The small non-coding RNA processing machinery of two living fossil species, lungfish and coelacanth, gives new insights into the evolution of the Argonaute protein family

Argonaute (AGO) family proteins play many roles in epigenetic programming, genome rearrangement, mRNA breakdown, inhibition of translation, and transposon silencing. Despite being a hotspot in current scientific research, their evolutionary history is still poorly understood and consequently the identification of evolutionary conserved structural features should also generate useful information for better understanding their functions. We report here for the first time the transcript sets of the two subfamilies, Ago and Piwi, in the West African lungfish Protopterus annectens and in the Indonesian coelacanth Latimeria menadoensis, two key species in the evolutionary lineage leading to tetrapods. The phylogenetic analysis of 142 inferred protein sequences in 22 fully sequenced species and the analysis of microsynteny performed in the major vertebrate lineages indicate an intricate pattern for the evolution of both subfamilies that has been shaped by whole genome duplications and lineage specific gains and losses. The argonaute subfamily was additionally expanded by local gene duplications at the base of the jawed vertebrate lineage. The subfamily of Piwi proteins is involved in several processes such as spermatogenesis, piRNA biogenesis, and transposon repression. Expression assessment of AGO genes and genes coding for proteins involved in small RNA biogenesis suggests a limited activity of the Piwi pathway in lungfish in agreement with the lungfish genome containing mainly old and inactive transposons

The arms race of ray-finned fish against the derepression of LTR retroelements

Transposable elements (TEs) are dynamic components of eukaryotic genomes that are important in speciation. Evolutionary pressure has led to the evolution of silencing mechanisms, such as the involvement of Krüppel box-associated zinc finger proteins (KRAB-ZFPs) that regulate TE transcription via TRIM28-mediated NuRD complex recruitment in sarcopterygians. The transcriptional activity of genes that encode proteins of the NuRD complex was also detected in actinopterygians, even though genes encoding crucial proteins such as TRIM28 and KRAB-ZNF are missing in this evolutionary lineage. This study hypothesized that TRIM33 could serve as a replacement for TRIM28 in this lineage and suggested an evolutionary relationship between the sarcopterygian KRAB-ZFPs, the actinopterygian KRAB-like ZNFs and the fish N-terminal zinc-associated domain (FiNZ) ZNFs that are specific to cyprinids. Through coimmunoprecipitation analyses conducted in the basal teleost Anguilla marmorata and the cyprinid Danio rerio, we evaluated the interaction of TRIM33 with the KRAB-like and FiNZ ZFPs. Moreover, we explored the expression profiles of TEs and genes that encode proteins that are potentially involved in their silencing during zebrafish development. Our results may provide new evidence for more thoroughly understanding the evolutionary mechanisms underlying the adaptation of ray-finned fish

A comparative view on sex differentiation and gametogenesis genes in lungfish and coelacanths

none8siGonadal sex differentiation andreproductionare the keys totheperpetuationof favorable gene combinations andpositively selected traits. In vertebrates, several gonad development features that differentiate tetrapods and fishes are likely to be, at least in part, related to the water-to-land transition. The collection of information from basal sarcopterygians, coelacanths, and lungfishes, is crucial to improve our understanding of the molecular evolution of pathways involved in reproductive functions, since these organisms are generally regarded as “living fossils” and as the direct ancestors of tetrapods. Here, we report for the first time the characterization of >50 genes related to sex differentiation and gametogenesis in Latimeria menadoensis and Protopterus annectens. Although the expression profiles of most genes is consistent with the intermediate position of basal sarcopterygians between actinopterygian fish and tetrapods, their phylogenetic placement and presence/absence patterns often reveal a closer affinity to the tetrapod orthologs. On the other hand, particular genes, for example, the male gonad factor gsdf (Gonadal Soma-Derived Factor), provide examples of ancestral traits sharedwith actinopterygians,which disappeared in the tetrapod lineage.openMaria Assunta Biscotti, Mateus Contar Adolfi, Marco Barucca, Mariko Forconi, Alberto Pallavicini, Marco Gerdol, Adriana Canapa, Manfred SchartlBiscotti, Maria Assunta; Contar Adolfi, Mateus; Barucca, Marco; Forconi, Mariko'; Pallavicini, Alberto; Gerdol, Marco; Canapa, Adriana; Schartl, Manfre

A bioinformatic approach to characterize the vitellogenin receptor and the low density lipoprotein receptor superfamily in the newt Cynops orientalis

The Low Density Lipoprotein receptors (LDLRs) gene family includes 15 receptors: very low-density lipoprotein receptor (VLDLR), LDLR, Sorting-related receptor with A-type repeats (SORLA), and 12 LDL receptor-related proteins (LRPs): LRP1, LRP1B, LRP2, LRP3, LRP4, LRP5, LRP6, LRP8, LRP10, LRP11, LRP12, LRP13. Most of these are involved in the transduction of key signals during embryonic development and in the regulation of cholesterol homeostasis. In oviparous animals, the VLDL receptor is also known as VTGR since it facilitates the uptake of vitellogenin in ovary. In tetrapods, information concerning genes encoding these proteins is limited to a few taxa. Here, we report the characterization of VTGR in the amphibian Cynops orientalis. The secondary structure analyses and the expression profiles obtained from hepatic and gonadal tissues of C. orientalis supported the role of VTGR as vitellogenin oocyte membrane receptor in this species. Moreover, to get a holistic view of the evolutionary history of this gene superfamily, we extended our investigation to all 15 genes belonging to the LDLR superfamily analyzing through a phylogenetic analysis a total of 161 sequences belonging to 11 genera of vertebrates. The position of LRP8 in the tree and its expression findings in C. orientalis ovary allowed us to suggest that other proteins of the LDLR superfamily could act as receptors during vitellogenesi

The Physics of Financial Networks

As the total value of the global financial market outgrew the value of the real economy, financial institutions created a global web of interactions that embodies systemic risks. Understanding these networks requires new theoretical approaches and new tools for quantitative analysis. Statistical physics contributed significantly to this challenge by developing new metrics and models for the study of financial network structure, dynamics, and stability and instability. In this Review, we introduce network representations originating from different financial relationships, including direct interactions such as loans, similarities such as co-ownership and higher-order relations such as contracts involving several parties (for example, credit default swaps) or multilayer connections (possibly extending to the real economy). We then review models of financial contagion capturing the diffusion and impact of shocks across each of these systems. We also discuss different notions of ‘equilibrium’ in economics and statistical physics, and how they lead to maximum entropy ensembles of graphs, providing tools for financial network inference and the identification of early-warning signals of system-wide instabilities

Analysis of the African coelacanth genome sheds light on tetrapod evolution

It was a zoological sensation when a living specimen of the coelacanth was first discovered in 1938, as this lineage of lobe-finned fish was thought to have gone extinct 70 million years ago. The modern coelacanth looks remarkably similar to many of its ancient relatives, and its evolutionary proximity to our own fish ancestors provides a glimpse of the fish that first walked on land. Here we report the genome sequence of the African coelacanth, Latimeria chalumnae. Through a phylogenomic analysis, we conclude that the lungfish, and not the coelacanth, is the closest living relative of tetrapods. Coelacanth protein-coding genes are significantly more slowly evolving than those of tetrapods, unlike other genomic features . Analyses of changes in genes and regulatory elements during the vertebrate adaptation to land highlight genes involved in immunity, nitrogen excretion and the development of fins, tail, ear, eye, brain, and olfaction. Functional assays of enhancers involved in the fin-to-limb transition and in the emergence of extra-embryonic tissues demonstrate the importance of the coelacanth genome as a blueprint for understanding tetrapod evolution

Karyological and genetic variation in Middle Eastern lacertid lizards, Lacerta laevis and the Lacerta kulzeri complex: a case of chromosomal allopatric speciation

Abstract Karyological (standard and C, Ag-NOR and Alu-I banding methods) and mtDNA analyses (cytochrome b and 12S rRNA) were conducted on specimens from eight allopatric populations of the Lacerta kulzeri complex. Parallel analyses were performed for comparison on Lacerta laevis specimens. Karyological and molecular studies support the morphological and ethological evidence indicating the speci¢c separation between Lacerta laevis and Lacerta kulzeri. In the Lacerta kulzeri complex, chromosomal analysis substantiated an interpopulation di¡erentiation roughly along a north^south trend, mainly regarding the sex chromosome morphology and heterochromatin. The cytochrome b and 12S rRNA gene analyses showed minor genetic di¡erences that were considerably smaller than those commonly found in genetically isolated populations. The L. kulzeri populations from Barouk, Druze and Hermon show a mean genetic distance that, in other saurians, characterises subspecies. The conditions found in L. laevis and L. kulzeri are reminiscent of King's model of chromosomal primary allopatry and support the hypothesis that in these lacertid lizards chromosome variations can become ¢xed before the accumulation of the genetic mutations

How does risk flow in the credit default swap market?

We develop a framework to analyse the credit default swap (CDS) market as a network of risk transfers among counterparties. From a theoretical perspective, we introduce the notion of flow-of-risk and provide sufficient conditions for a bow-tie network architecture to endogenously emerge as a result of intermediation. This architecture shows three distinct sets of counterparties: (i) Ultimate Risk Sellers (URS), (ii) Dealers (indirectly connected to each other), (iii) Ultimate Risk Buyers (URB). We show that the probability of widespread distress due to counterparty risk is higher in a bow-tie architecture than in more fragmented network structures. Empirically, we analyse a unique global dataset of bilateral CDS exposures on major sovereign and financial reference entities in 2011–2014. We find the presence of a bow-tie network architecture consistently across both reference entities and time, and that the flow-of-risk originates from a large number of URSs (e.g. hedge funds) and ends up in a few leading URBs, most of which are non-banks (in particular asset managers). Finally, the analysis of the CDS portfolio composition of the URBs shows a high level of concentration: in particular, the top URBs often show large exposures to potentially correlated reference entities