GECO Evolutionary and Computational Genomics

Bioinformatics, Phylogeny and Evolutionary Genomics Group

Mugal Carina

Chargée de recherche

CNRS

Address: 43 bd du 11 novembre 1918
69622 VILLEURBANNE cedex

I am an evolutionary geneticist particularly interested in understanding the molecular mechanisms and evolutionary processes that shape genetic variation within and among species. For this purpose, I use a multi-disciplinary approach spanning empirical and theoretical work within evolutionary genomics. On the empirical side, I primarily use birds and more specifically Ficedula flycatchers as a model organism, since birds show some interesting karyotype features, which make them an exciting model system in the field of genomics. On the theoretical side, I work on stochastic models solidly rooted in population genetics theory in order to improve our conceptual understanding of the genomic signatures generated by diverse evolutionary processes.

The research questions I address can be summarized into three main areas:

1) Causes and consequences of recombination rate regulation in birds

2) Speciation genomics in Ficedula flycatchers

3) A theoretical approach to the study of nonequilibrium dynamics in molecular evolution

Building on a background in mathematical sciences at the University of Graz, Austria, I completed my PhD studies in evolutionary genetics at the Department of Ecology and Genetics, Uppsala University, Sweden, in 2013. I then continued my post-doctoral research there, a period which coined my interest in birds as a study system. In 2017, I established as an independent researcher and focused on the study of closely related species, since closely related species form an excellent study system to investigate how different molecular mechanisms and population-level processes contribute to the build-up of genomic differences among species. I first continued my research at Uppsala University, and since 2022 I work as a CNRS researcher at the Laboratory of Biometry and Evolutionary Biology (LBBE), University of Lyon 1.

Publications

Display of 1 to 30 publications on 32 in total

Divergence in expression of a singing-related neuro-plasticity gene in the brains of two Ficedula flycatchers and their hybrids

David Wheatcroft, Niclas Backström, Ludovic Dutoit, S Eryn Mcfarlane, Carina Mugal, Mi Wang...

G3 .

DOI: 10.1093/g3journal/jkae293

2024

Journal article

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A Wright–Fisher graph model and the impact of directional selection on genetic variation

Ingemar Kaj, Carina Mugal, Rebekka Müller-Widmann

Theoretical Population Biology . 159 : 13-24

DOI: 10.1016/j.tpb.2024.07.004

2024

Journal article

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Regulatory and evolutionary impact of DNA methylation in two songbird species and their naturally occurring F1 hybrids

Jesper Boman, Anna Qvarnström, Carina Mugal

BMC Biology . 22 ( 1 ) : 124

DOI: 10.1186/s12915-024-01920-2

2024

Journal article

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The role of recombination dynamics in shaping signatures of direct and indirect selection across the Ficedula flycatcher genome

Madeline Chase, Maurine Vilcot, Carina Mugal

Proceedings of the Royal Society B: Biological Sciences . 291 ( 2015 ) : 20232382

DOI: 10.1098/rspb.2023.2382

2024

Journal article

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Evidence that genetic drift not adaptation drives fast‐Z and large‐Z effects in Ficedula flycatchers

Madeline Chase, Maurine Vilcot, Carina Mugal

Molecular Ecology . : e17262

DOI: 10.1111/mec.17262

2024

Journal article

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A Nearly Neutral Model of Molecular Signatures of Natural Selection after Change in Population Size

Rebekka Müller, Ingemar Kaj, Carina Mugal

Genome Biology and Evolution . 14 ( 5 )

DOI: 10.1093/gbe/evac058

2022

Journal article

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Positive selection plays a major role in shaping signatures of differentiation across the genomic landscape of two independent Ficedula flycatcher species pairs

Madeline Chase, Hans Ellegren, Carina Mugal

Evolution - International Journal of Organic Evolution . 75 ( 9 ) : 2179-2196

DOI: 10.1111/evo.14234

2021

Journal article

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The Effects of GC-Biased Gene Conversion on Patterns of Genetic Diversity among and across Butterfly Genomes

Jesper Boman, Carina Mugal, Niclas Backström

Genome Biology and Evolution . 13 ( 5 )

DOI: 10.1093/gbe/evab064

2021

Journal article

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Tissue-specific patterns of regulatory changes underlying gene expression differences among Ficedula flycatchers and their naturally occurring F 1 hybrids

Carina Mugal, Mi Wang, Niclas Backström, David Wheatcroft, Murielle Ålund, Marie Sémon...

Genome Research . 30 ( 12 ) : 1727-1739

DOI: 10.1101/gr.254508.119

2020

Journal article

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Polymorphism Data Assist Estimation of the Nonsynonymous over Synonymous Fixation Rate Ratio ω for Closely Related Species

Carina Mugal, Verena Kutschera, Fidel Botero-Castro, Jochen Wolf, Ingemar Kaj

Molecular Biology and Evolution . 37 ( 1 ) : 260-279

DOI: 10.1093/molbev/msz203

2020

Journal article

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GC-biased gene conversion conceals the prediction of the nearly neutral theory in avian genomes

Paulina Bolívar, Laurent Guéguen, Laurent Duret, Hans Ellegren, Carina Mugal

Genome Biology . 20 ( 1 )

DOI: 10.1186/s13059-018-1613-z

2019

Journal article

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Positive selection on human gamete-recognition genes

Michael Hart, Daryn Stover, Vanessa Guerra, Sahar Mozaffari, Carole Ober, Carina Mugal...

PeerJ . 6 : e4259

DOI: 10.7717/peerj.4259

2018

Journal article

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Biased Inference of Selection Due to GC-Biased Gene Conversion and the Rate of Protein Evolution in Flycatchers When Accounting for It

Paulina Bolívar, Carina Mugal, Matteo Rossi, Alexander Nater, Mi Wang, Ludovic Dutoit...

Molecular Biology and Evolution . 35 ( 10 ) : 2475-2486

DOI: 10.1093/molbev/msy149

2018

Journal article

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Sex‐biased gene expression, sexual antagonism and levels of genetic diversity in the collared flycatcher ( Ficedula albicollis ) genome

Ludovic Dutoit, Carina Mugal, Paulina Bolívar, Mi Wang, Krystyna Nadachowska-Brzyska, Linnéa Smeds...

Molecular Ecology . 27 ( 18 ) : 3572-3581

DOI: 10.1111/mec.14789

2018

Journal article

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Whole‐genome patterns of linkage disequilibrium across flycatcher populations clarify the causes and consequences of fine‐scale recombination rate variation in birds

Takeshi Kawakami, Carina Mugal, Alexander Suh, Alexander Nater, Reto Burri, Linnéa Smeds...

Molecular Ecology . 26 ( 16 ) : 4158-4172

DOI: 10.1111/mec.14197

2017

Journal article

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Covariation in levels of nucleotide diversity in homologous regions of the avian genome long after completion of lineage sorting

Ludovic Dutoit, Nagarjun Vijay, Carina Mugal, Christen Bossu, Reto Burri, Jochen Wolf...

Proceedings of the Royal Society B: Biological Sciences . 284 ( 1849 ) : 20162756

DOI: 10.1098/rspb.2016.2756

2017

Journal article

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Genomic distribution and estimation of nucleotide diversity in natural populations: perspectives from the collared flycatcher ( Ficedula albicollis ) genome

Ludovic Dutoit, Reto Burri, Alexander Nater, Carina Mugal, Hans Ellegren

Molecular Ecology Resources . 17 ( 4 ) : 586-597

DOI: 10.1111/1755-0998.12602

2017

Journal article

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High-Resolution Mapping of Crossover and Non-crossover Recombination Events by Whole-Genome Re-sequencing of an Avian Pedigree

Linnéa Smeds, Carina Mugal, Anna Qvarnström, Hans Ellegren

PLoS Genetics . 12 ( 5 ) : e1006044

DOI: 10.1371/journal.pgen.1006044

2016

Journal article

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Divergence in gene expression within and between two closely related flycatcher species

Severin Uebbing, Axel Künstner, Hannu Mäkinen, Niclas Backström, Paulina Bolivar, Reto Burri...

Molecular Ecology . 25 ( 9 ) : 2015-2028

DOI: 10.1111/mec.13596

2016

Journal article

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The non-equilibrium allele frequency spectrum in a Poisson random field framework

Ingemar Kaj, Carina Mugal

Theoretical Population Biology . 111 : 51-64

DOI: 10.1016/j.tpb.2016.06.003

2016

Journal article

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Evolutionary Consequences of DNA Methylation on the GC Content in Vertebrate Genomes

Carina Mugal, Peter Arndt, Lena Holm, Hans Ellegren

G3 . 5 ( 3 ) : 441-447

DOI: 10.1534/g3.114.015545

2015

Journal article

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Recombination Rate Variation Modulates Gene Sequence Evolution Mainly via GC-Biased Gene Conversion, Not Hill–Robertson Interference, in an Avian System

Paulina Bolívar, Carina Mugal, Alexander Nater, Hans Ellegren

Molecular Biology and Evolution . 33 ( 1 ) : 216-227

DOI: 10.1093/molbev/msv214

2015

Journal article

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GC‐biased gene conversion links the recombination landscape and demography to genomic base composition

Carina Mugal, Claudia Weber, Hans Ellegren

BioEssays . 37 ( 12 ) : 1317-1326

DOI: 10.1002/bies.201500058

2015

Journal article

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Linked selection and recombination rate variation drive the evolution of the genomic landscape of differentiation across the speciation continuum of Ficedula flycatchers

Reto Burri, Alexander Nater, Takeshi Kawakami, Carina Mugal, Pall Olason, Linnea Smeds...

Genome Research . 25 ( 11 ) : 1656-1665

DOI: 10.1101/gr.196485.115

2015

Journal article

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A high‐density linkage map enables a second‐generation collared flycatcher genome assembly and reveals the patterns of avian recombination rate variation and chromosomal evolution

Takeshi Kawakami, Linnéa Smeds, Niclas Backström, Arild Husby, Anna Qvarnström, Carina Mugal...

Molecular Ecology . 23 ( 16 ) : 4035-4058

DOI: 10.1111/mec.12810

2014

Journal article

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Why Time Matters: Codon Evolution and the Temporal Dynamics of dN/dS

Carina Mugal, Jochen B.W. Wolf, Ingemar Kaj

Molecular Biology and Evolution . 31 ( 1 ) : 212-231

DOI: 10.1093/molbev/mst192

2014

Journal article

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Genome-wide analysis in chicken reveals that local levels of genetic diversity are mainly governed by the rate of recombination

Carina Mugal, Benoit Nabholz, Hans Ellegren

BMC Genomics . 14 ( 1 ) : 86

DOI: 10.1186/1471-2164-14-86

2013

Journal article

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Twisted Signatures of GC-Biased Gene Conversion Embedded in an Evolutionary Stable Karyotype

Carina Mugal, Peter Arndt, Hans Ellegren

Molecular Biology and Evolution . 30 ( 7 ) : 1700-1712

DOI: 10.1093/molbev/mst067

2013

Journal article

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Substitution rate variation at human CpG sites correlates with non-CpG divergence, methylation level and GC content

Carina Mugal, Hans Ellegren

Genome Biology . 12 ( 6 ) : R58

DOI: 10.1186/gb-2011-12-6-r58

2011

Journal article

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Conservation of Neutral Substitution Rate and Substitutional Asymmetries in Mammalian Genes

Carina Mugal, J. Wolf, H. von Grünberg, H. Ellegren

Genome Biology and Evolution . 2 : 19-28

DOI: 10.1093/gbe/evp056

2010

Journal article

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Short summary of my scientific background

Publications

Divergence in expression of a singing-related neuro-plasticity gene in the brains of two Ficedula flycatchers and their hybrids

A Wright–Fisher graph model and the impact of directional selection on genetic variation

Regulatory and evolutionary impact of DNA methylation in two songbird species and their naturally occurring F1 hybrids

The role of recombination dynamics in shaping signatures of direct and indirect selection across the Ficedula flycatcher genome

Evidence that genetic drift not adaptation drives fast‐Z and large‐Z effects in Ficedula flycatchers

A Nearly Neutral Model of Molecular Signatures of Natural Selection after Change in Population Size

Positive selection plays a major role in shaping signatures of differentiation across the genomic landscape of two independent Ficedula flycatcher species pairs

The Effects of GC-Biased Gene Conversion on Patterns of Genetic Diversity among and across Butterfly Genomes

Tissue-specific patterns of regulatory changes underlying gene expression differences among Ficedula flycatchers and their naturally occurring F 1 hybrids

Polymorphism Data Assist Estimation of the Nonsynonymous over Synonymous Fixation Rate Ratio ω for Closely Related Species

GC-biased gene conversion conceals the prediction of the nearly neutral theory in avian genomes

Positive selection on human gamete-recognition genes

Biased Inference of Selection Due to GC-Biased Gene Conversion and the Rate of Protein Evolution in Flycatchers When Accounting for It

Sex‐biased gene expression, sexual antagonism and levels of genetic diversity in the collared flycatcher ( Ficedula albicollis ) genome

Whole‐genome patterns of linkage disequilibrium across flycatcher populations clarify the causes and consequences of fine‐scale recombination rate variation in birds

Covariation in levels of nucleotide diversity in homologous regions of the avian genome long after completion of lineage sorting

Genomic distribution and estimation of nucleotide diversity in natural populations: perspectives from the collared flycatcher ( Ficedula albicollis ) genome

High-Resolution Mapping of Crossover and Non-crossover Recombination Events by Whole-Genome Re-sequencing of an Avian Pedigree

Divergence in gene expression within and between two closely related flycatcher species

The non-equilibrium allele frequency spectrum in a Poisson random field framework

Evolutionary Consequences of DNA Methylation on the GC Content in Vertebrate Genomes

Recombination Rate Variation Modulates Gene Sequence Evolution Mainly via GC-Biased Gene Conversion, Not Hill–Robertson Interference, in an Avian System

GC‐biased gene conversion links the recombination landscape and demography to genomic base composition

Linked selection and recombination rate variation drive the evolution of the genomic landscape of differentiation across the speciation continuum of Ficedula flycatchers

A high‐density linkage map enables a second‐generation collared flycatcher genome assembly and reveals the patterns of avian recombination rate variation and chromosomal evolution

Why Time Matters: Codon Evolution and the Temporal Dynamics of dN/dS

Genome-wide analysis in chicken reveals that local levels of genetic diversity are mainly governed by the rate of recombination

Twisted Signatures of GC-Biased Gene Conversion Embedded in an Evolutionary Stable Karyotype

Substitution rate variation at human CpG sites correlates with non-CpG divergence, methylation level and GC content

Conservation of Neutral Substitution Rate and Substitutional Asymmetries in Mammalian Genes