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Article ; Online: Divergence and gene flow history at two large chromosomal inversions underlying ecotype differentiation in the long-snouted seahorse.

Meyer, Laura / Barry, Pierre / Riquet, Florentine / Foote, Andrew / Der Sarkissian, Clio / Cunha, Regina L / Arbiol, Christine / Cerqueira, Frédérique / Desmarais, Erick / Bordes, Anaïs / Bierne, Nicolas / Guinand, Bruno / Gagnaire, Pierre-Alexandre

Molecular ecology

2024 , Page(s) e17277

Abstract: Chromosomal inversions can play an important role in divergence and reproductive isolation by building and maintaining distinct allelic combinations between evolutionary lineages. Alternatively, they can take the form of balanced polymorphisms that ... ...

Abstract	Chromosomal inversions can play an important role in divergence and reproductive isolation by building and maintaining distinct allelic combinations between evolutionary lineages. Alternatively, they can take the form of balanced polymorphisms that segregate within populations until one arrangement becomes fixed. Many questions remain about how inversion polymorphisms arise, how they are maintained over the long term, and ultimately, whether and how they contribute to speciation. The long-snouted seahorse (Hippocampus guttulatus) is genetically subdivided into geographic lineages and marine-lagoon ecotypes, with shared structural variation underlying lineage and ecotype divergence. Here, we aim to characterize structural variants and to reconstruct their history and suspected role in ecotype formation. We generated a near chromosome-level genome assembly and described genome-wide patterns of diversity and divergence through the analysis of 112 whole-genome sequences from Atlantic, Mediterranean, and Black Sea populations. By also analysing linked-read sequencing data, we found evidence for two chromosomal inversions that were several megabases in length and showed contrasting allele frequency patterns between lineages and ecotypes across the species range. We reveal that these inversions represent ancient intraspecific polymorphisms, one likely being maintained by divergent selection and the other by pseudo-overdominance. A possible selective coupling between the two inversions was further supported by the absence of specific haplotype combinations and a putative functional interaction between the two inversions in reproduction. Lastly, we detected gene flux eroding divergence between inverted alleles at varying levels for the two inversions, with a likely impact on their dynamics and contribution to divergence and speciation.
Language	English
Publishing date	2024-01-27
Publishing country	England
Document type	Journal Article
ZDB-ID	1126687-9
ISSN	1365-294X ; 0962-1083
ISSN (online)	1365-294X
ISSN	0962-1083
DOI	10.1111/mec.17277
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Article ; Online: Advancing responsible genomic analyses of ancient mollusc shells.

Martin-Roy, Raphaël / Thyrring, Jakob / Mata, Xavier / Bangsgaard, Pernille / Bennike, Ole / Christiansen, Gunvor / Funder, Svend / Gotfredsen, Anne Birgitte / Gregersen, Kristian Murphy / Hansen, Camilla Haarby / Ilsøe, Peter Carsten / Klassen, Lutz / Kristensen, Inge Kjær / Ravnholt, Gerd Bindesbøl / Marin, Frédéric / Der Sarkissian, Clio

PloS one

2024 Volume 19, Issue 5, Page(s) e0302646

Abstract: The analysis of the DNA entrapped in ancient shells of molluscs has the potential to shed light on the evolution and ecology of this very diverse phylum. Ancient genomics could help reconstruct the responses of molluscs to past climate change, pollution, ...

Abstract	The analysis of the DNA entrapped in ancient shells of molluscs has the potential to shed light on the evolution and ecology of this very diverse phylum. Ancient genomics could help reconstruct the responses of molluscs to past climate change, pollution, and human subsistence practices at unprecedented temporal resolutions. Applications are however still in their infancy, partly due to our limited knowledge of DNA preservation in calcium carbonate shells and the need for optimized methods for responsible genomic data generation. To improve ancient shell genomic analyses, we applied high-throughput DNA sequencing to 27 Mytilus mussel shells dated to ~111-6500 years Before Present, and investigated the impact, on DNA recovery, of shell imaging, DNA extraction protocols and shell sub-sampling strategies. First, we detected no quantitative or qualitative deleterious effect of micro-computed tomography for recording shell 3D morphological information prior to sub-sampling. Then, we showed that double-digestion and bleach treatment of shell powder prior to silica-based DNA extraction improves shell DNA recovery, also suggesting that DNA is protected in preservation niches within ancient shells. Finally, all layers that compose Mytilus shells, i.e., the nacreous (aragonite) and prismatic (calcite) carbonate layers, with or without the outer organic layer (periostracum) proved to be valuable DNA reservoirs, with aragonite appearing as the best substrate for genomic analyses. Our work contributes to the understanding of long-term molecular preservation in biominerals and we anticipate that resulting recommendations will be helpful for future efficient and responsible genomic analyses of ancient mollusc shells.
MeSH term(s)	Animals ; Animal Shells ; Genomics/methods ; Mollusca/genetics ; X-Ray Microtomography ; Calcium Carbonate ; High-Throughput Nucleotide Sequencing ; Fossils
Chemical Substances	Calcium Carbonate (H0G9379FGK)
Language	English
Publishing date	2024-05-06
Publishing country	United States
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	2267670-3
ISSN	1932-6203 ; 1932-6203
ISSN (online)	1932-6203
ISSN	1932-6203
DOI	10.1371/journal.pone.0302646
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Article: Ancient Metagenomic Studies: Considerations for the Wider Scientific Community.

Der Sarkissian, Clio / Velsko, Irina M / Fotakis, Anna K / Vågene, Åshild J / Hübner, Alexander / Fellows Yates, James A

mSystems

2021 Volume 6, Issue 6, Page(s) e0131521

Abstract: Like modern metagenomics, ancient metagenomics is a highly data-rich discipline, with the added challenge that the DNA of interest is degraded and, depending on the sample type, in low abundance. This requires the application of specialized measures ... ...

Abstract	Like modern metagenomics, ancient metagenomics is a highly data-rich discipline, with the added challenge that the DNA of interest is degraded and, depending on the sample type, in low abundance. This requires the application of specialized measures during molecular experiments and computational analyses. Furthermore, researchers often work with finite sample sizes, which impedes optimal experimental design and control of confounding factors, and with ethically sensitive samples necessitating the consideration of additional guidelines. In September 2020, early career researchers in the field of ancient metagenomics met (Standards, Precautions & Advances in Ancient Metagenomics 2 [SPAAM2] community meeting) to discuss the state of the field and how to address current challenges. Here, in an effort to bridge the gap between ancient and modern metagenomics, we highlight and reflect upon some common misconceptions, provide a brief overview of the challenges in our field, and point toward useful resources for potential reviewers and newcomers to the field.
Language	English
Publishing date	2021-12-21
Publishing country	United States
Document type	Journal Article
ISSN	2379-5077
ISSN	2379-5077
DOI	10.1128/msystems.01315-21
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Article ; Online: metaBIT, an integrative and automated metagenomic pipeline for analysing microbial profiles from high-throughput sequencing shotgun data.

Louvel, Guillaume / Der Sarkissian, Clio / Hanghøj, Kristian / Orlando, Ludovic

Molecular ecology resources

2016 Volume 16, Issue 6, Page(s) 1415–1427

Abstract: Micro-organisms account for most of the Earth's biodiversity and yet remain largely unknown. The complexity and diversity of microbial communities present in clinical and environmental samples can now be robustly investigated in record times and prices ... ...

Abstract	Micro-organisms account for most of the Earth's biodiversity and yet remain largely unknown. The complexity and diversity of microbial communities present in clinical and environmental samples can now be robustly investigated in record times and prices thanks to recent advances in high-throughput DNA sequencing (HTS). Here, we develop metaBIT, an open-source computational pipeline automatizing routine microbial profiling of shotgun HTS data. Customizable by the user at different stringency levels, it performs robust taxonomy-based assignment and relative abundance calculation of microbial taxa, as well as cross-sample statistical analyses of microbial diversity distributions. We demonstrate the versatility of metaBIT within a range of published HTS data sets sampled from the environment (soil and seawater) and the human body (skin and gut), but also from archaeological specimens. We present the diversity of outputs provided by the pipeline for the visualization of microbial profiles (barplots, heatmaps) and for their characterization and comparison (diversity indices, hierarchical clustering and principal coordinates analyses). We show that metaBIT allows an automatic, fast and user-friendly profiling of the microbial DNA present in HTS shotgun data sets. The applications of metaBIT are vast, from monitoring of laboratory errors and contaminations, to the reconstruction of past and present microbiota, and the detection of candidate species, including pathogens.
MeSH term(s)	Automation ; Computational Biology/methods ; Environmental Microbiology ; High-Throughput Nucleotide Sequencing/methods ; Metagenomics/methods ; Microbiota ; Sequence Analysis, DNA/methods
Language	English
Publishing date	2016-11
Publishing country	England
Document type	Evaluation Studies ; Journal Article
ZDB-ID	2406833-0
ISSN	1755-0998 ; 1755-098X
ISSN (online)	1755-0998
ISSN	1755-098X
DOI	10.1111/1755-0998.12546
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Article ; Online: Major transitions in human evolution revisited: a tribute to ancient DNA.

Ermini, Luca / Der Sarkissian, Clio / Willerslev, Eske / Orlando, Ludovic

Journal of human evolution

2015 Volume 79, Page(s) 4–20

Abstract: The origin and diversification of modern humans have been characterized by major evolutionary transitions and demographic changes. Patterns of genetic variation within modern populations can help with reconstructing this ∼200 thousand year-long ... ...

Abstract	The origin and diversification of modern humans have been characterized by major evolutionary transitions and demographic changes. Patterns of genetic variation within modern populations can help with reconstructing this ∼200 thousand year-long population history. However, by combining this information with genomic data from ancient remains, one can now directly access our evolutionary past and reveal our population history in much greater detail. This review outlines the main recent achievements in ancient DNA research and illustrates how the field recently moved from the polymerase chain reaction (PCR) amplification of short mitochondrial fragments to whole-genome sequencing and thereby revisited our own history. Ancient DNA research has revealed the routes that our ancestors took when colonizing the planet, whom they admixed with, how they domesticated plant and animal species, how they genetically responded to changes in lifestyle, and also, which pathogens decimated their populations. These approaches promise to soon solve many pending controversies about our own origins that are indecipherable from modern patterns of genetic variation alone, and therefore provide an extremely powerful toolkit for a new generation of molecular anthropologists.
MeSH term(s)	Animals ; Biological Evolution ; DNA/analysis ; DNA/genetics ; Fossils ; Genome, Human/genetics ; Genomics ; Hominidae/genetics ; Humans ; Paleontology/methods
Chemical Substances	DNA (9007-49-2)
Language	English
Publishing date	2015-02
Publishing country	England
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	120141-4
ISSN	1095-8606 ; 0047-2484
ISSN (online)	1095-8606
ISSN	0047-2484
DOI	10.1016/j.jhevol.2014.06.015
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Article ; Online: No particular genomic features underpin the dramatic economic consequences of 17

Seguin-Orlando, Andaine / Costedoat, Caroline / Der Sarkissian, Clio / Tzortzis, Stéfan / Kamel, Célia / Telmon, Norbert / Dalén, Love / Thèves, Catherine / Signoli, Michel / Orlando, Ludovic

iScience

2021 Volume 24, Issue 4, Page(s) 102383

Abstract: ... The ... ...

Abstract	The 17
Language	English
Publishing date	2021-03-31
Publishing country	United States
Document type	Journal Article
ISSN	2589-0042
ISSN (online)	2589-0042
DOI	10.1016/j.isci.2021.102383
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Article ; Online: Heterogeneous Hunter-Gatherer and Steppe-Related Ancestries in Late Neolithic and Bell Beaker Genomes from Present-Day France.

Seguin-Orlando, Andaine / Donat, Richard / Der Sarkissian, Clio / Southon, John / Thèves, Catherine / Manen, Claire / Tchérémissinoff, Yaramila / Crubézy, Eric / Shapiro, Beth / Deleuze, Jean-François / Dalén, Love / Guilaine, Jean / Orlando, Ludovic

Current biology : CB

2021 Volume 31, Issue 5, Page(s) 1072–1083.e10

Abstract: The transition from the Late Neolithic to the Bronze Age has witnessed important population and societal changes in western Europe. ...

Abstract	The transition from the Late Neolithic to the Bronze Age has witnessed important population and societal changes in western Europe.
MeSH term(s)	DNA, Ancient ; Europe ; France ; Genome, Human ; Genomics ; History, Ancient ; Human Migration ; Humans
Chemical Substances	DNA, Ancient
Language	English
Publishing date	2021-01-12
Publishing country	England
Document type	Historical Article ; Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	1071731-6
ISSN	1879-0445 ; 0960-9822
ISSN (online)	1879-0445
ISSN	0960-9822
DOI	10.1016/j.cub.2020.12.015
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Article: Assessing the predictive taxonomic power of the bony labyrinth 3D shape in horses, donkeys and their F1-hybrids

Clavel, Pierre / Dumoncel, Jean / Der Sarkissian, Clio / Seguin-Orlando, Andaine / Calvière-Tonasso, Laure / Schiavinato, Stephanie / Chauvey, Lorelei / Perdereau, Aude / Aury, Jean-Marc / Wincker, Patrick / Onar, Vedat / Clavel, Benoît / Lepetz, Sébastien / Braga, José / Orlando, Ludovic

Journal of archaeological science. 2021 July, v. 131

2021

Abstract: Horses and donkeys have had a far-reaching impact on human history, providing mechanical power for agriculture and transportation. Their F1-hybrids, especially mules, have also been of considerable importance due to their exceptional strength, endurance ... ...

Abstract	Horses and donkeys have had a far-reaching impact on human history, providing mechanical power for agriculture and transportation. Their F1-hybrids, especially mules, have also been of considerable importance due to their exceptional strength, endurance and resistance. The reconstruction of the respective role that horses, donkeys and mules played in past societies requires prior identification of their osseous elements in archaeological assemblages. This, however, remains difficult on the basis of morphological data alone and in the absence of complete skeletal elements. While DNA sequencing provides almost certain identification success, this approach requires dedicated infrastructure and sufficient ancient DNA (aDNA) preservation. Here, we assessed the performance of a cost-effective alternative approach based on geometric morphometric (GMM) analysis of the bony labyrinth, a structure carried within the petrosal bone. This extremely compact osseous structure provides good aDNA preservation and is frequently found in archaeological assemblages. To assess the GMM performance, we first used High-throughput DNA sequencing to identify 41 horses, 24 donkeys, 36 mules and one hinny from 11 archaeological sites from France and Turkey spanning different time periods. This provided a panel of 102 ancient equine remains for micro-computed tomography (microCT) and GMM assessment of the variation of the bony labyrinth shape, including the cochlea and the semicircular canals. Our new method shows good-to-excellent prediction rates (85.7%–95.2%) for the identification of species and hybrids when considering the cochlea and semicircular canals together. It provides a cheap, non-destructive alternative to aDNA for the taxonomic identification of past equine assemblages.
Keywords	DNA ; archaeology ; cost effectiveness ; geometry ; hinnies ; horses ; infrastructure ; micro-computed tomography ; morphometry ; prediction ; species identification ; transportation ; France
Language	English
Dates of publication	2021-07
Publishing place	Elsevier Ltd
Document type	Article
Note	NAL-AP-2-clean
ZDB-ID	1468969-8
ISSN	0305-4403
ISSN	0305-4403
DOI	10.1016/j.jas.2021.105383
Database	NAL-Catalogue (AGRICOLA)

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Article ; Online: Combining bleach and mild predigestion improves ancient DNA recovery from bones.

Boessenkool, Sanne / Hanghøj, Kristian / Nistelberger, Heidi M / Der Sarkissian, Clio / Gondek, Agata T / Orlando, Ludovic / Barrett, James H / Star, Bastiaan

Molecular ecology resources

2017 Volume 17, Issue 4, Page(s) 742–751

Abstract: The feasibility of genome-scale studies from archaeological material remains critically dependent on the ability to access endogenous, authentic DNA. In the majority of cases, this represents a few per cent of the DNA extract, at most. A number of ... ...

Abstract	The feasibility of genome-scale studies from archaeological material remains critically dependent on the ability to access endogenous, authentic DNA. In the majority of cases, this represents a few per cent of the DNA extract, at most. A number of specific pre-extraction protocols for bone powder aimed to improve ancient DNA recovery before library amplification have recently been developed. Here, we test the effects of combining two of such protocols, a bleach wash and a predigestion step, on 12 bone samples of Atlantic cod and domestic horse aged 750-1350 cal. years before present. Using high-throughput sequencing, we show that combined together, bleach wash and predigestion consistently yield DNA libraries with higher endogenous content than either of these methods alone. Additionally, the molecular complexity of these libraries is improved and endogenous DNA templates show larger size distributions. Other library characteristics, such as DNA damage profiles or the composition of microbial communities, are little affected by the pre-extraction protocols. Application of the combined protocol presented in this study will facilitate the genetic analysis of an increasing number of ancient remains and will reduce the cost of whole-genome sequencing.
Language	English
Publishing date	2017-07
Publishing country	England
Document type	Journal Article
ZDB-ID	2406833-0
ISSN	1755-0998 ; 1755-098X
ISSN (online)	1755-0998
ISSN	1755-098X
DOI	10.1111/1755-0998.12623
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Article: Vibrio tapetis

Dias, Graciela M / Bidault, Adeline / Le Chevalier, Patrick / Choquet, Gwenaëlle / Der Sarkissian, Clio / Orlando, Ludovic / Medigue, Claudine / Barbe, Valerie / Mangenot, Sophie / Thompson, Cristiane C / Thompson, Fabiano L / Jacq, Annick / Pichereau, Vianney / Paillard, Christine

Frontiers in microbiology

2018 Volume 9, Page(s) 227

Abstract: The Brown Ring Disease (BRD) caused high mortality rates since 1986 in the Manila ... ...

Abstract	The Brown Ring Disease (BRD) caused high mortality rates since 1986 in the Manila clam
Language	English
Publishing date	2018-02-19
Publishing country	Switzerland
Document type	Journal Article
ZDB-ID	2587354-4
ISSN	1664-302X
ISSN	1664-302X
DOI	10.3389/fmicb.2018.00227
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