Genome sequence, comparative analysis, and population genetics of the domestic horse

We report a high-quality draft sequence of the genome of the horse (Equus caballus). The genome is relatively repetitive but has little segmental duplication. Chromosomes appear to have undergone few historical rearrangements: 53% of equine chromosomes show conserved synteny to a single human chromosome. Equine chromosome 11 is shown to have an evolutionary new centromere devoid of centromeric satellite DNA, suggesting that centromeric function may arise before satellite repeat accumulation. Linkage disequilibrium, showing the influences of early domestication of large herds of female horses, is intermediate in length between dog and human, and there is long-range haplotype sharing among breeds.

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.

Genetic analysis of white facial and leg markings in the Swiss Franches-Montagnes Horse Breed

White markings and spotting patterns in animal species are thought to be a result of the domestication process. They often serve for the identification of individuals but sometimes are accompanied by complex pathological syndromes. In the Swiss Franches-Montagnes horse population, white markings increased vastly in size and occurrence during the past 30 years, although the breeding goal demands a horse with as little depigmented areas as possible. In order to improve selection and avoid more excessive depigmentation on the population level, we estimated population parameters and breeding values for white head and anterior and posterior leg markings. Heritabilities and genetic correlations for the traits were high (h(2) > 0.5). A strong positive correlation was found between the chestnut allele at the melanocortin-1-receptor gene locus and the extent of white markings. Segregation analysis revealed that our data fit best to a model including a polygenic effect and a biallelic locus with a dominant-recessive mode of inheritance. The recessive allele was found to be the white trait-increasing allele. Multilocus linkage disequilibrium analysis allowed the mapping of the putative major locus to a chromosomal region on ECA3q harboring the KIT gene.

Benthos fauna in the North Sea from 2 surveys in 1986 and 1987

During two surveys in the North Sea, in summer 1986 and in winter 1987, larger epibenthos was collected with a 2 m beam trawl. The distributions of the species were checked for average linkage by means of the JACCARD-index cluster analysis. In summer two main clusters can be recognized. These are situated to the north and to the south of the Dogger Bank. In winter two main clusters may be recognized as well, but these clusters divide the North Sea into a western and an eastern part. We conclude, that these differences of epibenthos characteristics are correlated with seasonal changes in water body distributions.

Biomarker and radiogenic isotopes from sediment core POS362-2_33

The termination of the African Humid Period in northeastern Africa during the early Holocene was marked by the southward migration of the rain belt and the disappearance of the Green Sahara. This interval of drastic environmental changes was also marked by the initiation of food production by North African huntergatherer populations and thus provides critical information on human-environment relationships. However, existing records of regional climatic and environmental changes exhibit large differences in timing and modes of the wet/dry transition at the end of the African Humid Period. Here we present independent records of changes in river runoff, vegetation and erosion in the Nile River watershed during the Holocene obtained from a unique sedimentary sequence on the Nile River fan using organic and inorganic proxy data. This high-resolution reconstruction allows to examine the phase relationship between the changes of these three parameters and provides a detailed picture of the environmental conditions during the Paleolithic/Neolithic transition. The data show that river runoff decreased gradually during the wet/arid transition at the end of the AHP whereas rapid shifts of vegetation and erosion occurred earlier between 8.7 and about 6 ka BP. These asynchronous changes are compared to other regional records and provide new insights into the threshold responses of the environment to climatic changes. Our record demonstrates that the degradation of the environment in northeastern Africa was more abrupt and occurred earlier than previously thought and may have accelerated the process of domestication in order to secure sustainable food resources for the Neolithic African populations.

Percepción dispersa: Arquitectura y tactilidad en la sociedad de la comunicación

El tema de la tesis se centra en el pensamiento de Walter Benjamin y en el concepto de percepción distraída, desarrollado en el ensayo La obra de arte en la época de su reproducibilidad técnica (1936). El título percepción dispersa deriva de una profundización de los conceptos benjaminianos en términos lingüísticos, adoptando otros significados de la palabra distracción que relacionan este concepto a cuestiones de ámbito espacial y atmosférico. Benjamin sostiene que la arquitectura, en una época en la que se desarrollan y se difunden nuevas técnicas de reproducción/ comunicación, no se puede percibir solo de manera visual sino también táctil, interrelacionando la difusión de nuevas técnicas de reproducción, la tensión entre diferentes modalidades perceptivas y la arquitectura: según él, la dispersión de la vista a favor de la percepción táctil/háptica es un rasgo característico de una sociedad en la que se desarrollan y se difunden nuevas técnicas de reproducción. La tesis profundiza en estos temas, actualizando el concepto de distracción/dispersión para valorar las repercusiones de esta intuición en el ámbito de una parte de la producción arquitectónica contemporánea: se propone una contextualización histórica y una conceptual, relativas a los proyectos recientes de algunos de los autores que profundizan en el impacto de las nuevas tecnologías en el ámbito del proyecto de arquitectura. La hipótesis que se quiere demostrar es que se está desarrollando una tendencia que lleva proyectos o edificios de alto nivel tecnológico y informático desde un ámbito de (supuesto) predominio de la percepción visual, hasta una arquitectura que proporciona experiencias multisensoriales: espacios que se pueden medir con el movimiento, los músculos y el tacto, que desarrollan un conjunto de sensaciones táctiles/hápticas y no solo visuales. Finalmente se quiere verificar si, revertiendo siglos de evolución visual, la visión táctil y cercana siga siendo uno de los polos dialécticos que estructuran la experiencia de la arquitectura, como previsto por Benjamin hace 75 años. ABSTRACT The thesis focuses on the thought of Walter Benjamin and the concept of distracted perception, developed in the essay The Work of Art in the Age of Mechanical Reproduction (1936). The title derives from a linguistic approach to this concept which further explores the meaning of the word distraction, finally relating this kind of perception to spatial and atmospheric issues. Benjamin argues that architecture, thanks to the development of new reproduction/communication technologies, cannot be perceived exclusively in a visual way but also in a tactile way, interrelating new technologies of reproduction, perceptual modalities and architecture: according to him, the dispersion of the view in favor of tactile/ haptic perception is a fundamental characteristic of a technologically developed society. The thesis explores these issues, updating the concept of distraction/dispersion to assess its implications in the works of some architects that are exploring with their buildings the impact of new communication technologies in the field of architectural design. The hypothesis at the base of this work is that we are facing a new trend in this particular field: many of the most advanced buildings provide multisensory experience, and define spaces that can be better perceived with the sense of touch (haptic sense), going beyond a mere visual perception. Finally the thesis wants to verify if, reversing centuries of visual evolution, tactile and close vision remains one of the dialectical poles that stay at the base of the experience of architecture, as foreseen by Benjamin 75 years ago. ABSTRACT La tesi si basa sul pensiero di Walter Benjamin e sul concetto di percezione distratta, sviluppato nel saggio La opera d’arte nell’epoca della sua riproducibilità tecnica (1936). Il titolo, percezione dispersa, deriva da un approfondimento dei concetti benjaminiani in termini linguistici, adottando ulteriori significati della parola che il filosofo utilizza per indicare la distrazione e che relazionano questo termine a questioni di ambito spaziale ed atmosferico. Benjamin sostiene che l’architettura, in un’epoca nella quale si sviluppano e si diffondono nuove tecniche di riproduzione (o meglio: nuove tecnologie di comunicazione), non possa essere percepita solamente in maniera visuale, ma anche tattile, mettendo in relazione la diffusione di nuove tecnologie, la tensione tra differenti modalità percettive e l’architettura: secondo Benjamin, la dispersione della vista a favore di una ricezione tattile/aptica della realtà è una caratteristica tipica di quei momenti storici nei quali si manifestano grandi trasformazioni di ambito sociale e culturale dovute allo sviluppo di nuove tecnologie di comunicazione. La tesi approfondisce questi temi, aggiornando il concetto di distrazione/dispersione per valutarne le ripercussioni su una certa parte della produzione architettonica contemporanea: si propone una contestualizzazione storica ed una concettuale, relative ai progetti di alcuni architetti che lavorano da tempo sull’impatto delle nuove tecnologie nell’ambito del progetto di architettura. La ipotesi che si dimostra con questa tesi è che si sta sviluppando una contro-tendenza tattile, a seguito della quale molti degli edifici tecnologicamente ed informaticamente più avanzati strutturano la relazione con i propri utenti sulla base di esperienze multisensoriali, definendo spazi che possono essere percepiti attraverso una percezione aptica, piuttosto che visuale. In definitiva la tesi verifica che, superando secoli di evoluzione visuale, la visione tattile e ravvicinata e - più in generale - una percezione di tipo aptico continuano ad essere uno dei poli dialettici che strutturano l’esperienza dell’architettura, come previsto da Benjamin più di 75 anni fa.

Investigation of the bottleneck leading to the domestication of maize

Maize (Zea mays ssp. mays) is genetically diverse, yet it is also morphologically distinct from its wild relatives. These two observations are somewhat contradictory: the first observation is consistent with a large historical population size for maize, but the latter observation is consistent with strong, diversity-limiting selection during maize domestication. In this study, we sampled sequence diversity, coupled with simulations of the coalescent process, to study the dynamics of a population bottleneck during the domestication of maize. To do this, we determined the DNA sequence of a 1,400-bp region of the Adh1 locus from 19 individuals representing maize, its presumed progenitor (Z. mays ssp. parviglumis), and a more distant relative (Zea luxurians). The sequence data were used to guide coalescent simulations of population bottlenecks associated with domestication. Our study confirms high genetic diversity in maize—maize contains 75% of the variation found in its progenitor and is more diverse than its wild relative, Z. luxurians—but it also suggests that sequence diversity in maize can be explained by a bottleneck of short duration and very small size. For example, the breadth of genetic diversity in maize is consistent with a founding population of only 20 individuals when the domestication event is 10 generations in length.

The earliest archaeological maize (Zea mays L.) from highland Mexico: New accelerator mass spectrometry dates and their implications

Accelerator mass spectrometry age determinations of maize cobs (Zea mays L.) from Guilá Naquitz Cave in Oaxaca, Mexico, produced dates of 5,400 carbon-14 years before the present (about 6,250 calendar years ago), making those cobs the oldest in the Americas. Macrofossils and phytoliths characteristic of wild and domesticated Zea fruits are absent from older strata from the site, although Zea pollen has previously been identified from those levels. These results, together with the modern geographical distribution of wild Zea mays, suggest that the cultural practices that led to Zea domestication probably occurred elsewhere in Mexico. Guilá Naquitz Cave has now yielded the earliest macrofossil evidence for the domestication of two major American crop plants, squash (Cucurbita pepo) and maize.

Archaeological evidence of teosinte domestication from Guilá Naquitz, Oaxaca

Analysis of the three most ancient Zea mays inflorescence fragments from Guilá Naquitz, Oaxaca, Mexico shows they did not disarticulate naturally, indicating that agricultural selection of domesticated teosinte was underway by 5,400 14C years before the present (about 4,200 dendrocalibrated years B.C.). The cooccurrence of two-ranked specimens with two rows and four rows of grain and numerous additional morphological characteristics of these specimens support hypotheses based on molecular and quantitative genetic analyses that maize evolved from teosinte. Domestication of the wild ancestor of maize occurred before the end of the 5th millennium B.C.

Genome projects and gene pools: New germplasm for plant breeding?

Crop gene pools have adapted to and sustained the demands of agricultural systems for thousands of years. Yet, very little is known about their content, distribution, architecture, or circuitry. The presumably shallow elite gene pools often continue to yield genetic gains while the exotic pools remain mostly untapped, uncharacterized, and underutilized. The concept and content of a crop’s gene pools are being changed by advancements in plant science and technology. In the first generation of plant genomics, DNA markers have refined some perceptions of genetic variation by providing a glimpse of a primary source, DNA polymorphism. The markers have provided new and more powerful ways of assessing genetic relationships, diversity, and merit by infusing genetic information for the first time in many scenarios or in a more comprehensive manner for others. As a result, crop gene pools may be supplemented through more rapid and directed methods from a greater variety of sources. Previously limited by the barriers of sexual reproduction, the native gene pools will soon be complemented by another gene pool (transgenes) and perhaps by other native exotic gene pools through comparative analyses of plants’ biological repertoire. Plant genomics will be an important force of change for crop improvement. The plant science community and crop gene pools may be united and enriched as never before. Also, the genomes and gene pools, the products of evolution and crop domestication, will be reduced and subjected to the vagaries and potential divisiveness of intellectual property considerations. Let the gains begin.

Gene genealogies and population variation in plants

Early in the development of plant evolutionary biology, genetic drift, fluctuations in population size, and isolation were identified as critical processes that affect the course of evolution in plant species. Attempts to assess these processes in natural populations became possible only with the development of neutral genetic markers in the 1960s. More recently, the application of historically ordered neutral molecular variation (within the conceptual framework of coalescent theory) has allowed a reevaluation of these microevolutionary processes. Gene genealogies trace the evolutionary relationships among haplotypes (alleles) with populations. Processes such as selection, fluctuation in population size, and population substructuring affect the geographical and genealogical relationships among these alleles. Therefore, examination of these genealogical data can provide insights into the evolutionary history of a species. For example, studies of Arabidopsis thaliana have suggested that this species underwent rapid expansion, with populations showing little genetic differentiation. The new discipline of phylogeography examines the distribution of allele genealogies in an explicit geographical context. Phylogeographic studies of plants have documented the recolonization of European tree species from refugia subsequent to Pleistocene glaciation, and such studies have been instructive in understanding the origin and domestication of the crop cassava. Currently, several technical limitations hinder the widespread application of a genealogical approach to plant evolutionary studies. However, as these technical issues are solved, a genealogical approach holds great promise for understanding these previously elusive processes in plant evolution.

Mitochondrial diversity and the origins of African and European cattle.

The nature of domestic cattle origins in Africa are unclear as archaeological data are relatively sparse. The earliest domesticates were humpless, or Bos taurus, in morphology and may have shared a common origin with the ancestors of European cattle in the Near East. Alternatively, local strains of the wild ox, the aurochs, may have been adopted by peoples in either continent either before or after cultural influence from the Levant. This study examines mitochondrial DNA displacement loop sequence variation in 90 extant bovines drawn from Africa, Europe, and India. Phylogeny estimation and analysis of molecular variance verify that sequences cluster significantly into continental groups. The Indian Bos indicus samples are most markedly distinct from the others, which is indicative of a B. taurus nature for both European and African ancestors. When a calibration of sequence divergence is performed using comparisons with bison sequences and an estimate of 1 Myr since the Bison/Bos Leptobos common ancestor, estimates of 117-275,000 B.P. and 22-26,000 B.P. are obtained for the separation between Indians and others and between African and European ancestors, respectively. As cattle domestication is thought to have occurred approximately 10,000 B.P., these estimates suggest the domestication of genetically discrete aurochsen strains as the origins of each continental population. Additionally, patterns of variation that are indicative of population expansions (probably associated with the domestication process) are discernible in Africa and Europe. Notably, the genetic signatures of these expansions are clearly younger than the corresponding signature of African/European divergence.

Alma dispersa.

Mode of access: Internet.

De la variation des animaux et des plantes sous l'action de la domestication /

Mode of access: Internet.

Acclimatation et domestication des animaux utiles /

Mode of access: Internet.