Publications

2024

Mathon et al (2024) 3D conservation planning of multiple fish biodiversity metrics achieves deep-sea 30x30 CBD target.  Conservation Biology

Vilcot M, Faure N, Andrews KR, Bowen WB, Leprieur F, Manel  S (2024) Neutral processes and taxonomic scale drive beta species-genetic diversity correlations in a submesophotic tropical reef fish. Molecular Ecology. 

Mace B et al. (2024) The Tree of Life eDNA metabarcoding reveals a similar taxonomic richness but dissimilar evolutionary lineages between seaports and marine reserves. Molecular Ecology

Melissa J,  Albouy C,  Bach W, Waldock C, Marques V, Maire E, Juhel JB, Andrello M, Valentini A, Manel S, Dejean T, Mouillot D, Pellissier L (2024) Environmental DNA recovers fish composition turnover of the coral reefs of West Indian Ocean islands. Ecology and Environment.

Sanchez L, Loiseau N, GrahamE, Hautecoeur C, Leprieur F, Manel S, McLean M,  Stuart-Smith R,  Velez L, Mouillot D (2024) Rarity mediates species-specific responses of tropical reef fishes to protection. Ecology Letters.

Andrello M, Manel S (2024) Evaluating different approaches to integrate genome-wide geetic diversity in spatial conservation prirization. Biological Conservation.

Manel S,   Mathon L,  Mouillot D,  Bruno M,  Valentini A,  Lecaillon G,  Gudefin A,  Deter J,  Boissery P, Alicia Dalongeville (2024) Benchmarking fish biodiversity of seaports with eDNA and nearby marine reserves. Conservation Letters. https://conbio.onlinelibrary.wiley.com/doi/full/10.1111/conl.13001

2023

Marques V, Blanchet  S, Loot  G, Miaud  C, Planes S,  Peyran  Claire, Arnal V, Calvet C, Pioch S, Manel S (2023) Optimizing detectability of the endangered fan mussel using eDNA and ddPCR. Ecology and Evolution.

Keggin T, Waldcok C, Skeels A, Hagen O, Albouy C, Manel S, Pellissier L (2023) Diversity across organisational scale emerges through dispersal ability and speciation dynamics in tropical fish. BMC Biology.

Lamperti L, Sanchez T., Si Moussi S, Mouillot D., Albouy C., Fl%uck B., Bruno M., Valentini A., Pellissier L., Manel S.  (2023) New deep learning-based methods for visualizing ecosystem properties using environmental DNA metabarcoding data. Molecular Ecology Resources. 23: 1946-1958.

Manel S., Boulanger E., Benestan  L., Mouillot D., Dalongeville.  (2023) Revisiting long dispersal distance in a coastal marine fish. Ecography. 

 Andrello M, Manel S, Vilcot M, Xuereb A, D'Aloia CC (2023) Benefits of genetic data for spatial conservation planning in coastal habitats. Coastal Futures.

Mathon et al. (2023) The distribution of coastal fish eDNA sequences in the Anthropocene. Global Ecology and Biogeography. 32:1336-1352.

Faure N, Manel S, Macé B, Arnal V, Guellati N, Holon F, Barroil A, Pichot F, Riutort JJ, Inscacco G, Zava B, Mouillot D, Deter J (2023) A quantitative PCR-based environmental DNA assay for the detection of Critically Endangered angel sharks ( Squatina sp.). Aquatic Conservation: Marine and Freshwater Ecosystems. 33: 1088-1097.

Vilcot M, Albouy C, Donati G,  Claverie T, Julius P, Manel S, Pellissier L, Leprieur F (2023) Spatial genetic differentiation correlates with species assemblage turnover across tropical reef fish lineage. Global Ecology and Biogeography.32:535-547.

Duhamet et al. (2023) The global depth range of marine fishes and their genetic coverage for eDNA metabarcoding. Ecology and Evolution.13:e9672.

Dauphin, B., Rellstab, C., Wüest, R.O., Karger, D.N., Holderegger, R., Gugerli, F., and Manel, S. (2023). Re-thinking the environment in landscape genomics. Trends in Ecology & Evolution. 38:261-274.

Benestan, L., Loiseau, N., Guérin, P.-E., Pérez-Ruzafa, A., Forcada, A., Arcas, E., Lenfant, P., Mallol, S., Goñi, R., Velez, L., et al. (2023). Contrasting influence of seascape, space and marine reserves on genomic variation in multiple species. Ecography e06127.

2022

Muff M, Jacquier M, Marques V, Ballesta L, Deter J, Bockel T, Hocdé R, Juhel, JB, Boulanger E, Guellati N, Polanco AF, Valentini A, Dejean T, Manel S, Albouy C, Durville P, Mouillot D, Holon F, Pellissier L. Environmental DNA highlights fish biodiversity in mesophotic ecosystems (2022) Environmental DNA

Polanco F., Andrea; Waldock, Conor; Keggin, Thomas; Marques, Virginie; Rozanski, Romane; Valentini, Alice; Dejean, Tony; Manel, Stephanie; Vermeij, Mark; Albouy, Camille; Pellissier, Loïc, 2022. Ecological indices from environmental DNA to contrast coastal reefs under different anthropogenic pressures. Ecology and Evolution.

Dalongeville, Alicia; Boulanger, Emilie; Marques, Virginie; Charbonnel, Eric; Hartmann, Virginie; Santoni, Marie-Catherine; Deter, Julie; Valentini, Alice; Lenfant, Philippe; Boissery, PIerre; Dejean, Tony; Velez, Laure; Pichot, Franck; Sanchez, Loic; Arnal, Véronique; Bockel, Thomas; Delarue, Gwenaelle; Holon, Florian; Milhau, Tristan; Romant, Lola; Manel, Stephanie; Mouillot, David (2022) Benchmarking eleven biodiversity indicators based on environmental DNA surveys: more diverse functional traits and evolutionary lineages inside marine reserves. Journal of Animal Ecology. 59:2803-2813.

Flück B, Mathon L, Manel S, Valentini A, Dejean T, Albouy C, Mouillot D, Thuiller W, Murienne J, Brosse S, et al. (2022) Applying convolutional neural networks to speed up environmental DNA annotation in a highly diverse ecosystem. Scientific Reports 12:10247.

Walsh CAJ, Momigliano P, Boussarie G, Robbins WD, Bonnin L, Fauvelot C, Kiszka JJ, Mouillot D, Vigliola L, Manel S. (2022) Genomic insights into the historical and contemporary demographics of the grey reef shark. Heredity 128:225-235.

Sanchez, L., Boulanger, E., Arnal, V., Boissery, P., Dalongeville, A., Dejean T., . .Manel S, . Mouillot, D. (2022). Ecological indicators based on quantitative eDNA metabarcoding: the case of marine reserves. Ecological Indicators, 140: 108966. 

Mathon L, Marques V, Mouillot D, Albouy C, Andrello M, Baletaud F, Borrero-Perez GH, Dejean T, Edgar GJ, Grondin J, Guerin PE, Hocdé R, Juhel JB, Kadarusman, Maire E, Marian G, McLean M, Poland AF, Pouyaud L, Stuart-Smith RD, Sugeha HY, Valentini A, Vigliola L, Vimono IB, Pellissier L, Manel S.  (2022) Cross-ocean patterns and processes in fish biodiversity on coral reefs through the lens of eDNA metabarcoding. Proceedings of  the Royal Society B. 289.

Boussarie G, Momigliano P, Robbins WD, Bonnin L, Cornu J-F, Fauvelot C, Kiszka JJ, Manel S, Mouillot D, Vigliola L. (2022) Identifying barriers to gene flow and hierarchical conservation units from seascape genomics: a modelling framework applied to a marine predator. Ecography. 2022:e06158.

Andrello M, D’Aloia C, Dalongeville A, Escalante MA, Guerrero J, Perrier C, Torres-Florez JP, Xuereb A, Manel S (2022) Evolving spatial conservation prioritization with intraspecific genetic data. Trends In Ecology & Evolution 37:553-564.

Tournebize R, Borner L, Manel S, Meynard CN, Vigouroux Y, Crouzillat D, Fournier C, Kassam M, Descombes P, Tranchant-Dubreuil C, et al. (2022) Ecological and genomic vulnerability to climate change across native populations of Robusta coffee (Coffea canephora). Global Change Biology 28:4124-4142.

de Aquino SO, Kiwuka C, Tournebize R, Gain C, Marraccini P, Mariac C, Bethune K, Couderc M, Cubry P, Andrade AC, et al. (2022). Adaptive potential of Coffea canephora from Uganda in response to climate change. Molecular Ecology. 31:1800-1819

Mace B, Hocdé R, Marques V, Guerin PE, Valentini A, Arnal V, Pellissier L, Manel S. (2022)  Evaluating bioinformatics pipelines for population level inference using environmental DNA. Environmental DNA. 

Boulanger E, Benestan L, Guerin P-E, Dalongeville A, Mouillot D, Manel S. (2022) Climate differently influences the genomic patterns of two sympatric marine fish species. Journal of Animal Ecology 91:1180-1195.

2021

Stauffer  et al. (2021) How many replicates to accurately estimate fish biodiversity using environmental DNA on coral reefs. Ecology and Evolution. 11:14630-14643.

Donati G, Zemp N, Manel S, et al . (2021) Species ecology explains the spatial components of genetic diversity in tropical reef fishes. Proceedings of  Royal Society B, 288.

Leigh DM, van Rees CB, Millette KL, Breed MF, Schmidt C, Bertola LD, Hand BK, Hunter ME, Jensen EL, Kershaw F, Liggins , Gordon L,  Manel S, Mergeay J, Miller  JM,  Segelbacher G,  Hoban S,  Paz-Vinas I (2021) Opportunities and challenges of macrogenetic studies. Nature Reviews Genetics. 22:791-807.

Polanco FA, Martinezguerra MM, Marques V, Villa-Navarro F, Perez GHB, Cheutin MC, Dejean T, Hocde R, Juhel JB, Maire E, Manel S, Spescha, Valentini A, Mouillot D, Albouy C, Pellissier  L (2021) Detecting aquatic and terrestrial biodiversity in a tropical estuary using environmental DNA. Biotropica. 53:1606-1619.

Polanco et al. (2021) Comparing the performance of 12S mitochondrial primers for fish environmental DNA across ecosystems. Environmental DNA.

Loiseau et al. (2021) Maximizing regional biodiversity requires a mosaic of protection levels. Plos Biology. 19. e3001195.

Benestan L, Fietz K, Loiseau N, Guerin PE, Trofimenko E, Rühs S, Schmidt C, Rath W, Biastoch A, Perez-Rufaza A, Baixauli P, Forcada A, Arcas E, Lenfant P, Goni R, Velez L, Höppner M, Kininmonth S, Mouillot D, Puebla O, Manel S (2021) Restricted dispersal in a sea of gene flow. Proceedings of the Royal Society B 288. 

Mathon L, Valentini A, Guerin PE, Noel C, Lionnet C, Boulanger E, Wilfried Thuiller, Bernatchez L, Mouillot D, Dejan T, Manel S (2021) Benchmarking bioinformatics tools for fast accurate eDNA metabarcoding species identification. Mol Ecol Resources. 21:2565-2579.

Concepción M, Díaz D, Fietz K, Forcada A, Ford A, García-Charton JA, Goñi R, Lenfant P, Mallol S, Mouillot D, Pérez-Marcos M, Puebla O, Manel S, Pérez-Ruzafa A  (2021) Reviewing the ecosystem services, societal goods and benefits of marine protected areas. Frontiers in Marine Science. 8.

Boulanger E, Loiseau N, Valentini A, Arnal A, Boissery B, Dejean T, Deter J, Guellati G,  Holon F, Juhel JB, Lenfant P, Manel S, Mouillot D Environmental DNA metabarcoding reveals and unpacks a biodiversity conservation paradox in Mediterranean marine reserves (2021) Proceedings of the Royal Society B.  288:20210112.

Andrello M., Noirot C, Debarre F, Manel S. (2021) MetaPopGen2.0: a multilocus genetic simulator to model populations of large size. Molecular Ecology Resources. 21:596-608.

Polanco Fernández A, Marques V, Fopp F, Juhel J-B, Borrero-Pérez GH, Cheutin M-C, Dejean T, González Corredor JD, Acosta-Chaparro A, Hocdé R, et al. (2021) Comparing environmental DNA metabarcoding and underwater visual census to monitor tropical reef fishes. Environmental DNA 3, 142-156.

Juhel JB et al. (2021) Detection of the elusive Dwarf sperm whale (Kogia sima) using environmental DNA at Malpelo island (Eastern Pacific, Colombia). Ecology and Evolution. 11:2956-2962.

Blanco-Pastor JL et al. (2021) Canonical correlations reveal adaptive loci and phenotypic responses to climate in perennial ryegrass. Molecular Ecology Resources.

Marques V, Milhau T,  Albouy C, Dejean T, Manel S, Mouillot D, Juhel JB (2020)  GAPeDNA: An application for assessment and visualization of genetic databases completeness for eDNA metabarcoding . Diversity and Distribution.

2020

Escalante M, Perrier C, Garcia de Leon F,   ...    , Manel S ( 2020) Genotyping by sequencin reveals the effect of riverscape, climate and interspecific introgression on the genetic diversity and local adaptation of the endangered Mexican golden trout. Conservation Genetics. 21:907-926.

Marques V, Guérin PE, Rocle M, Valentini A, Manel S, Mouillot  D and Dejean   T (2020) Blind assessment of vertebrate taxonomic diversity across spatial scales by clustering environmental DNA metabarcoding sequences. Ecography. 43:1-12.

Boulanger E, Dalongeville E, Andrello M, Mouillot D, Manel S (2020) Spatial graph highlight how multi-generational dispersal shapes landscape genetics patterns. Ecography. 43:1667-1179.

Fietz K, Trofimenko E, Guerin PE, Arnal V, Montserrat T-O, Lobréaux S, Pérez-Ruzafa A, Manel S, Puebla O (2020) New genomic resources for three exploited Mediterranean fishes. Genomics. 112, 4297-4303.  

Manel S, Guerin PE , Mouillot D., Blanchet S., Velez L., Albouy C, Pellisser L (2020) Global determinants of freshwater and marine fish genetic diversity. Nature Communications. 11, 692.

2019

Manel S. (2019) Smoothing technical and computational obstacles in gene-environment associations. Molecular Ecology Resources. 19: 1385-1387.

Manel S, Loiseau N, Puebla O (2019) Long-distance marine connectivity : poorly understood but potentially important. Trends in Ecology & Evolution. 34:688-689.

Blanco-Pastor JL, Manel S. et al (2019) Pleistocene climate changes, and not agricultural spread, accounts for range expansion and admixture in the dominant grassland species Lolium perenne L. Journal of Biogeography. 46:1451-1465.

Razgour O,  Forester B., Taggard JB, Bekaert M, Juste J, Ibanez C, Puechmaille J, Fernandez-Novella R, Alberdi A, Manel S (2019)  Considering adaptive genetic variation in climate change vulnerability assessment reduces species range loss projections. Proceedings of the National Academy of Sciences, 116:10418-10423.

Manel S, Loiseau  N., Andrello M, et al (2019).  Benefits of Marine Reserves: Myth or Reality? Trends in Ecology & Evolution. 34:342-354.

Tournebize R, Vigouroux Y, Jakobsson, Poncet V, Manel S (2019) McSwan: a joint site frequency spectrum method to detect and date selective sweeps across multiple population genomes. Molecular Ecology Resources. 19: 283-295.

2018

Pfeifer V, Ford B, Housset J, McCombs A, Blanco-Pastor JL, Goin N, Manel S, Bertin A (2018) Partitioning genetic and species diversity refines our understanding of species-genetic diversty relationships. Ecology and Evolution. 8: 12351-12364.  

Manel S, Andrello M, Henry K, Verdelet D, Darracq A, Guerin PE, Desprez B, Devaux P. (2018) Predicting genotypes environmental range from genome-environment associations. Molecular Ecology, 27: 2823-2833.

Dalongeville A., Andrello M., Mouillot D., Lobreaux S., Fortin M. J., Lasram F., Belmaker J., Rocklin D., Manel S. (2018) Geographic isolation and larval dispersal shape seascape genetic patterns differently according to spatial scale. Evolutionary Applications. 11: 1437-1447.

Escalante MA, Garcia-De Leon FJ, Ruiz-Luna A, Landguth E, Manel S (2018) The interplay of riverscape features and exotic introgression on the genetic structure of the Mexican golden trout (Oncorhynchus chrysogaster), a simulation approach.  Journal of Biogeography. 45:1500-1514.

Guerrero J, Andrello M, Burgarella C, Manel S (2018) Soil environment is a key driver of adaptation in Medicago truncatula: new insight from landscape genomics. New Phytologist. 219:378-390.

Boussarie G, Bakker J, Wangensteen OS, Mariani S, Bonnin L, Juhel JB, Kiszka JJ, Kulbicki M, Manel S, Robbins WD, et al. 2018. Environmental DNA illuminates the dark diversity of sharks. Science Advances 4.

Dalongeville A., Benestan L, Mouillot D, Lobreaux S, Manel S (2018) Combing six genome scan methods to detect candidate genes to salinity in the Mediterranean striped red mullet (Mullus surmuletus). BMC Genomics. 19.

Magris RA, Andrello M, Pressey RL, Mouillot D, Dalongeville A, Jacobi MN, Manel S. (2018)  Biologically representative  and well-connected marine reserves  enhance biodiversity in conservation planning. Conservation Letters. 11:UNSP e12439.

Schoville S,  Dalongeville A, Viennois G,  Gugerli F, Taberlet P, Lequette L,  Alvarez N,  Manel  S (2018) Preserving genetic connectivity in the European Alps protected area network. Biological Conservation. 218:99-109.

Razgour O, Taggard JB, Manel S, Juste J, Ibanez C, Rebelo H, ALberdi A, Gareth J, Park  K (2018) An integrated framework to identify wildlife populations under threath from climate change. Molecular Ecology Resources. 18:18-31.

2017

Tournebize R, Manel S, Vigouroux Y, Munoz F, de Kockko A, Poncet V (2017) Two disjunct pleiostene populations and anisotropic postglacial expansion shaped the current genetic structure of the relict plant Amborella trichopoda. Plos One. 12(8): e0183412.

Rochat E, Manel S, Deschamps-Cottin M, Widmer I, Joost S (2017) Persistence of butterfly populations in fragmented landscape habitats along urban density gradients: motility helps. Heredity. 119:328-338.

Andrello M, Henry K, Devaux P, Verdelet D, Desprez B, Manel S (2017) Insights into the genetic relationships among plants of Beta section Beta using SNP markers. Theoretical and applied genetics. 130:1857-1866.

Andrello A,  Guilhaumon  F,  Albouy  C, Parravicini V,  Scholtens J,  Verley  P,  Barange M,   Sumaila UR, Manel S,  Mouillot   (2017) Global mismatch between fishing dependency and larval supply from marine reserves? Nature Communications. 8:16039.

Paradis E, Gosselin T, Grundwald NJ, Jombart T, Manel S, Lapp H (2017) Towards an integrated ecosystem of R package for the analysis of population genetic data. Mol Ecol Res. 17:1-4.

Bertin A, Gouin N,  Baumel A, Gianoli E,  Serratosa J,  Osorio R and Manel S (2017) Genetic variation of loci potentially under selection confounds species-genetic diversity correlations in a fragmented habitat. Molecular Ecology. 26:431-443. 

Kamvar  ZN, Lopez-Uribe MM, Coughlan S, Grunwald NJ, Lapp H, Manel S (2017) Developping educational resources for population genetics in R: an open and collaborative approach. Mol Ecol Ress. 17: 120-128.

2016

Talbot B, Chen TW, Zimmerman S, Joost S, Eckert A, Crow TM, Semizer-Cuming D, Seshdri S, Manel S (2016) Combining genotype, phenotype and environment to infer potential candidate genes. Journal of Heredity.  108:207-216.

Manel S., Luikart G, Sonké B., Couteron P. (2016 ) Detecting poaching from natural populations using genetic forensic  approaches. In AA Aguirre & R. Sukumar, eds.  Tropical conservation: perspectives on local and global priorities. Oxford University Press, New York..

Garrido-Garduno T, Tellez-Valdez O, Manel S, Vazquez-Dominguez E. 2016. Role of habitat heterogeneity and landscape connectivity in shaping gene flow and spatial population structure of a dominant rodent species in a tropical dry forest. Journal of Zoology. 298: 293-301. 

Andrello M, Henry K, Devaux P, Desprez B & Manel S. 2016. Taxonomic, spatial and adaptive genetic variation of Beta section Beta. Theoretical and applied genetics. 129: 257-271. 

Dalongeville A, Andrello M, Mouillot D, Albouy C, Manel S. 2016. Ecological traits shape genetic diversity patterns across the Mediterranean Sea: a quantitative review on fishes. Journal of Biogeography. 43: 845-857.