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Sérgio's last PhD chapter on skull modularity in ant-eating placental mammals published!

Frederic Delsuc

Jun 30
1 min

Sérgio's last PhD chapter on skull modularity in ant-eating placental mammals published!

Sérgio's fourth and final PhD paper on modularity of the skull in convergently evolved myrmecophagous placental mammals has just been published in BMC Ecology and Evolution (doi:10.1186/s12862-022-02030-9). In this paper, we show that extreme rostrum elongation and tooth loss in myrmecophagid anteaters have resulted in a shift in intermodule correlations in the proximal region of the rostrum. In contrast, the similarly toothless pangolins show a weaker correlation between the

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Frédéric appointed as Community Gateway advisor on Evolution and Ecology at Open Research Europe

Frederic Delsuc

Jun 15
1 min

Frédéric appointed as Community Gateway advisor on Evolution and Ecology at Open Research Europe

Frédéric accepted an invitation to serve as a Community Gateway advisor on Evolution and Ecology at Open Research Europe (https://open-research-europe.ec.europa.eu/gateways/evolution-and-ecology/). ORE is a new open access journal created by the European Commission ensuring the free publication with open peer review of research stemming from Horizon 2020, Horizon Europe, and Euratom funding across all subject areas. The newly created Community Gateways are designed to attrac

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New publication by Sophie with members of the Animal Microbiome Research Group

Frederic Delsuc

Feb 12
1 min

New publication by Sophie with members of the Animal Microbiome Research Group

Following from her participation to the 2nd annual Animal Microbiome Research Group (AMRG) virtual meeting (https://amrg.mystrikingly.com/), Sophie, together with two other fellow early career animal microbiome researchers, participated in the publication of a meeting report in Evolutionary Anthropology. In addition to describing the latest advances in animal microbiome research presented at the meeting, the paper also exposes the actions undertaken to grow and maintain this

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First publication of the European Reference Genome Atlas (ERGA) consortium

Frederic Delsuc

Jan 23
1 min

First publication of the European Reference Genome Atlas (ERGA) consortium

As a member of the recently created European Reference Genome Atlas (ERGA), Frédéric participated to the first paper of the consortium published in Trends in Ecology and Evolution (doi:10.1016/j.tree.2021.11.008). The ERGA is a pan-European scientific initiative aimed at generating high-quality complete genome resources for eukaryote species of continental Europe. This first consortium paper highlights the usefulness of producing high-quality complete genome resources in larg

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Chris' new paper on gene loss in the melatonin pathway published in Open Research Europe

Frederic Delsuc

Dec 12, 2021
2 min

Chris' new paper on gene loss in the melatonin pathway published in Open Research Europe

Chris' study on the molecular evolution and loss of function of the genes involved in the melatonin pathway in vertebrates has been published in Open Research Europe (doi:10.12688/openreseurope.13795.1) a new gold open access journal edited by the European Commission with a transparent process of peer-review. In this work, we studied the molecular evolution of genes involved in the synthesis (AANAT, ASMT) and signaling (MTNR1A, MTNR1B) of melatonin, a hormone secreted by the

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High molecular weight bacterial DNA extraction protocol from fecal samples shared on Protocols.io

Frederic Delsuc

Jun 27, 2021
1 min

High molecular weight bacterial DNA extraction protocol from fecal samples shared on Protocols.io

We are happy to share our optimized protocol for extracting high molecular weight bacterial DNA from field-collected fecal samples. This protocol has been designed to obtain fecal DNA suitable for long read metagenomic sequencing on the portable MinION instrument enabling field-sequencing of fecal samples. Try it on your own samples! Magdeleine A., Tilak M.-K., Teullet S. & Delsuc F. (2021). High molecular weight bacterial DNA extraction from field-collected fecal samples pre

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Rémi's roadkill genomics paper published in eLife!

Frederic Delsuc

Mar 15, 2021
2 min

Rémi's roadkill genomics paper published in eLife!

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

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Book chapter describing the OMM_MACSE pipeline

Frederic Delsuc

Jan 12, 2021
1 min

Book chapter describing the OMM_MACSE pipeline

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

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Sérgio's new paper on comparative myology of the masticatory apparatus in anteaters

Frederic Delsuc

Sep 4, 2020
1 min

Sérgio's new paper on comparative myology of the masticatory apparatus in anteaters

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

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New Open Access book "Phylogenetics in the Genomic Era" released

Frederic Delsuc

Apr 14, 2020
1 min

New Open Access book "Phylogenetics in the Genomic Era" released

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

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Rémi's MitoFinder paper published in Molecular Ecology Resources

Frederic Delsuc

Apr 8, 2020
1 min

Rémi's MitoFinder paper published in Molecular Ecology Resources

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

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New paper on the evolution the vertebrate gut microbiome out in mBio!

Frederic Delsuc

Jan 7, 2020
2 min

New paper on the evolution the vertebrate gut microbiome out in mBio!

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

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New paper by Sérgio on skull shape variation in pangolins

Frederic Delsuc

Nov 9, 2019
1 min

New paper by Sérgio on skull shape variation in pangolins

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

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Protocol for sequencing mammalian roadkill tissues with the MinION shared on Protocols.io

Frederic Delsuc

Aug 8, 2019
1 min

Protocol for sequencing mammalian roadkill tissues with the MinION shared on Protocols.io

We are happy to share our optimized protocol for sequencing long reads from mammalian roadkill tissues with the Oxford Nanopore Technology (ONT). This protocol was specifically developed to optimize DNA extraction and sequencing roadkill tissues containing necrotized cells and impurities that result in DNA degradation. First, we observed that DNA preservation was generally better in RNAlater than in 95% EtOH preserved tissues. Second, we found that physically removing necroti

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A major update of our OrthoMaM database of orthologous mammalian markers

Frederic Delsuc

Feb 5, 2019
1 min

A major update of our OrthoMaM database of orthologous mammalian markers

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://orthomam.mbb.

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New paper on the molecular evolution and loss of function of the ODAM gene in mammals

Frederic Delsuc

Jan 24, 2019
1 min

New paper on the molecular evolution and loss of function of the ODAM gene in mammals

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

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Outreach article in French on the evolution of chitinase genes in placental mammals

Frederic Delsuc

Jan 23, 2019
1 min

Outreach article in French on the evolution of chitinase genes in placental mammals

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! Citation: Delsuc F., Emerling C.A. & Nachman M.W. (2019). Les chitinases, témoins de la radiation des mammifères placentaires. Médecine/Sciences 35:12-15. doi

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Sérgio's first PhD paper published in Current Biology!

Frederic Delsuc

Jan 17, 2019
1 min

Sérgio's first PhD paper published in Current Biology!

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! Citation: Ferreira-Cardoso S., Delsuc F. & Hautier L. (2019). Evolutionary tinkering of the mandibular canal linked t

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New updated version of our frameshift-aware alignment MACSE program

Frederic Delsuc

Oct 1, 2018
1 min

New updated version of our frameshift-aware alignment MACSE program

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

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Study on the evolution of chitinase genes in placental mammals published in Science Advances

Frederic Delsuc

May 16, 2018
1 min

Study on the evolution of chitinase genes in placental mammals published in Science Advances

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. Citation: Emerling C.A., Delsuc F. & Nachman M.W. (2018). Chitinase genes (CHIA

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