History repeats itself: genomic divergence in copepods

Press stop, erase everything from now till some arbitrary time in the past and start recording life as it evolves once again. Would you see the same tape of life playing itself over and over, or would a different story unfold every time? The late Steven Jay Gould called this experiment replaying the tape of life and argued that any replay of the tape would lead evolution down a pathway radically different from the road actually taken (Gould 1989). This thought experiment has puzzled evolutionary biologists for a long time: how repeatable are evolutionary events? And if history does indeed repeat itself, what are the factors that may help us predict the path taken? A powerful means to address these questions at a small evolutionary scale is to study closely related populations that have evolved independently, under similar environmental conditions. This is precisely what Pereira et al. ( 2016 ) set out to do using marine copepods Tigriopus californicus, and present their results in this issue of Molecular Ecology. They show that evolution can be repeatable and even partly predictable, at least at the molecular level. As expected from theory, patterns of divergence were shaped by natural selection. At the same time, strong genetic drift due to small population sizes also constrained evolution down a similar evolutionary road, and probably contributed to repeatable patterns of genomic divergence.     

Through the looking-glass: Observing HSCs through the lens of infection reveals unexpected insights into HSC function

Comment on: Hall CJ, et al. Cell Stem Cell 2012; 10:198-209.     

Observing development through evolutionary eyes: a practical approach.

An argument is made that only through a detailed comparison of mutational mechanisms underlying the evolution of the genetic systems governing development, can the 'logic' of individual development be fully comprehended. To do this, it is essential to choose two or more genes (or their products) that interact in the establishment of a given function, and to compare the molecular basis of that interaction in closely related species. The rationale to this approach arises from observations of molecular co-evolution between interacting partners involved with given functions which have led to species specificity in the manner in which such functions are effected. Molecular coevolution reveals that divergence in sequence can be tolerated whilst biological functions are maintained, not because it is neutral and dispensable but because successful, compensatory changes can evolve in eukaryotic genomes that are in continuous states of flux.     

The mu transpososome through a topological lens

Phage Mu is the most efficient transposable element known, its high efficiency being conferred by an enhancer DNA element. Transposition is the end result of a series of well choreographed steps that juxtapose the enhancer and the two Mu ends within a nucleoprotein complex called the 'transpososome.' The particular arrangement of DNA and protein components lends extraordinary stability to the transpososome and regulates the frequency, precision, directionality, and mechanism of transposition. The structure of the transpososome, therefore, holds the key to understanding all of these attributes, and ultimately to explaining the runaway genetic success of transposable elements throughout the biological world. This review focuses on the path of the DNA within the Mu transpososome, as uncovered by recent topological analyses. It discusses why Mu topology cannot be analyzed by standard methods, and how knowledge of the geometry of site alignment during Flp and Cre site-specific recombination was harnessed to design a new methodology called 'difference topology.' This methodology has also revealed the order and dynamics of association of the three interacting DNA sites, as well as the role of the enhancer in assembly of the Mu transpososome.     

Rangeland stewardship envisioned through a planetary lens

Rangelands comprise approximately 50% of ecologically intact landscapes available to mitigate biodiversity loss and to provide natural climate solutions. However, their planetary value is often overshadowed by local priorities on select provisioning services. A transformative stewardship strategy will require an inversion of priorities placed on ecosystem service categories supplied by rangelands.     

Minireview: Apoptosis as seen through a lens

The lens represents an ideal model system for studying many of the cellular and molecular events of differentiation. It is composed of two ectodermally-derived cell types: the lens epithelial cells and the lens fibre cells, which are derived from the lens epithelial cells by differentiation. Programmed removal of nuclei and other organelles from the lens fibre cells ensures that an optically clear structure is created, while the morphology of the degenerating nuclei is similar to that observed during apoptosis and is accompanied by DNA fragmentation. These observations suggest the existence of biochemical parallels between the process of lens fibre cell organelle loss and classical apoptosis. For example, proteins encoded by the bcl-2 and caspase gene families are expressed in developing lenses and nuclear degeneration in lens fibre cells can be inhibited in vivo by overexpression of bcl-2 and in vitro by incubation of differentiating lens epithelial cell cultures with caspase inhibitors. Thus, the developing lens may represent a particularly useful model system for researchers interested in apoptosis. In this review, the recent literature pertaining to lens fibre cell organelle loss and its relationship to apoptosis is reviewed and possible future research directions are suggested.     

Archeal lectins: An identification through a genomic search

Forty‐six lectin domains which have homologues among well established eukaryotic and bacterial lectins of known three‐dimensional structure, have been identified through a search of 165 archeal genomes using a multipronged approach involving domain recognition, sequence search and analysis of binding sites. Twenty‐one of them have the 7‐bladed β‐propeller lectin fold while 16 have the β‐trefoil fold and 7 the legume lectin fold. The remainder assumes the C‐type lectin, the β‐prism I and the tachylectin folds. Acceptable models of almost all of them could be generated using the appropriate lectins of known three‐dimensional structure as templates, with binding sites at one or more expected locations. The work represents the first comprehensive bioinformatic study of archeal lectins. The presence of lectins with the same fold in all domains of life indicates their ancient origin well before the divergence of the three branches. Further work is necessary to identify archeal lectins which have no homologues among eukaryotic and bacterial species. Proteins 2016; 84:21–30. © 2015 Wiley Periodicals, Inc.     

Voltage-gated sodium channels viewed through a structural biology lens

Bacterial voltage-gated sodium (BacNav) channels provide insight into eukaryotic Nav channel gating, ion selectivity and pharmacology.

     

Gene prioritization through genomic data fusion

The identification of genes involved in health and disease remains a challenge. We describe a bioinformatics approach, together with a freely accessible, interactive and flexible software termed Endeavour, to prioritize candidate genes underlying biological processes or diseases, based on their similarity to known genes involved in these phenomena. Unlike previous approaches, ours generates distinct prioritizations for multiple heterogeneous data sources, which are then integrated, or fused, into a global ranking using order statistics. In addition, it offers the flexibility of including additional data sources. Validation of our approach revealed it was able to efficiently prioritize 627 genes in disease data sets and 76 genes in biological pathway sets, identify candidates of 16 mono- or polygenic diseases, and discover regulatory genes of myeloid differentiation. Furthermore, the approach identified a novel gene involved in craniofacial development from a 2-Mb chromosomal region, deleted in some patients with DiGeorge-like birth defects. The approach described here offers an alternative integrative method for gene discovery.     

A survey of carbon fixation pathways through a quantitative lens

While the reductive pentose phosphate cycle is responsible for the fixation of most of the carbon in the biosphere, it has several natural substitutes. In fact, due to the characterization of three new carbon fixation pathways in the last decade, the diversity of known metabolic solutions for autotrophic growth has doubled. In this review, the different pathways are analysed and compared according to various criteria, trying to connect each of the different metabolic alternatives to suitable environments or metabolic goals. The different roles of carbon fixation are discussed; in addition to sustaining autotrophic growth it can also be used for energy conservation and as an electron sink for the recycling of reduced electron carriers. Our main focus in this review is on thermodynamic and kinetic aspects, including thermodynamically challenging reactions, the ATP requirement of each pathway, energetic constraints on carbon fixation, and factors that are expected to limit the rate of the pathways. Finally, possible metabolic structures of yet unknown carbon fixation pathways are suggested and discussed.     

Maximizing crossbred performance through purebred genomic selection

Background

In livestock production, many animals are crossbred, with two distinct advantages: heterosis and breed complementarity. Genomic selection (GS) can be used to select purebred parental lines for crossbred performance (CP). Dominance being the likely genetic basis of heterosis, explicitly including dominance in the GS model may be an advantage to select purebreds for CP. Estimated breeding values for CP can be calculated from additive and dominance effects of alleles that are estimated using pure line data. The objective of this simulation study was to investigate the benefits of applying GS to select purebred animals for CP, based on purebred phenotypic and genotypic information. A second objective was to compare the use of two separate pure line reference populations to that of a single reference population that combines both pure lines. These objectives were investigated under two conditions, i.e. either a low or a high correlation of linkage disequilibrium (LD) phase between the pure lines.

Results

The results demonstrate that the gain in CP was higher when parental lines were selected for CP, rather than purebred performance, both with a low and a high correlation of LD phase. For a low correlation of LD phase between the pure lines, the use of two separate reference populations yielded a higher gain in CP than use of a single reference population that combines both pure lines. However, for a high correlation of LD phase, marker effects that were estimated using a single combined reference population increased the gain in CP.

Conclusions

Under the hypothesis that performance of crossbred animals differs from that of purebred animals due to dominance, a dominance model can be used for GS of purebred individuals for CP, without using crossbred data. Furthermore, if the correlation of LD phase between pure lines is high, accuracy of selection can be increased by combining the two pure lines into a single reference population to estimate marker effects.

Electronic supplementary material

The online version of this article (doi:10.1186/s12711-015-0099-3) contains supplementary material, which is available to authorized users.     

Mexico through a superdiversity lens: already-existing diversity meets new immigration

New migration flows to Mexico are challenging long-established sociocultural configurations. So far, most studies on immigrants in Mexico have focused on singular ethno-national groups rather than paying attention to the intermingling of people. This paper presents an examination of diversification processes occurring in Guadalajara, Mexico. We contend that these are particularly strained because of the continuing frictions with which the country has to deal due to its already-existing diversity. The many forms of discrimination and racism that many Mexicans are subjected to by their co-nationals are often extended to new arrivals. The increasing complexity of migrant inflows challenges established forms of prejudice in everyday interactions. We argue in this paper that the use of superdiversity as a lens to study diversification processes allows us to better understand the changing dynamics currently taking place in Mexico.     

Huntington's disease: seeing the pathogenic process through a genetic lens

Thirteen years ago, the culmination of genetic rather than biochemical strategies resulted in the identification of the root cause of Huntington's disease: an expanded CAG trinucleotide repeat that leads to an elongated polyglutamine tract in the huntingtin protein. Since then, biochemical and cell biological attempts to elucidate pathogenesis have largely focused on N-terminal polyglutamine-containing huntingtin fragments. However, continued application of genetic strategies has suggested that the disease process is, in fact, triggered by the presence of expanded polyglutamine in intact huntingtin. An increased emphasis on the earliest presymptomatic stages of the disease, facilitated by incorporating genetic lessons from human patients into the search for biochemical targets, could provide a route to a rational treatment to prevent or slow the onset of this devastating neurodegenerative disorder.