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Additional file 1: Table S1. Statistics for the window selection analysis. Table S2. Groups of breeds that were compared in this study. Table S3. Estimates of effective population size (Ne) over time (from 13 to 142 generations ago). Table S4. Single-SNP-based FST distances between pairs of rabbit populations. Table S5. Window-based FST distances between pairs of rabbit populations. Table S6. The most relevant results obtained from the PCAdapt analysis that overlap with those of the FST analyses. Table S8. Pearson���s correlations for genome windows FST values obtained from Method 1 and Method 2 (P-value

Additional file 2: Figure S1. Window-based Neighbor Joining tree. Figure S2. Multidimensional scaling plot. The first three components are provided. Figure S3. Scree plot used to identify the number of principal components that describe well the population structure of the investigated rabbit breeds. The plot displays in decreasing order the percentage of variance explained by each principal component. Figure S4. Manhattan plots of the PCAdapt analysis. Each dot represents a 350-kb genome window. The red line identifies the threshold value (0.1 Bonferroni corrected P-value). Unassembled scaffolds are not reported. Figure S5. Genome regions carrying signatures of selection (99.8th percentile; expanded windows) identified in the studied breeds. Only the assembled autosomes are presented and unassembled scaffolds are not reported. Figure S6. Manhattan plots of the genome-wide FST analyses based on Method 1 (M1). Each dot represents a 350-kb genome window. The blue line identifies the threshold value (99.8th percentile of the distribution). Unassembled scaffolds are not reported. Figure S7. Manhattan plots of the genome-wide FST analyses based on Method 2 (M2). Each dot represents a 350-kb genome window. The blue line identifies the threshold value (99.8th percentile of the distribution). Unassembled scaffolds are not reported.

Sangre y leche fueron símbolos omnipresentes en los territorios de la «Monarquía Católica», en España y su Imperio colonial. Situados a medio camino entre la naturaleza y la cultura, a lo largo de las edades Media y Moderna, la sangre y la leche tejieron una poderosa analogía entre la reproducción fisiológica y la reproducción cultural. Como exploran los artículos de este libro, estos símbolos desempeñaron un papel determinante en los procesos de ordenación, jerarquización, y por supuesto también, de exclusión social dentro de la monarquía. Partiendo de perspectivas tan diversas como la religiosa, la social, la jurídica o la antropológica, los autores de este libro analizan esta privilegiada encrucijada simbólica para interrogarse sobre el origen y desarrollo del discurso de la «raza» en la España altomoderna., Índice: Introducción, por Mercedes García-Arenal y Felipe Pereda. SANGRE. LA POLÍTICA DEL LINAJE Y LA SANGRE. -Genealogía, linaje e identidad etnocultural en la Granada nazarí, por Mohamad Ballan. -Religión y raza en la Edad Media cristiana e islámica, por David Nirenberg. -Linaje, conversión y naturalezas inestables en el Atlántico ibérico: comparación entre la incorporación y la exclusión de los moriscos y de los pueblos indígenas, por Karoline P. Cook. -Limpieza de sangre: la batalla por la reforma desde Salucio hasta Quevedo, por Francisco Bethencourt. LA SANGRE, VEHÍCULO DE LA NATURALEZA INMUTABLE. -Sangre de mi sangre: lo que no se podía adquirir, o casi no, por Jean-Frédéric Schaub. -Demonios, estrellas e imaginación. El cuerpo a principios de la modernidad en los trópicos, por Jorge Cañizares-Esguerra. -«Sua malicia vem-se a conaturizar»: Sangre, color de piel y conversión en el mundo ibérico moderno, por Giuseppe Marcocci. -Los «judíos menstruantes». Sangre, bautismo y la retórica de la evidencia en un tratado de Juan de Quiñones (1632), por Stefania Pastore. SANGRE & LECHE. EL DISCURSO SIMBÓLICO DE LOS FLUIDOS SACROS .-Líquidos sagrados y la formación de protestantes (españoles), por James S. Amelang. -Divinos pechos, como cántaros: estética, política y género de las imágenes del Barroco español, por Felipe Pereda. -La puesta en escena de la limpieza de sangre en la España del siglo XVII, por Rachel Burk. REPRESENTACIONES Y FICCIONES. -Saberes médicos e ideología esencialista: sangre, esperma, leche y construcción del ser, por Christine Orobitg. -Ficciones genealógicas. El morisco Román Ramírez y los libros de caballerías, por Miguel Martínez. -Del morisco real al imaginado. Construcciones de la alteridad en la Península Ibérica moderna, por Francisco J. Moreno Díaz del Campo y Borja Franco Llopis. A MODO DE COLOFÓN. -De sangre y leche: debates y categorías sobre racialización. Una lectura retrospectiva, por Max S. Hering Torres. -¿Eran racistas los europeos de la modernidad temprana?, por Joan Pau Rubiès.

This dissertation explores the relationship between intellectual networks, royal patronage and developments in political thought in late medieval Islamic Spain and North Africa. It proposes a new reading of the history of the Nasrid Kingdom of Granada (635/1238–897/1492) that examines these broader issues by closely studying the life and works of Lisān al-Dīn Muḥammad b. al-Khaṭīb (713/1313–776/1374), the most prominent Spanish Muslim historian, chancellor and philosopher during the 8th/14th century, situating this figure within a larger network of scholars, statesmen and functionaries in the late medieval Islamic West. This dissertation illustrates the manner in which the crisis and transformation that characterized the territorial fragmentation of Islamic Spain and North Africa contributed to the rise of a distinct class of scholar-officials who reshaped the intellectual and political culture of the Western Mediterranean. It argues that the gradual concentration of executive political authority in the hands of scholar-officials, such as Ibn al-Khaṭīb, was part of the process of the consolidation of royal power at the expense of the nobility during the late Middle Ages. For their part, these scholar-officials composed works across a variety of genres that sought to legitimate and rationalize the centralization of royal authority. To examine this phenomenon, this dissertation draws upon a corpus of Arabic, Castilian and Aragonese manuscripts, as well as coinage and epigraphy. It investigates the lives of those individuals who existed in close proximity to royal power during the late medieval period in order to explore how their own experiences and ideas fashioned discourses about sovereignty, governmentality and the craft of history during the 14th century. The rise of a distinct class of scholar-officials, whose members included Christians, Muslims and Jews working for different (often competing) dynasties, was underpinned by similar networks of patronage, intellectual interests and a shared geography. These highly-educated individuals rose to prominence as chancellors, treasurers, and councilors within the royal courts in Iberia and were responsible for producing a multitude of works, while patronizing pieces of art and architecture that embodied their particular worldview. Lisān al-Dīn b. al-Khaṭīb provides us with an illustrative example of this class of individuals during the 8th/14th century. This figure followed in the footsteps of leading Spanish Muslim scholar-officials such as Abū Bakr b. al-Khaṭṭāb, Ibn ‘Amīra, Ibn Sa‘īd and Ibn al-Abbār, individuals who had exercised significant administrative and political authority while also being deeply involved in various intellectual and literary pursuits during the 7th/13th century. Ibn al-Khaṭīb authored over 50 works, including historical chronicles, epistolography, biographical dictionaries, poetry, medical texts, and political treatises, throughout his career. This dissertation illustrates his role at the intersection of intellectual and political developments and demonstrates how his literary production was closely intertwined with his function as a statesman. It provides the first comprehensive study in English of Ibn al-Khaṭīb’s life, from his birth into a minor family in the small town of Loja in 713/1313 to his rise as a physician and scribe in the Nasrid court, his transformation from a client and servant of the Nasrid dynasty into an itinerant scholar-official who sought to establish his own individual power and influence across the Islamic West, to his controversial assassination in Fez in 776/1374. It looks particularly closely at the letters that he exchanged with his broader network of scholars, nobles, functionaries and kings across the Mediterranean world to think about the question of loyalty, ties of obligation and individual strategies of survival in the Islamic West during this period.

Runs of homozygosity (ROH) are defined as long stretches of DNA homozygous at each polymorphic position. The proportion of genome covered by ROH and their length are indicators of the level and origin of inbreeding. In this study, we analysed SNP chip datasets (obtained using the Axiom OrcunSNP Array) of a total of 702 rabbits from 12 fancy breeds and four meat breeds to identify ROH with different approaches and calculate several genomic inbreeding parameters. The highest average number of ROH per animal was detected in Belgian Hare (~150) and the lowest in Italian Silver (~106). The average length of ROH ranged from 4.001 ± 0.556Mb in Italian White to 6.268 ± 1.355Mb in Ermine. The same two breeds had the lowest (427.9 ± 86.4 Mb, Italian White) and the highest (921.3 ± 179.8 Mb, Ermine) average values of the sum of all ROH segments. More fancy breeds had a higher level of genomic inbreeding (as defined by ROH) than meat breeds. Several ROH islands contain genes involved in body size, body length, pigmentation processes, carcass traits, growth, and reproduction traits (e.g.: AOX1, GPX5, IFRD1, ITGB8, NELL1, NR3C1, OCA2, TRIB1, TRIB2). Genomic inbreeding parameters can be useful to overcome the lack of information in the management of rabbit genetic resources. ROH provided information to understand, to some extent, the genetic history of rabbit breeds and to identify signatures of selection in the rabbit genome.

Background Domestication of the rabbit (Oryctolagus cuniculus) has led to a multi-purpose species that includes many breeds and lines with a broad phenotypic diversity, mainly for external traits (e.g. coat colours and patterns, fur structure, and morphometric traits) that are valued by fancy rabbit breeders. As a consequence of this human-driven selection, distinct signatures are expected to be present in the rabbit genome, defined as signatures of selection or selective sweeps. Here, we investigated the genome of three Italian commercial meat rabbit breeds (Italian Silver, Italian Spotted and Italian White) and 12 fancy rabbit breeds (Belgian Hare, Burgundy Fawn, Champagne d’Argent, Checkered Giant, Coloured Dwarf, Dwarf Lop, Ermine, Giant Grey, Giant White, Rex, Rhinelander and Thuringian) by using high-density single nucleotide polymorphism data. Signatures of selection were identified based on the fixation index (FST) statistic with different approaches, including single-breed and group-based methods, the latter comparing breeds that are grouped based on external traits (different coat colours and body sizes) and types (i.e. meat vs. fancy breeds). Results We identified 309 genomic regions that contained signatures of selection and that included genes that are known to affect coat colour (ASIP, MC1R and TYR), coat structure (LIPH), and body size (LCORL/NCAPG, COL11A1 and HOXD) in rabbits and that characterize the investigated breeds. Their identification proves the suitability of the applied methodologies for capturing recent selection events. Other regions included novel candidate genes that might contribute to the phenotypic variation among the analyzed breeds, including genes for pigmentation-related traits (EDNRA, EDNRB, MITF and OCA2) and body size, with a strong candidate for dwarfism in rabbit (COL2A1). Conclusions We report a genome-wide view of genetic loci that underlie the main phenotypic differences in the analyzed rabbit breeds, which can be useful to understand the shift from the domestication process to the development of breeds in O. cuniculus. These results enhance our knowledge about the major genetic loci involved in rabbit external traits and add novel information to understand the complexity of the genetic architecture underlying body size in mammals.