Coalescent-based genome analyses resolve the early branches of the euarchontoglires

Despite numerous large-scale phylogenomic studies, certain parts of the mammalian tree are extraordinarily difficult to resolve. We used the coding regions from 19 completely sequenced genomes to study the relationships within the super-clade Euarchontoglires (Primates, Rodentia, Lagomorpha, Dermoptera and Scandentia) because the placement of Scandentia within this clade is controversial. The difficulty in resolving this issue is due to the short time spans between the early divergences of Euarchontoglires, which may cause incongruent gene trees. The conflict in the data can be depicted by network analyses and the contentious relationships are best reconstructed by coalescent-based analyses. This method is expected to be superior to analyses of concatenated data in reconstructing a species tree from numerous gene trees. The total concatenated dataset used to study the relationships in this group comprises 5,875 protein-coding genes (9,799,170 nucleotides) from all orders except Dermoptera (flying lemurs). Reconstruction of the species tree from 1,006 gene trees using coalescent models placed Scandentia as sister group to the primates, which is in agreement with maximum likelihood analyses of concatenated nucleotide sequence data. Additionally, both analytical approaches favoured the Tarsier to be sister taxon to Anthropoidea, thus belonging to the Haplorrhine clade. When divergence times are short such as in radiations over periods of a few million years, even genome scale analyses struggle to resolve phylogenetic relationships. On these short branches processes such as incomplete lineage sorting and possibly hybridization occur and make it preferable to base phylogenomic analyses on coalescent methods

Running Speed in Mammals Increases with Muscle n-6 Polyunsaturated Fatty Acid Content

Polyunsaturated fatty acids (PUFAs) are important dietary components that mammals cannot synthesize de novo. Beneficial effects of PUFAs, in particular of the n-3 class, for certain aspects of animal and human health (e.g., cardiovascular function) are well known. Several observations suggest, however, that PUFAs may also affect the performance of skeletal muscles in vertebrates. For instance, it has been shown that experimentally n-6 PUFA-enriched diets increase the maximum swimming speed in salmon. Also, we recently found that the proportion of PUFAs in the muscle phospholipids of an extremely fast runner, the brown hare (Lepus europaeus), are very high compared to other mammals. Therefore, we predicted that locomotor performance, namely running speed, should be associated with differences in muscle fatty acid profiles. To test this hypothesis, we determined phospholipid fatty acid profiles in skeletal muscles of 36 mammalian species ranging from shrews to elephants. We found that there is indeed a general positive, surprisingly strong relation between the n-6 PUFAs content in muscle phospholipids and maximum running speed of mammals. This finding suggests that muscle fatty acid composition directly affects a highly fitness-relevant trait, which may be decisive for the ability of animals to escape from predators or catch prey

Social Phobia in an Italian region: do Italian studies show lower frequencies than community surveys conducted in other European countries?

BACKGROUND: The lifetime prevalence of Social Phobia (SP) in European countries other than Italy has been estimated to range from 3.5% to 16.0%. The aim of this study was to assess the frequency of SP in Sardinia (Italy) in order to verify the evidence of a lower frequency of SP in Italy observed in previous studies (from 1.0% to 3.1%). METHODS: A randomised cross sample of 1040 subjects, living in Cagliari, in rural areas, and in a mining district in Sardinia were interviewed using a Simplified version of the Composite International Diagnostic Interview (CIDIS). Diagnoses were made according to the 10(th )International Classification of Diseases (ICD-10). RESULTS: Lifetime prevalence of SP was 2.2% (males: 1.5%, females: 2.8%) whereas 6-month prevalence resulted in 1.5% (males: 0.9%, females: 2.1%). Mean age at onset was 16.2 ± 9.3 years. A statistically significant association was found with Depressive Episode, Dysthymia and Generalized Anxiety Disorder. CONCLUSIONS: The study is consistent with findings reported in several previous studies of a lower prevalence of SP in Italy. Furthermore, the results confirm the fact that SP, due to its early onset, might constitute an ideal target for early treatment aimed at preventing both the accumulation of social disabilities and impairments caused by anxiety and avoidance behaviour, as well as the onset of more serious, associated complications in later stages of the illness

Grounds for engagement: Dissonances and overlaps at the intersection of contemporary civilizations analysis and postcolonial sociology

This article elucidates grounds for engagement between two fields of the social sciences engaged in critique of Eurocentrism: contemporary civilizations analysis and postcolonial sociology. Between the two fields there are both evident dissonances and points of potential dialogue and engagement. The article identifies three areas of high contention: divergent perceptions of essentialism, commitments to transformative politics and evaluations of the paradigm of multiple modernities. Despite extensive theoretical and normative differences, a notional intersection of the two fields is outlined in the form of three conceptual and methodological shifts. The first is a displacement of ideal typology. The second move is the most original. ‘Intercivilizational encounters’ and ‘intracivilizational encounters’ are re-cast as ‘intercivilizational engagement’. The goal is the demarcation of a discrete position based on a strong version of interaction that goes further than the notion of intercivilizational encounters recently re-developed in civilizational analysis. To illustrate potential grounds for engagement on this point, the article reviews the historiography of ‘connected histories’ and the insights of relational historians. Finally, the article urges for a nuanced definition of ‘region’ and deeper appreciation of the multiplicity of regionalisms as a meeting point for both fields of critique of Eurocentrism

Evolutionary relationships and divergence times among the native rats of Australia

Background The genus Rattus is highly speciose and has a complex taxonomy that is not fully resolved. As shown previously there are two major groups within the genus, an Asian and an Australo-Papuan group. This study focuses on the Australo-Papuan group and particularly on the Australian rats. There are uncertainties regarding the number of species within the group and the relationships among them. We analysed 16 mitochondrial genomes, including seven novel genomes from six species, to help elucidate the evolutionary history of the Australian rats. We also demonstrate, from a larger dataset, the usefulness of short regions of the mitochondrial genome in identifying these rats at the species level. Results Analyses of 16 mitochondrial genomes representing species sampled from Australo-Papuan and Asian clades of Rattus indicate divergence of these two groups ~2.7 million years ago (Mya). Subsequent diversification of at least 4 lineages within the Australo-Papuan clade was rapid and occurred over the period from ~ 0.9-1.7 Mya, a finding that explains the difficulty in resolving some relationships within this clade. Phylogenetic analyses of our 126 taxon, but shorter sequence (1952 nucleotides long), Rattus database generally give well supported species clades. Conclusions Our whole mitochondrial genome analyses are concordant with a taxonomic division that places the native Australian rats into the Rattus fuscipes species group. We suggest the following order of divergence of the Australian species. R. fuscipes is the oldest lineage among the Australian rats and is not part of a New Guinean radiation. R. lutreolus is also within this Australian clade and shallower than R. tunneyi while the R. sordidus group is the shallowest lineage in the clade. The divergences within the R. sordidus and R. leucopus lineages occurring about half a million years ago support the hypotheses of more recent interchanges of rats between Australia and New Guinea. While problematic for inference of deeper divergences, we report that the analysis of shorter mitochondrial sequences is very useful for species identification in rats

A Drastic Reduction in the Life Span of Cystatin C L68Q Carriers Due to Life-Style Changes during the Last Two Centuries

Hereditary cystatin C amyloid angiopathy (HCCAA) is an autosomal dominant disease with high penetrance, manifest by brain hemorrhages in young normotensive adults. In Iceland, this condition is caused by the L68Q mutation in the cystatin C gene, with contemporary carriers reaching an average age of only 30 years. Here, we report, based both on linkage disequilibrium and genealogical evidence, that all known copies of this mutation derive from a common ancestor born roughly 18 generations ago. Intriguingly, the genealogies reveal that obligate L68Q carriers born 1825 to 1900 experienced a drastic reduction in life span, from 65 years to the present-day average. At the same time, a parent-of-origin effect emerged, whereby maternal inheritance of the mutation was associated with a 9 year reduction in life span relative to paternal inheritance. As these trends can be observed in several different extended families, many generations after the mutational event, it seems likely that some environmental factor is responsible, perhaps linked to radical changes in the life-style of Icelanders during this period. A mutation with such radically different phenotypic effects in reaction to normal variation in human life-style not only opens the possibility of preventive strategies for HCCAA, but it may also provide novel insights into the complex relationship between genotype and environment in human disease

Investigation of the Origin and Spread of a Mammalian Transposable Element Based on Current Sequence Diversity

Almost half the human genome consists of mobile DNA elements, and their analysis is a vital part of understanding the human genome as a whole. Many of these elements are ancient and have persisted in the genome for tens or hundreds of millions of years, providing a window into the evolution of modern mammals. The Golem family have been used as model transposons to highlight computational analyses which can be used to investigate these elements, particularly the use of molecular dating with large transposon families. Whole-genome searches found Golem sequences in 20 mammalian species. Golem A and B subsequences were only found in primates and squirrel. Interestingly, the full-length Golem, found as a few copies in many mammalian genomes, was found abundantly in horse. A phylogenetic profile suggested that Golem originated after the eutherian–metatherian divergence and that the A and B subfamilies originated at a much later date. Molecular dating based on sequence diversity suggests an early age, of 175 Mya, for the origin of the family and that the A and B lineages originated much earlier than expected from their current taxonomic distribution and have subsequently been lost in some lineages. Using publically available data, it is possible to investigate the evolutionary history of transposon families. Determining in which organisms a transposon can be found is often used to date the origin and expansion of the families. However, in this analysis, molecular dating, commonly used for determining the age of gene sequences, has been used, reducing the likelihood of errors from deleted lineages

1989 as a mimetic revolution: Russia and the challenge of post-communism

Various terms have been used to describe the momentous events of 1989, including Jürgen Habermas’s ‘rectifying revolution,’ and my own notion of 1989 as a type of ‘anti-revolution’: repudiating not only what had come before, but also denying the political logic of communist power, as well as the emancipatory potential of revolutionary socialism in its entirety. In the event, while the negative agenda of 1989 has been fulfilled, it failed in the end to transcend the political logic of the systems that collapsed at that time. This paper explores the unfulfilled potential of 1989. Finally, 1989 became more of a counter- rather than an anti-revolution, replicating in an inverted form the practices of the mature state socialist regimes. The paucity of institutional and intellectual innovation arising from 1989 is striking. The dominant motif was ‘returnism,’ the attempt to join an established enterprise rather than transforming it. Thus, 1989 can be seen as mimetic revolution, in the sense that it emulated systems that were not organically developed in the societies in which they were implanted. For Eastern Europe ‘returning’ to Europe appeared natural, but for Russia the civilizational challenge of post-communism was of an entirely different order. There could be no return, and instead of a linear transition outlined by the classic transitological literature, Russia’s post-communism demonstrated that the history of others could not be mechanically transplanted from one society to another

Impact of Carnivory on Human Development and Evolution Revealed by a New Unifying Model of Weaning in Mammals

Our large brain, long life span and high fertility are key elements of human evolutionary success and are often thought to have evolved in interplay with tool use, carnivory and hunting. However, the specific impact of carnivory on human evolution, life history and development remains controversial. Here we show in quantitative terms that dietary profile is a key factor influencing time to weaning across a wide taxonomic range of mammals, including humans. In a model encompassing a total of 67 species and genera from 12 mammalian orders, adult brain mass and two dichotomous variables reflecting species differences regarding limb biomechanics and dietary profile, accounted for 75.5%, 10.3% and 3.4% of variance in time to weaning, respectively, together capturing 89.2% of total variance. Crucially, carnivory predicted the time point of early weaning in humans with remarkable precision, yielding a prediction error of less than 5% with a sample of forty-six human natural fertility societies as reference. Hence, carnivory appears to provide both a necessary and sufficient explanation as to why humans wean so much earlier than the great apes. While early weaning is regarded as essentially differentiating the genus Homo from the great apes, its timing seems to be determined by the same limited set of factors in humans as in mammals in general, despite some 90 million years of evolution. Our analysis emphasizes the high degree of similarity of relative time scales in mammalian development and life history across 67 genera from 12 mammalian orders and shows that the impact of carnivory on time to weaning in humans is quantifiable, and critical. Since early weaning yields shorter interbirth intervals and higher rates of reproduction, with profound effects on population dynamics, our findings highlight the emergence of carnivory as a process fundamentally determining human evolution