Molecular dating of caprines using ancient DNA sequences of Myotragus balearicus, an extinct endemic Balearic mammal

Background: Myotragus balearicus was an endemic bovid from the Balearic Islands (Western Mediterranean) that became extinct around 6,000-4,000 years ago. The Myotragus evolutionary lineage became isolated in the islands most probably at the end of the Messinian crisis, when the desiccation of the Mediterranean ended, in a geological date established at 5.35 Mya. Thus, the sequences of Myotragus could be very valuable for calibrating the mammalian mitochondrial DNA clock and, in particular, the tree of the Caprinae subfamily, to which Myotragus belongs. Results: We have retrieved the complete mitochondrial cytochrome b gene (1,143 base pairs), plus fragments of the mitochondrial 12S gene and the nuclear 28S rDNA multi-copy gene from a well preserved Myotragus subfossil bone. The best resolved phylogenetic trees, obtained with the cytochrome b gene, placed Myotragus in a position basal to the Ovis group. Using the calibration provided by the isolation of Balearic Islands, we calculated that the initial radiation of caprines can be dated at 6.2 ± 0.4 Mya. In addition, alpine and southern chamois, considered until recently the same species, split around 1.6 ± 0.3 Mya, indicating that the two chamois species have been separated much longer than previously thought. Conclusion: Since there are almost no extant endemic mammals in Mediterranean islands, the sequence of the extinct Balearic endemic Myotragus has been crucial for allowing us to use the Messinian crisis calibration point for dating the caprines phylogenetic tree.

Ancient DNA of the extinct Lava shearwater (Puffinus olsoni) from the Canary Islands reveals incipient differentiation within the P. puffinus complex

The loss of species during the Holocene was, dramatically more important on islands than on continents. Seabirds from islands are very vulnerable to human-induced alterations such as habitat destruction, hunting and exotic predators. For example, in the genus Puffinus (family Procellariidae) the extinction of at least five species has been recorded during the Holocene, two of them coming from the Canary Islands.

The whereabouts of an ancient wonderer: Global phylogeography of the solitary ascidian Styela plicata

Genetic tools have greatly aided in tracing the sources and colonization history of introduced species. However, recurrent introductions and repeated shuffling of populations may have blurred some of the genetic signals left by ancient introductions. Styela plicata is a solitary ascidian distributed worldwide. Although its origin remains unclear, this species is believed to have spread worldwide by travelling on ship's hulls. The goals of this study were to infer the genetic structure and global phylogeography of S. plicata and to look for present-day and historical genetic patterns. Two genetic markers were used: a fragment of the mitochondrial gene Cytochrome Oxidase subunit I (COI) and a fragment of the nuclear gene Adenine Nucleotide Transporter/ADP-ATP Translocase (ANT). A total of 368 individuals for COI and 315 for ANT were sequenced from 17 locations worldwide. The levels of gene diversity were moderate for COI to high for ANT. The Mediterranean populations showed the least diversity and allelic richness for both markers, while the Indian, Atlantic and Pacific Oceans had the highest gene and nucleotide diversities. Network and phylogenetic analyses with COI and ANT revealed two groups of alleles separated by 15 and 4 mutational steps, respectively. The existence of different lineages suggested an ancient population split. However, the geographic distributions of these groups did not show any consistent pattern, indicating different phylogeographic histories for each gene. Genetic divergence was significant for many population-pairs irrespective of the geographic distance among them. Stochastic introduction events are reflected in the uneven distribution of COI and ANT allele frequencies and groups among many populations. Our results confirmed that S. plicata has been present in all studied oceans for a long time, and that recurrent colonization events and occasional shuffling among populations have determined the actual genetic structure of this species.

Fragmentation of contaminant and endogenous DNA in ancient samples determined by shotgun sequencing; prospects for human palaeogenomics

Despite the successful retrieval of genomes from past remains, the prospects for human palaeogenomics remain unclear because of the difficulty of distinguishing contaminant from endogenous DNA sequences. Previous sequence data generated on high-throughput sequencing platforms indicate that fragmentation of ancient DNA sequences is a characteristic trait primarily arising due to depurination processes that create abasic sites leading to DNA breaks.

Evolution: the end of an ancient asexual scandal.

Bdelloid rotifers were believed to have persisted and diversified in the absence of sex. Two papers now show they exchange genes with each other, via horizontal gene transfers as known in bacteria and/or via other forms of non-canonical sex.

Ancient DNA analysis of 8000 B.C. near eastern farmers supports an early neolithic pioneer maritime colonization of Mainland Europe through Cyprus and the Aegean Islands

The genetic impact associated to the Neolithic spread in Europe has been widely debated over the last 20 years. Within this context, ancient DNA studies have provided a more reliable picture by directly analyzing the protagonist populations at different regions in Europe. However, the lack of available data from the original Near Eastern farmers has limited the achieved conclusions, preventing the formulation of continental models of Neolithic expansion. Here we address this issue by presenting mitochondrial DNA data of the original Near-Eastern Neolithic communities with the aim of providing the adequate background for the interpretation of Neolithic genetic data from European samples. Sixty-three skeletons from the Pre Pottery Neolithic B (PPNB) sites of Tell Halula, Tell Ramad and Dja'de El Mughara dating between 8,700-6,600 cal. B.C. were analyzed, and 15 validated mitochondrial DNA profiles were recovered. In order to estimate the demographic contribution of the first farmers to both Central European and Western Mediterranean Neolithic cultures, haplotype and haplogroup diversities in the PPNB sample were compared using phylogeographic and population genetic analyses to available ancient DNA data from human remains belonging to the Linearbandkeramik-Alföldi Vonaldiszes Kerámia and Cardial/Epicardial cultures. We also searched for possible signatures of the original Neolithic expansion over the modern Near Eastern and South European genetic pools, and tried to infer possible routes of expansion by comparing the obtained results to a database of 60 modern populations from both regions. Comparisons performed among the 3 ancient datasets allowed us to identify K and N-derived mitochondrial DNA haplogroups as potential markers of the Neolithic expansion, whose genetic signature would have reached both the Iberian coasts and the Central European plain. Moreover, the observed genetic affinities between the PPNB samples and the modern populations of Cyprus and Crete seem to suggest that the Neolithic was first introduced into Europe through pioneer seafaring colonization.

Truths ancient and modern

The paper presents a comparison of the theories of truth, and the solutions of the liar paradox, proposed by Thomas Bradwardine (c. 1290-1349), Jean Buridan (c. 1295-1358), and Alfred Tarski (1901-1983).

Defining the art of grammar: Ancient perceptions of γραμματική and grammatical

The subject of this dissertation, which belongs to the field of Classical Philology, are the definitions of the art of grammar found in Greek and Latin sources from the Classical era to the second century CE. Definitions survive from grammarians, philosophers, and general scholars. I have examined these definitions from two main points of view: how they are formed, and how they reflect the development of the art itself. Defining formed part of dialectic, in practice also of rhetoric, and was perceived as important from the Classical era onwards. Definitions of grammar seem to have become established as part of preliminary discussions, located at the beginning of grammatical manuals (tékhnai, artes). These discussions included certain principal notions of the art; in addition to the definition, a list of the parts of the art was also typically included. These lists were formed by two different methods: division (diaíresis, divisio) and partition (merismós, partitio). Many of the grammarians may actually have been unfamiliar with these methods, unlike the two most important scholars of the Late Republic, Varro and Cicero. Significant attention was devoted to the question whether the art of grammar is based on lógos or empeiría. This epistemological question had its roots in medical theories, which were prominent in Alexandria. In the history of the concept of grammatiké or grammatica, three stages become evident. In the Classical era, the Greek term is used to refer to a very concrete art of letters (grámmata); from the Hellenistic era onwards it refers to the art developed by the Alexandrian scholars, a matter of textual and literary criticism. Towards the end of the Hellenistic era, the grammarian also becomes involved with the question of correct language, which gradually begins to appear in the definitions as well.

Nietzsche's eternal recurrence of the same : the effect of logic abridgement, contradictions and inconsistencies

I will argue that the doctrine of eternal recurrence of the same no better interprets cosmology than pink elephants interpret zoology. I will also argue that the eternal-reiurn-of-the-same doctrine as what Magnus calls "existential imperative" is without possibility of application and thus futile. To facilitate those arguments, the validity of the doctrine of the eternal recurrence of the same will be tested under distinct rubrics. Although each rubric will stand alone, one per chapter, as an evaluation of some specific aspect of eternal recurrence, the rubric sequence has been selected to accommodate the identification of what I shall be calling logic abridgments. The conclusions to be extracted from each rubric are grouped under the heading CONCLUSION and appear immediately following rubric ten. Then, or if, at the end of a rubric a reader is inclined to wonder which rubric or topic is next, and why, the answer can be found at the top of the following page. The question is usually answered in the very first sentence, but always answered in the first paragraph. The first rubric has been placed in order by chronological entitlement in that it deals with the evolution of the idea of eternal recurrence from the time of the ancient Greeks to Nietzsche's August, 1881 inspiration. This much-recommended technique is also known as starting at the beginning. Rubric 1 also deals with 20th. Century philosophers' assessments of the relationship between Nietzsche and ancient Greek thought. The only experience of E-R, Zarathustra's mountain vision, is second only because it sets the scene alluded to in following rubrics. The third rubric explores .ii?.ih T jc,i -I'w Nietzsche's evaluation of rationality so that his thought processes will be understood appropriately. The actual mechanism of E-R is tested in rubric four...The scientific proof Nietzsche assembled in support of E-R is assessed by contemporary philosophers in rubric five. E-R's function as an ethical imperative is debated in rubrics six and seven.. .The extent to which E-R fulfills its purpose in overcoming nihilism is measured against the comfort assured by major world religions in rubric eight. Whether E-R also serves as a redemption for revenge is questioned in rubric nine. Rubric ten assures that E-R refers to return of the identically same and not merely the similar. In addition to assemblage and evaluation of all ten rubrics, at the end of each rubric a brief recapitulation of its principal points concludes the chapter. In this essay I will assess the theoretical conditions under which the doctrine cannot be applicable and will show what contradictions and inconsistencies follow if the doctrine is taken to be operable. Harold Alderman in his book Nietzsche's Gift wrote, the "doctrine of eternal recurrence gives us a problem not in Platonic cosmology, but in Socratic selfreflection." ^ I will illustrate that the recurrence doctrine's cosmogony is unworkable and that if it were workable, it would negate self-reflection on the grounds that selfreflection cannot find its cause in eternal recurrence of the same. Thus, when the cosmology is shown to be impossible, any expected ensuing results or benefits will be rendered also impossible. The so-called "heaviest burden" will be exposed as complex, engrossing "what if speculations deserving no linkings to reality. To identify ^Alderman p. 84 abridgments of logic, contradictions and inconsistencies in Nietzsche's doctrine of eternal recurrence of the same, I. will examine the subject under the following schedule. In Chapter 1 the ancient origins of recurrence theories will be introduced. ..This chapter is intended to establish the boundaries within which the subsequent chapters, except Chapter 10, will be confined. Chapter 2, Zarathustra's vision of E-R, assesses the sections of Thus Spoke Zarathustra in which the phenomenon of recurrence of the same is reported. ..Nihilism as a psychological difficulty is introduced in this rubric, but that subject will be studied in detail in Chapter 8. In Chapter 2 the symbols of eternal recurrence of the same will be considered. Whether the recurrence image should be of a closed ring or as a coil will be of significance in many sections of my essay. I will argue that neither symbolic configuration can accommodate Nietzsche's supposed intention. Chapter 3 defends the description of E-R given by Zarathustra. Chapter 4, the cosmological mechanics of E-R, speculates on the seriousness with which Nietzsche might have intended the doctrine of eternal recurrence to be taken. My essay reports, and then assesses, the argument of those who suppose the doctrine to have been merely exploratory musings by Nietzsche on cosmological hypotheses...The cosmogony of E-R is examined. In Chapter 5, cosmological proofs tested, the proofs for Nietzsche's doctrine of return of the same are evaluated. This chapter features the position taken by Martin ' Heidegger. My essay suggests that while Heidegger's argument that recurrence of the same is a genuine cosmic agenda is admirable, it is not at all persuasive. Chapter 6, E-R is an ethical imperative, is in essence the reporting of a debate between two scholars regarding the possibility of an imperative in the doctrine of recurrence. Their debate polarizes the arguments I intend to develop. Chapter 7, does E-R of the same preclude alteration of attitudes, is a continuation of the debate presented in Chapter 6 with the focus shifted to the psychological from the cosmological aspects of eternal recurrence of the same. Chapter 8, Can E-R Overcome Nihilism?, is divided into two parts. In the first, nihilism as it applies to Nietzsche's theory is discussed. ..In part 2, the broader consequences, sources and definitions of nihilism are outlined. My essay argues that Nietzsche's doctrine is more nihilistic than are the world's major religions. Chapter 9, Is E-R a redemption for revenge?, examines the suggestion extracted from Thus Spoke Zarathustra that the doctrine of eternal recurrence is intended, among other purposes, as a redemption for mankind from the destructiveness of revenge. Chapter 10, E-R of the similar refuted, analyses a position that an element of chance can influence the doctrine of recurrence. This view appears to allow, not for recurrence of the same, but recurrence of the similar. A summary will recount briefly the various significant logic abridgments, contradictions, and inconsistencies associated with Nietzsche's doctrine of eternal recurrence of the same. In the 'conclusion' section of my essay my own opinions and observations will be assembled from the body of the essay.

The true history regarding alleged connection of the order of ancient, free and accepted Masons: with the abduction and murder of William Morgan in western New York, in 1826... (1886)

Cover title: Masonic light on the abduction and murder of Wm. Morgan.