Rémi's new study about genomics of carnivores based on roadkill samples is finally published in eLife after using their new pre-print review system. In this paper, we generated two reference genomes using hybrid Nanopore/Illumina sequencing to study the genetic differentiation between the allopatric populations of aardwolf (Proteles cristatus) and bat-eared fox (Otocyon megalotis). First, we estimated the genetic diversity among carnivores for the COX1 and CYTB mitochondrial

Together with Vincent Ranwez and Nathalie Chantret, Frédéric participated in the writing of a book chapter on the practical use our multiple alignement program MACSE for protein-coding sequences. This chapter presents a practical overview and guidelines on the use of MACSE v2 and its integration into bioinformatic pipelines for handling large phylogenomic datasets. In particular we provide a detailed description of the OMM_MACSE pipeline that can be used as a singularity cont

Sérgio's third PhD paper on comparative masticatory myology in anteaters and its implications for interpreting morphological convergence in myrmecophagous placentals has just been published in PeerJ (https://peerj.com/articles/9690/). This paper is based on both classical and digital dissections using contrast-enhanced µ-CT scanning of masticatory muscles on heads of the pygmy (Cyclopes didactylus), collared (Tamandua tetradactyla) and giant (Myrmecophaga tridactyla) anteater

Together with Céline Scornavacca and Nicolas Galtier from the Institut des Sciences de l'Evolution de Montpellier, Frédéric edited the first Open Access book on phylogenomics entitled "Phylogenetics in the Genomic Era" (https://hal.inria.fr/PGE/). The book contains 27 chapters covering various aspects of phylogenomics, from concepts and algorithms to programs and applications. The full book is freely available as a single pdf or can be downloaded chapter by chapter. We're ver

Rémi's first PhD paper describing the MitoFinder bioinformatic pipeline designed to automatically extract mitogenomic signal from genomic data has been published in Molecular Ecology Resources. MitoFinder software can be downloaded from GitHub (https://github.com/RemiAllio/MitoFinder). We illustrated MitoFinder efficiency with ant UCE libraries but it also works well with other type of capture data in which numerous off-target reads are sequenced, as well as with RNAseq trans

The results of the vertebrate microbiome project in collaboration with Rob Knight's lab at the University of California in San Diego are finally being published in mBio. This paper is based on comparisons of the gut microbiomes of over 900 vertebrate species. We found that not only do birds and bats have more similar gut microbiome compositions, but they seem to be similar in how they change across host evolution compared to nonflying mammals. While most mammal gut microbiome

Sérgio's second PhD paper on skull shape variation in extant pangolins and its implications for systematics just appeared in the Zoological Journal of the Linnean Society (https://doi.org/10.1093/zoolinnean/zlz096). This paper is based on geometric morphometrics analyses of 243 museum specimens from the eight extant species of pangolins. Our results shed light on the morphological diversity of the skull of these enigmatic myrmecophagous mammals and confirm the genus-level cla

We just published an updated version our OrthoMaM database of mammalian orthologs in Molecular Biology and Evolution (doi:10.1093/molbev/msz015). The new OMM v10 version more than doubles the number of species for which curated alignments of CDSs and exons and associated ML trees could be downloaded. It now includes alignments and ML trees of 14,509 CDSs and 6888 exons for 116 mammal species and can be accessed through a completely revamped web interface: http://www.orthomam.

Chris and Frédéric participated in a study on the molecular evolution and loss of function of the ameloblast-associated gene ODAM in mammals published in BMC Evolutionary Biology (doi:10.1186/s12862-019-1359-6). In this study, we discovered inactivating mutations in the ODAM gene in all species of placental mammals that either lack teeth or lack enamel on their teeth. Surprisingly, ODAM is also inactivated in all toothed whales that were examined. We hypothesize that ODAM ina

Frédéric wrote a short scientific outreach article in French in Médecine/Sciences (doi:10.1051/medsci/2018317) giving some general context on our recent study on the evolution of chitinase genes in placental mammals published last year in Science Advances (doi:10.1126/sciadv.aar6478). A first paper in French for Chris! #Anteaters #Aardvark #Armadillos #Microbiome #Publication #Collaboration #Pseudogenes

So proud of Sérgio's first PhD paper on the evolution of mandibular innervation after tooth regression in placental mammals just published in Current Biology (https://doi.org/10.1016/j.cub.2018.12.023). This paper is the result of countless hours of work by Sergio to segment the numerous micro-CT scans of museum specimens included in this study. Huge congrats! #Anteaters #Aardvark #Armadillos #Microbiome #Publication #Collaboration #Pseudogenes

We published an updated and augmented version our multiple alignement program MACSE accounting for frameshifts in protein-coding sequences in Molecular Biology and Evolution (doi.org/10.1093/molbev/msy159). This new MACSE v2 version is enriched by a series of subprograms aimed at facilitating the production and handling of multiple alignments of protein-coding sequences. In order to make the program more accessible, we now provide a graphical user interface (GUI) facilitating

Our study on the evolution of chitinase genes and pseudogenes in placental mammal genomes is published in Science Advances (doi:10.1126/sciadv.aar6478). The stunning picture of a spectral tarsier kindly provided by Quentin Martinez (http://www.quentinmartinez.com/) to illustrate our study was featured on the journal website and has been also used in numerous press outlets highlighting our results. Associated media coverage: Berkeley News: What we inherited from our bug-eating

Our paper on the effect of captivity on the composition of mammalian gut microbiomes led by Valerie McKenzie has been published in Integrative and Comparative Biology (doi:10.1093/icb/icx090). The amazing picture of a giant anteater kindly provided by Gerardo Ceballos to illustrate our study has been selected as the cover picture of the journal issue. Awesome! #Anteaters #Aardvark #Armadillos #Microbiome #Fieldwork #Publication #Collaboration