Natural history collections and the future legacy of ecological research

Oecologia - Natural history collections are now being championed as key to broad ecological studies, especially those involving human impacts in the Anthropocene. However, collections are going...     

Breast cancer family history and allele-specific DNA methylation in the legacy girls study

Family history, a well-established risk factor for breast cancer, can have both genetic and environmental contributions. Shared environment in families as well as epigenetic changes that also may be influenced by shared genetics and environment may also explain familial clustering of cancers. Epigenetic regulation, such as DNA methylation, can change the activity of a DNA segment without a change in the sequence; environmental exposures experienced across the life course can induce such changes. However, genetic-epigenetic interactions, detected as methylation quantitative trait loci (mQTLs; a.k.a. meQTLs) and haplotype-dependent allele-specific methylation (hap-ASM), can also contribute to inter-individual differences in DNA methylation patterns. To identify differentially methylated regions (DMRs) associated with breast cancer susceptibility, we examined differences in white blood cell DNA methylation in 29 candidate genes in 426 girls (ages 6–13 years) from the LEGACY Girls Study, 239 with and 187 without a breast cancer family history (BCFH). We measured methylation by targeted massively parallel bisulfite sequencing (bis-seq) and observed BCFH DMRs in two genes: ESR1 (Δ4.9%, P = 0.003) and SEC16B (Δ3.6%, P = 0.026), each of which has been previously implicated in breast cancer susceptibility and pubertal development. These DMRs showed high inter-individual variability in methylation, suggesting the presence of mQTLs/hap-ASM. Using single nucleotide polymorphisms data in the bis-seq amplicon, we found strong hap-ASM in SEC16B (with allele specific-differences ranging from 42% to 74%). These findings suggest that differential methylation in genes relevant to breast cancer susceptibility may be present early in life, and that inherited genetic factors underlie some of these epigenetic differences.     

The life history legacy of evolutionary body size change in carnivores

We estimate the body sizes of direct ancestors of extant carnivores, and examine selected aspects of life history as a function not only of species' current size, but also of recent changes in size. Carnivore species that have undergone marked recent evolutionary size change show life history characteristics typically associated with species closer to the ancestral body size. Thus, phyletic giants tend to mature earlier and have larger litters of smaller offspring at shorter intervals than do species of the same body size that are not phyletic giants. Phyletic dwarfs, by contrast, have slower life histories than nondwarf species of the same body size. We discuss two possible mechanisms for the legacy of recent size change: lag (in which life history variables cannot evolve as quickly as body size, leading to species having the 'wrong' life history for their body size) and body size optimization (in which life history and hence body size evolve in response to changes in energy availability); at present, we cannot distinguish between these alternatives. Our finding that recent body size changes help explain residual variation around life history allometries shows that a more dynamic view of character change enables comparative studies to make more precise predictions about species traits in the context of their evolutionary background.     

The history of linguistic anthropology as a device for a new integrated perspective

The history of the emergence of linguistic anthropology helps us not only to reflect on the path-dependency of our own scientific categories, but also to enlarge our own perspective beyond these categories. The following paper tries to develop on the basis of Latour's network theory a new integrated perspective that reflects our own historical position in the network of constructing scientific facts, in the context of political problems, of social claims of objects that we are using in order to constitute our scientific field.     

A plant dialect of the histone language

The genome contains all the information needed to build an organism. However, during differentiation and development, additional epigenetic information determines the functional state of cells and tissues. This epigenetic information can be introduced by cytosine methylation and by marking nucleosomal histones. The code written on histones consists of post-translational modifications, including acetylation and methylation. In contrast to the universal nature of the DNA code, the histone language and its decoding machinery differ among animals, plants and fungi. Plant cells have retained totipotency to generate the entire plant and maintained the ability to dedifferentiate, which suggests that the establishment and maintenance of epigenetic information differs from animals. Here, I aim to summarize the histone code and plant-specific aspects of setting and translating the code.     

Platelets and the immune continuum

Platelets are anucleate cells that are crucial mediators of haemostasis. Most immunologists probably don't think about platelets every day, and may even consider these cells to be 'nuisances' in certain in vitro studies. However, it is becoming increasingly clear that platelets have inflammatory functions and can influence both innate and adaptive immune responses. Here, we discuss the mechanisms by which platelets contribute to immunity: these small cells are more immunologically savvy than we once thought.     

Vitality and erosion of Molise Croatian dialect

This paper gives a presentation of the condition of an endangered language located on the southern part of the Italian peninsula, spoken by a small community of transplanted Slavic population who fled the Eastern Adriatic coast during the Turkish invasion of the Balkan peninsula and have lived in complete isolation from related Slavic languages for five centuries surrounded by a majority of Italian speaking population. The overview of contact induced changes shows a high level of interferences at all structural levels resulting in a relatively stable mixed idiom. Preservation and revitalization efforts are discussed particularly in relation to the importance of writing and codification of the language as well as possible steps that can be undertaken in view of the link between language and the group cultural identity.     

The genetic legacy of the Mongols

We have identified a Y-chromosomal lineage with several unusual features. It was found in 16 populations throughout a large region of Asia, stretching from the Pacific to the Caspian Sea, and was present at high frequency: approximately 8% of the men in this region carry it, and it thus makes up approximately 0.5% of the world total. The pattern of variation within the lineage suggested that it originated in Mongolia approximately 1,000 years ago. Such a rapid spread cannot have occurred by chance; it must have been a result of selection. The lineage is carried by likely male-line descendants of Genghis Khan, and we therefore propose that it has spread by a novel form of social selection resulting from their behavior.     

Measuring the diffusion of linguistic change

We examine situations in which linguistic changes have probably been propagated via normal contact as opposed to via conquest, recent settlement and large-scale migration. We proceed then from two simplifying assumptions: first, that all linguistic variation is the result of either diffusion or independent innovation, and, second, that we may operationalize social contact as geographical distance. It is clear that both of these assumptions are imperfect, but they allow us to examine diffusion via the distribution of linguistic variation as a function of geographical distance. Several studies in quantitative linguistics have examined this relation, starting with Séguy (Séguy 1971 Rev. Linguist. Romane 35, 335-357), and virtually all report a sublinear growth in aggregate linguistic variation as a function of geographical distance. The literature from dialectology and historical linguistics has mostly traced the diffusion of individual features, however, so that it is sensible to ask what sort of dynamic in the diffusion of individual features is compatible with Séguy's curve. We examine some simulations of diffusion in an effort to shed light on this question.     

Instability of the sexual continuum

Maynard Smith and Szathmary have posed the problem of demonstrating the conjectured instability of a continuum of sexual types with finite interbreeding. Here, I propose a model in which one can analyse exactly when and how the existence of the instability can depend on an Allee effect, and how the growth rate and typical scale of the unstable perturbations depend on the strength and range of competition, mating preference, fecundity and offspring variance due to Mendelian segregation and mutation. Instabilities of various kinds are shown to occur in the majority of parameter regimes. In short, the continuum often breaks up into incipient species.     

Punctuationism,cladistics and the legacy of medieval neoplatonism

The current dominant orthoxy in paleoanthropology has adopted the stance of cladistics and/or punctuationism and abandonned any concern for the mechanics by which selection has operated to control the course of human evolution. Rather than being a «new» intellectual development, this is simply the most recent manifestation of a tradition of thinking that goes back via Linnaeus to medieval scholasticism where reality was assumed to consist of discrete entities that can be dealt with solely by the exercis of deductive logic. While the construction of cladograms serves the useful function of proposing testable hypotheses, the promotion of cladistic logic as the only valid approach represents a great leap backwards into medieval intellectual stagnation. If an inductive component is not restored to paleoanthropology, it will cease to maintain its credibility as a productive science.     

Multi-locus phylogenies of the genus Barteria (Passifloraceae) portray complex patterns in the evolution of myrmecophytism

The four species of the central African genus Barteria show variation in habitat and in degree of association with ants. Whereas B. solida, restricted to submontane forests, attracts opportunistic ants to extrafloral nectar, the three other species, found in lowland rainforests (B. fistulosa, B. dewevrei) and in littoral scrub (B. nigritana), possess stem domatia of varying shapes and degrees of specialisation, hosting either non-specific arboreal ants (B. nigritana, some B. dewevrei) or two large species of ants of the genus Tetraponera Smith, 1852 that are specific to some species of Barteria (B. fistulosa, some B. dewevrei). We aimed to investigate whether this variation represents an evolutionary trend toward increasing specialisation of mutualism or the reduction or loss of myrmecophytic traits. For this, we determined phylogenetic relationships within the genus using DNA sequences (primarily nuclear ITS) and microsatellite genotypes (11 loci) on a large sample of individuals, mostly from Cameroon and Gabon. The two types of markers support an initial dichotomy that groups B. dewevrei with B. nigritana and B. fistulosa with B. solida respectively. Within these pairs, species do not appear reciprocally monophyletic. At microsatellite loci, B. nigritana forms a clade embedded within B. dewevrei; and within both B. solida and B. fistulosa, geographical populations show levels of differentiation similar to that observed between populations of B. solida and B. fistulosa. Geographic distance alone does not account for genetic differentiation between species, which indicates reproductive isolation. Divergence in each of the two pairs implies evolutionary transitions in habitat and in myrmecophytism. Specialised mutualism with specific ant species of the genus Tetraponera has been lost in species found in more marginal habitats.