Genome polarisation for detecting barriers to geneflow

J 2023

Genome polarisation for detecting barriers to geneflow

BAIRD, Stuart James Edmisti; Jan PETRUŽELA; Izar JAROŇ; Pavel ŠKRABÁNEK; Natália MARTÍNKOVÁ et al.

Základní údaje

Originální název

Genome polarisation for detecting barriers to geneflow

Autoři

BAIRD, Stuart James Edmisti; Jan PETRUŽELA; Izar JAROŇ; Pavel ŠKRABÁNEK a Natália MARTÍNKOVÁ

Vydání

Methods in Ecology and Evolution, Wiley, 2023, 2041-210X

Další údaje

Jazyk

angličtina

Typ výsledku

Článek v odborném periodiku

Obor

10511 Environmental sciences

Stát vydavatele

Spojené státy

Utajení

není předmětem státního či obchodního tajemství

Odkazy

URL

Impakt faktor

Impact factor: 6.300

Označené pro přenos do RIV

Ano

Kód RIV

RIV/00216224:14310/23:00130074

Organizační jednotka

Přírodovědecká fakulta

Klíčová slova anglicky

gene capture; geneflow; genome admixture; genome polarisation; hybrid zone; hybridisation; introgression; reduced representation genomics

Štítky

143180, rivok

Příznaky

Mezinárodní význam, Recenzováno

Změněno: 10. 6. 2025 15:40, Mgr. Michaela Hylsová, Ph.D.

Anotace

V originále

Semi-permeable barriers to geneflow in principle allow distantly related organisms to capture and exchange pre-adapted genes potentially speeding adaptation. However, describing barriers to geneflow on a genomic scale is non-trivial. We extend classic diagnostic allele counting measures of geneflow across a barrier to the case of genome-scale data. Diagnostic index expectation maximisation (diem) polarises the labelling of bistate markers with respect to the sides of a barrier. An initial state of ignorance is enforced by starting with randomly generated marker polarisations. This means there is no prior on population or taxon membership of the genomes concerned. Using a deterministic data labelling, small numbers of classic diagnostic markers can be replaced by large numbers of markers, each with a diagnostic index. Individuals' hybrid indices (genome admixture proportions) are then calculated genome wide conditioned on marker diagnosticity; within diploid, haplodiploid and/or haploid genome compartments; or indeed over any subset of markers, allowing classical cline width/barrier strength comparisons along genomes. Along-genome barrier strength heterogeneity allows for barrier regions to be identified. Furthermore, blocks of genetic material that have introgressed across a barrier are easily identified with high power. diem indicates panmixis among Myotis myotis bat genomes, with a barrier separating low data quality outliers. In a Mus musculus domesticus/Mus spretus system, diem adds multiple introgressions of olfactory (and vomeronasal) gene clusters in one direction to previous demonstrations of a pesticide resistance gene introgressing in the opposite direction across a strong species barrier. diem is a genome analysis solution, which scales over reduced representation genomics of thousands of markers to treatment of all variant sites in large genomes. While the method lends itself to visualisation, its output of markers with barrier-informative annotation will fuel research in population genetics, phylogenetics and association studies. diem can equip such downstream applications with millions of informative markers.

Návaznosti

EF17_043/0009632, projekt VaV

Název: CETOCOEN Excellence

LM2018140, projekt VaV

Název: e-Infrastruktura CZ (Akronym: e-INFRA CZ)

Investor: Ministerstvo školství, mládeže a tělovýchovy ČR, e-Infrastruktura CZ

90121, velká výzkumná infrastruktura

Název: RECETOX RI

Citovat

BAIRD, Stuart James Edmisti; Jan PETRUŽELA; Izar JAROŇ; Pavel ŠKRABÁNEK a Natália MARTÍNKOVÁ. Genome polarisation for detecting barriers to geneflow. Methods in Ecology and Evolution. Wiley, 2023, roč. 14, č. 2, s. 512-528. ISSN 2041-210X. Dostupné z: https://doi.org/10.1111/2041-210X.14010.

@article{2233475,
   author = {Baird, Stuart James Edmisti and Petružela, Jan and Jaroň, Izar and Škrabánek, Pavel and Martínková, Natália},
   article_number = {2},
   doi = {https://doi.org/10.1111/2041-210X.14010},
   keywords = {gene capture; geneflow; genome admixture; genome polarisation; hybrid zone; hybridisation; introgression; reduced representation genomics},
   language = {eng},
   issn = {2041-210X},
   journal = {Methods in Ecology and Evolution},
   title = {Genome polarisation for detecting barriers to geneflow},
   url = {https://doi.org/10.1111/2041-210X.14010},
   volume = {14},
   year = {2023}
}

TY  - JOUR
ID  - 2233475
AU  - Baird, Stuart James Edmisti - Petružela, Jan - Jaroň, Izar - Škrabánek, Pavel - Martínková, Natália
PY  - 2023
TI  - Genome polarisation for detecting barriers to geneflow
JF  - Methods in Ecology and Evolution
VL  - 14
IS  - 2
SP  - 512-528
EP  - 512-528
PB  - Wiley
SN  - 2041210X
KW  - gene capture
KW  - geneflow
KW  - genome admixture
KW  - genome polarisation
KW  - hybrid zone
KW  - hybridisation
KW  - introgression
KW  - reduced representation genomics
UR  - https://doi.org/10.1111/2041-210X.14010
N2  - Semi-permeable barriers to geneflow in principle allow distantly related organisms to capture and exchange pre-adapted genes potentially speeding adaptation. However, describing barriers to geneflow on a genomic scale is non-trivial. We extend classic diagnostic allele counting measures of geneflow across a barrier to the case of genome-scale data. Diagnostic index expectation maximisation (diem) polarises the labelling of bistate markers with respect to the sides of a barrier. An initial state of ignorance is enforced by starting with randomly generated marker polarisations. This means there is no prior on population or taxon membership of the genomes concerned. Using a deterministic data labelling, small numbers of classic diagnostic markers can be replaced by large numbers of markers, each with a diagnostic index. Individuals' hybrid indices (genome admixture proportions) are then calculated genome wide conditioned on marker diagnosticity; within diploid, haplodiploid and/or haploid genome compartments; or indeed over any subset of markers, allowing classical cline width/barrier strength comparisons along genomes. Along-genome barrier strength heterogeneity allows for barrier regions to be identified. Furthermore, blocks of genetic material that have introgressed across a barrier are easily identified with high power. diem indicates panmixis among Myotis myotis bat genomes, with a barrier separating low data quality outliers. In a Mus musculus domesticus/Mus spretus system, diem adds multiple introgressions of olfactory (and vomeronasal) gene clusters in one direction to previous demonstrations of a pesticide resistance gene introgressing in the opposite direction across a strong species barrier. diem is a genome analysis solution, which scales over reduced representation genomics of thousands of markers to treatment of all variant sites in large genomes. While the method lends itself to visualisation, its output of markers with barrier-informative annotation will fuel research in population genetics, phylogenetics and association studies. diem can equip such downstream applications with millions of informative markers.
ER  -

BAIRD, Stuart James Edmisti; Jan PETRUŽELA; Izar JAROŇ; Pavel ŠKRABÁNEK a Natália MARTÍNKOVÁ. Genome polarisation for detecting barriers to geneflow. \textit{Methods in Ecology and Evolution}. Wiley, 2023, roč.~14, č.~2, s.~512-528. ISSN~2041-210X. Dostupné z: https://doi.org/10.1111/2041-210X.14010.

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