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List of works by Nicolas Salamin

60 million years of co-divergence in the fig-wasp symbiosis

scientific article (publication date: 22 December 2005)

A cautionary note on the use of genotype callers in Phylogenomics

scientific article published on 21 October 2020

A dedicated target capture approach reveals variable genetic markers across micro- and macro-evolutionary time scales in palms

scientific article published on 03 November 2018

A generalized mechanistic codon model

scientific article

A multi‐platform package for the analysis of intra‐ and interspecific trait evolution

scientific article published in 2020

A process‐based model supports an association between dispersal and the prevalence of species traits in tropical reef fish assemblages

scientific article published on 26 September 2019

Accelerating Bayesian inference for evolutionary biology models

scientific article

Adaptive divergence of ancient gene duplicates in the avian MHC class II beta.

scientific article published on 12 May 2010

Assessing internal support with large phylogenetic DNA matrices

scientific article published on 01 June 2003

Assessing rapid evolution in a changing environment

scientific article

Back to Gondwanaland: can ancient vicariance explain (some) Indian Ocean disjunct plant distributions?

scientific article

Bayesian estimation of speciation and extinction from incomplete fossil occurrence data

scientific article

Biogeographic origin and radiation of the Old World crocidurine shrews (Mammalia: Soricidae) inferred from mitochondrial and nuclear genes

scientific article

Bridging Inter- and Intraspecific Trait Evolution with a Hierarchical Bayesian Approach

scientific article published on 23 February 2016

Building Supertrees: An Empirical Assessment Using the Grass Family (Poaceae)

article published in 2002

C4 Photosynthesis evolved in grasses via parallel adaptive genetic changes.

scientific article published on 5 July 2007

Climate change effects on animal and plant phylogenetic diversity in southern Africa

article

Clownfishes evolution below and above the species level.

scientific article published in February 2018

Coev-web: a web platform designed to simulate and evaluate coevolving positions along a phylogenetic tree

scientific article published on 23 November 2015

CoevDB: a database of intramolecular coevolution among protein-coding genes of the bony vertebrates

article

Combining food web and species distribution models for improved community projections

scientific article

Comparative performance of supertree algorithms in large data sets using the soapberry family (Sapindaceae) as a case study

scientific article

Conceptual and empirical bridges between micro- and macroevolution

scientific article published in 2023

Convergent changes in gene expression associated with repeated transitions between hummingbird and bee pollinated flowers

Convergent evolution of floral signals underlies the success of Neotropical orchids

scientific article published on 26 June 2013

Correction to 'Land plants and DNA barcodes: short-term and long-term goals'.

scientific article published on April 2016

DNA banking for plant breeding, biotechnology and biodiversity evaluation

scientific article published in January 2007

Decoupled evolution of floral traits and climatic preferences in a clade of Neotropical Gesneriaceae

scientific article published on 10 November 2015

Detecting patterns of species diversification in the presence of both rate shifts and mass extinctions ⬇️

scientific article

Development and testing of novel chloroplast microsatellite markers for Lolium perenne and other grasses (Poaceae) from de novo sequencing and in silico sequences

article

Developmental and comparative transcriptomic identification of iridophore contribution to white barring in clownfish

scientific article published on 29 January 2019

Different rates of defense evolution and niche preferences in clonal and nonclonal milkweeds (Asclepias spp.).

scientific article published on 17 September 2015

Duplication history and molecular evolution of the rbcS multigene family in angiosperms

scientific article published on 01 November 2019

ENDOTHERMY, THERMAL NICHE EVOLUTION AND THE DISTRIBUTION OF VERTEBRATE DIVERSITY

Early Arrival and Climatically-Linked Geographic Expansion of New World Monkeys from Tiny African Ancestors

scientific article published on 01 January 2019

Effect of genetic convergence on phylogenetic inference

scientific article published on 14 December 2011

Effects of a fire response trait on diversification in replicated radiations

scientific article published on 9 October 2013

Effects of phylogenetic signal on ancestral state reconstruction

scientific article published on 4 January 2012

Environment and evolutionary history shape phylogenetic turnover in European tetrapods

scientific article published in Nature Communications

Evolution of C(4) phosphoenolpyruvate carboxykinase in grasses, from genotype to phenotype

scientific article published on 6 November 2008

Evolution of a supergene that regulates a trans-species social polymorphism

scientific article published on 20 January 2020

Evolution of life cycles and reproductive traits: Insights from the brown algae

scientific article published in 2021

Evolutionary footprint of coevolving positions in genes.

scientific article published on 11 January 2014

Evolutionary history of New World monkeys revealed by molecular and fossil data

Evolutionary insights on C4 photosynthetic subtypes in grasses from genomics and phylogenetics

scientific article

Evolutionary patterns of MHC class II B in owls and their implications for the understanding of avian MHC evolution

scientific article published on 20 March 2008

Evolutionary switch and genetic convergence on rbcL following the evolution of C4 photosynthesis

scientific article published on 11 August 2008

Exotic taxa less related to native species are more invasive ⬇️

scholarly article

Exploring the Macroevolutionary Signature of Asymmetric Inheritance at Speciation

First draft genome of an iconic clownfish species (Amphiprion frenatus).

scientific article published on 17 February 2018

Flowering date of taxonomic families predicts phenological sensitivity to temperature: Implications for forecasting the effects of climate change on unstudied taxa

scientific article

Fossil biogeography: a new model to infer dispersal, extinction and sampling from palaeontological data

scientific article

Fossil-Informed Models Reveal a Boreotropical Origin and Divergent Evolutionary Trajectories in the Walnut Family (Juglandaceae)

scientific article published in 2021

Fossils matter: improved estimates of divergence times in Pinus reveal older diversification

article

Fossils matter: improved estimates of divergence times in Pinus reveal older diversification.

scientific article

Genetic consequences of Quaternary climatic oscillations in the Himalayas: Primula tibetica as a case study based on restriction site-associated DNA sequencing

scientific article

Genomic footprints of repeated evolution of CAM photosynthesis in a Neotropical species radiation

scientific article published on 16 July 2020

Genomics of clownfish adaptation to sea anemones: investigating the genetic bases of the acquisition of the mutualism and the diversification along host usage and habitat gradients

scientific article published on 14 August 2019

Genomics of the divergence continuum in an African plant biodiversity hotspot, I: drivers of population divergence in Restio capensis (Restionaceae).

scientific article

High Rate of Protein Coding Sequence Evolution and Species Diversification in the Lycaenids

scientific article published in 2017

Host specialist clownfishes are environmental niche generalists

scientific article

How a haemosporidian parasite of bats gets around: the genetic structure of a parasite, vector and host compared.

scientific article published on 3 February 2015

Howling from the past: historical phylogeography and diversity losses in European grey wolves

scientific article published on 01 August 2018

Hummingbird pollination and the diversification of angiosperms: an old and successful association in Gesneriaceae.

scientific article

Hybridisation and diversification in the adaptive radiation of clownfishes

scientific article

Implementation of biotic interactions in niche analyses unravels the patterns underneath community composition in clownfishes

Improved estimation of macroevolutionary rates from fossil data using a Bayesian framework

scientific article published on 12 September 2019

Improving spatial predictions of taxonomic, functional and phylogenetic diversity

scholarly article by Manuela D'Amen et al published 12 June 2017 in Journal of Ecology

Incompletely resolved phylogenetic trees inflate estimates of phylogenetic conservatism

scientific article

Insights into the Genomics of Clownfish Adaptive Radiation: Genetic Basis of the Mutualism with Sea Anemones

scientific article published in 2019

Insularity and the evolution of melanism, sexual dichromatism and body size in the worldwide-distributed barn owl.

scientific article published on 5 March 2010

Integrating phylogeny into studies of C4 variation in the grasses

scientific article published in January 2009

Interspecific correlation between red blood cell mitochondrial ROS production, cardiolipin content and longevity in birds

scientific article

Land plants and DNA barcodes: short-term and long-term goals

scientific article published in October 2005

Large multi-gene phylogenetic trees of the grasses (Poaceae): progress towards complete tribal and generic level sampling

scientific article

Large-Scale Comparative Analysis of Codon Models Accounting for Protein and Nucleotide Selection

scientific article published in 2019

Linking life-history traits, ecology, and niche breadth evolution in North American eriogonoids (Polygonaceae).

scientific article

Linking micro and macroevolution in the presence of migration

scientific article published on 20 November 2019

Loss of interactions with ants under cold climate in a regional myrmecophilous butterfly fauna

article by Loïc Pellissier et al published 12 July 2012 in Journal of Biogeography

Measurement errors should always be incorporated in phylogenetic comparative analysis

article

Modeling Codon Rate Variation: Robust Inference of Protein and Nucleotide Selection

Molecular dating, evolutionary rates, and the age of the grasses.

scientific article

Molecular ecology studies of species radiations: current research gaps, opportunities and challenges

scientific article published on 18 March 2017

Molecular evolutionary rates are not correlated with temperature and latitude in Squamata: an exception to the metabolic theory of ecology?

scientific article (publication date: 20 May 2016)

Molecular phylogenetics of shrews (Mammalia: Soricidae) reveal timing of transcontinental colonizations

scientific article published on 19 December 2006

Mutualism with sea anemones triggered the adaptive radiation of clownfishes

scientific article

New grass phylogeny resolves deep evolutionary relationships and discovers C4 origins

scientific article (publication date: 24 November 2011)

Niche width impacts vertebrate diversification

scientific article published on 10 June 2016

No evidence for the radiation time lag model after whole genome duplications in Teleostei

scientific article

No evidence for the radiation time lag model after whole genome duplications in Teleostei

Non-monophyly of the woody bamboos (Bambuseae; Poaceae): a multi-gene region phylogenetic analysis of Bambusoideae s.s.

scientific article

Nonredundant regulation of rice arbuscular mycorrhizal symbiosis by two members of the phosphate transporter1 gene family

scientific article (publication date: October 2012)

Oligocene CO2 decline promoted C4 photosynthesis in grasses.

scientific article published on 20 December 2007

On the effect of asymmetrical trait inheritance on models of trait evolution

scientific article published on 18 July 2020

One Year Genome Evolution of Lausannevirus in Allopatric versus Sympatric Conditions

scientific article published on 19 May 2017

Optimization strategies for fast detection of positive selection on phylogenetic trees

scientific article published on 23 January 2014

Phylogenetic analyses of plastid and nuclear DNA sequences indicate a rapid late Miocene radiation of the temperate bamboo tribe Arundinarieae (Poaceae, Bambusoideae)

scientific article published in 2010

Phylogenetic conservatism in plant phenology

article

Phylogenetic plant community structure along elevation is lineage specific

scientific article (publication date: December 2013)

Phylogenetics of Miscanthus , Saccharum and related genera (Saccharinae, Andropogoneae, Poaceae) based on DNA sequences from ITS nuclear ribosomal DNA and plastid trnL intron and trnL-F intergenic spacers

scientific article published in October 2002

Phylogenomics of C(4) photosynthesis in sedges (Cyperaceae): multiple appearances and genetic convergence.

scientific article

Phylogenomics of Gesneriaceae using targeted capture of nuclear genes

scientific article published on 09 January 2021

Phylogeny Reconstruction and Functional Constraints in Organellar Genomes: Plastid atpB and rbcL Sequences Versus Animal Mitochondrion

scholarly article by Vincent Savolainen et al published 1 July 2002 in Systematic Biology

Phylogeny and biogeography of Primula sect. Armerina: implications for plant evolution under climate change and the uplift of the Qinghai-Tibet Plateau

scientific article

Plant DNA barcodes and the influence of gene flow

scientific article published on 07 March 2012

Plant functional and phylogenetic turnover correlate with climate and land use in the Western Swiss Alps

article

Plastid genome characterisation in Brassica and Brassicaceae using a new set of nine SSRs

scientific article published on 15 August 2006

Polymorphic sites preferentially avoid co-evolving residues in MHC class I proteins.

scientific article published on 21 May 2018

Population Genetic Structure and Demographic History of Primula fasciculata in Southwest China

scientific article published on 02 July 2020

Prototypic SNARE Proteins Are Encoded in the Genomes of Heimdallarchaeota, Potentially Bridging the Gap between the Prokaryotes and Eukaryotes

scientific article published on 14 May 2020

Publisher Correction: The impact of endothermy on the climatic niche evolution and the distribution of vertebrate diversity

scientific article published on 01 March 2018

PyRate: a new program to estimate speciation and extinction rates from incomplete fossil data

article published in 2014

Rapid climate change results in long-lasting spatial homogenization of phylogenetic diversity

scientific article published on 16 September 2020

Resprouter fraction in Cape Restionaceae assemblages varies with climate and soil type

article published in 2016

Scale-dependent adaptive evolution and morphological convergence to climatic niche in Californian eriogonoids (Polygonaceae)

Selection on a eumelanic ornament is stronger in the tropics than in temperate zones in the worldwide-distributed barn owl.

scientific article published on 15 November 2008

Selection on the Major Color Gene Melanocortin-1-Receptor Shaped the Evolution of the Melanocortin System Genes

scientific article published on 5 December 2017

Selectome update: quality control and computational improvements to a database of positive selection

scientific article

Sensitivity of Spring Phenology to Warming Across Temporal and Spatial Climate Gradients in Two Independent Databases

article

Simultaneous Bayesian inference of phylogeny and molecular coevolution

scholarly article by Xavier Meyer et al published 12 March 2019 in Proceedings of the National Academy of Sciences of the United States of America

SlimCodeML: An Optimized Version of CodeML for the Branch-Site Model

scientific article published in May 2012

Slowly but surely: gradual diversification and phenotypic evolution in the hyper-diverse tree fern family Cyatheaceae

scientific article published on 01 January 2020

Soil fungal communities of grasslands are environmentally structured at a regional scale in the Alps

scientific article

Spatial predictions of phylogenetic diversity in conservation decision making

scientific article

State aggregation for fast likelihood computations in molecular evolution

scientific article

Sympatric speciation in palms on an oceanic island

scientific article

Targeted Capture of Hundreds of Nuclear Genes Unravels Phylogenetic Relationships of the Diverse Neotropical Palm Tribe Geonomateae

scientific article published on 12 July 2019

Taxogenomics of the order Chlamydiales

scientific article published on 29 January 2015

Temporal and spatial origin of Gesneriaceae in the New World inferred from plastid DNA sequences

scientific article published in 2012

The SIB Swiss Institute of Bioinformatics' resources: focus on curated databases

scientific article (publication date: 4 January 2016)

The evolutionary host switches of Polychromophilus: a multi-gene phylogeny of the bat malaria genus suggests a second invasion of mammals by a haemosporidian parasite ⬇️

scientific article published in 2012

The impact of endothermy on the climatic niche evolution and the distribution of vertebrate diversity

article published in 2018

The origins and diversification of C4grasses and savanna-adapted ungulates

The origins of C4 grasslands: integrating evolutionary and ecosystem science.

scientific article

The radiation of the clownfishes has two geographical replicates

The role of clade competition in the diversification of North American canids

scientific article

The role of climatic tolerances and seed traits in reduced extinction rates of temperate polygonaceae

scientific article

The simultaneous inducibility of phytochemicals related to plant direct and indirect defences against herbivores is stronger at low elevation

article

Thyroid hormones regulate the formation and environmental plasticity of white bars in clownfishes

scientific article published in 2021

Towards building the tree of life: a simulation study for all angiosperm genera

scientific article published in April 2005

Transcriptomic resources for an endemic Neotropical plant lineage (Gesneriaceae).

scientific article

Trophic specialization influences the rate of environmental niche evolution in damselfishes (Pomacentridae)

scientific article (publication date: 22 September 2012)

Turnover of plant lineages shapes herbivore phylogenetic beta diversity along ecological gradients

scientific article published in March 2013

Warming experiments underpredict plant phenological responses to climate change

scientific article published on 2 May 2012

Why are some species older than others? A large-scale study of vertebrates

scientific article

ecospat: an R package to support spatial analyses and modeling of species niches and distributions

article

gcodeml: a Grid-enabled tool for detecting positive selection in biological evolution.

scientific article published in January 2012

‘Next generation’ biogeography: towards understanding the drivers of species diversification and persistence

article

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