutionary genomics.ResultsWe constructed the reference genome of bezoar and sequenced representative breeds of domestic goats to search for genomic changes that likely have accompanied goat domestication and breed formation. Thirteen copy number variation genes associated with coat color were identified in domestic goats, among which ASIP gene duplication contributes to the generation of light coat-color phenotype in domestic goats. Analysis of rapidly evolving genes identified genic changes underlying behavior-related traits, immune response and production-related traits.ConclusionBased on the comparison studies of copy number variation genes and rapidly evolving genes between wild and domestic goat, our findings and methodology shed light on the genetic mechanism of animal domestication and will facilitate future goat breeding.Electronic supplementary materialThe online version of this article (doi:10.1186/s12864-015-1606-1) contains supplementary material, which is available to authorized users.