Paper on color patterns in clownfishes

New paper by Salis et al. on “Developmental and comparative transcriptomic identification of iridophore contribution to white barring in clownfish” in Pigment Cell Melanoma Res.

Abstract: Actinopterygian fishes harbor at least eight distinct pigment cell types, leading to a fascinating diversity of colors. Among this diversity, the cellular origin of the white color appears to be linked to several pigment cell types such as iridophores or leucophores. We used the clownfish Amphiprion ocellaris, which has a color pattern consisting of white bars over a darker body, to characterize the pigment cells that underlie the white hue. We observe by electron microscopy that cells in white bars are similar to iridophores. In addition, the transcriptomic signature of clownfish white bars exhibits similarities with that of zebrafish iridophores. We further show by pharmacological treatments that these cells are necessary for the white color. Among the top differentially expressed genes in white skin, we identified several genes (fhl2a, fhl2b, saiyan, gpnmb, and apoD1a) and show that three of them are expressed in iridophores. Finally, we show by CRISPR/Cas9 mutagenesis that these genes are critical for iridophore development in zebrafish. Our analyses provide clues to the genomic underpinning of color diversity and allow identification of new iridophore genes in fish.

Paper on phylogenetic turnover in tetrapods

New paper by Saladin et al. on “Environment and evolutionary history shape phylogenetic turnover in European tetrapods” published in Nature Comm.

Abstract: Phylogenetic turnover quantifies the evolutionary distance among species assemblages and iscentral to understanding the main drivers shaping biodiversity. It is affected both by geo-graphic and environmental distance between sites. Therefore, analyzing phylogenetic turn-over in environmental space requires removing the effect of geographic distance. Here, weapply a novel approach by deciphering phylogenetic turnover of European tetrapods inenvironmental space after removing geographic land distance effects. We demonstrate thatphylogenetic turnover is strongly structured in environmental space, particularly in ecto-thermic tetrapods, and is well explained by macroecological characteristics such as nichesize, species richness and relative phylogenetic diversity. In ectotherms, rather recent evo-lutionary processes were important in structuring phylogenetic turnover along environmentalgradients. In contrast, early evolutionary processes had already shaped the current structureof phylogenetic turnover in endotherms. Our approach enables the disentangling of theidiosyncrasies of evolutionary processes such as the degree of niche conservatism anddiversification rates in structuring biodiversity.

Paper on coevolution database

Paper by Meyer et al on “​CoevDB: a database of intramolecular coevolution among protein-coding genes of the bony vertebrates” in Nucleic Acid Research.

Abstract: The study of molecular coevolution, due to its potential to identify gene regions under functional or structural constraints, has recently been subject to numerous scientific inquiries. Particular efforts have been conducted to develop methods predicting the presence of coevolution in molecular sequences. Among these methods, a few aim to model the underlying evolutionary process of coevolution, which enable to differentiate the shared history of genes to coevolution and thus improve their accuracy. However, the usage of such methods remains sparse due to their expensive computational cost and the lack of resources alleviating this issue. Here we present CoevDB (http://phylodb.unil.ch/CoevDB), a database containing the result of a large-scale analysis of intramolecular coevolution of 8201 protein-coding genes of bony vertebrates. The web interface of CoevDB gives access to the results to 800 millions of statistical tests corresponding to all the pairs of sites analyzed. Several type of queries enable users to explore the database by either targeting specific genes or by discovering genes having promising estimations of coevolution.

Paper on evolution of New World monkes

New paper by Silvestro et al on “Early Arrival and Climatically-Linked Geographic Expansion of New World Monkeys from Tiny African Ancestors” in Syst Biol.

Abstract: New World Monkeys (NWM) (platyrrhines) are one of the most diverse groups of primates, occupying today a wide range of ecosystems in the American tropics and exhibiting large variations in ecology, morphology, and behavior. Although the relationships among the almost 200 living species are relatively well understood, we lack robust estimates of the timing of origin, ancestral morphology, and geographic range evolution of the clade. Herein, we integrate paleontological and molecular evidence to assess the evolutionary dynamics of extinct and extant platyrrhines. We develop novel analytical frameworks to infer the evolution of body mass, changes in latitudinal ranges through time, and species diversification rates using a phylogenetic tree of living and fossil taxa. Our results show that platyrrhines originated 5–10 million years earlier than previously assumed, dating back to the Middle Eocene. The estimated ancestral platyrrhine was small—weighing 0.4 kg—and matched the size of their presumed African ancestors. As the three platyrrhine families diverged, we recover a rapid change in body mass range. During the Miocene Climatic Optimum, fossil diversity peaked and platyrrhines reached their widest latitudinal range, expanding as far South as Patagonia, favored by warm and humid climate and the lower elevation of the Andes. Finally, global cooling and aridification after the middle Miocene triggered a geographic contraction of NWM and increased their extinction rates. These results unveil the full evolutionary trajectory of an iconic and ecologically important radiation of monkeys and showcase the necessity of integrating fossil and molecular data for reliably estimating evolutionary rates and trends.