Genome polarisation for detecting barriers to geneflow

Result code in IS VaVaI

<a href="https://www.isvavai.cz/riv?ss=detail&h=RIV%2F68081766%3A_____%2F23%3A00565367" target="_blank" >RIV/68081766:_____/23:00565367 - isvavai.cz</a>

Alternative codes found

RIV/00216305:26210/22:PU146558 RIV/00216224:14310/23:00130074

Result on the web

<a href="https://besjournals.onlinelibrary.wiley.com/doi/10.1111/2041-210X.14010" target="_blank" >https://besjournals.onlinelibrary.wiley.com/doi/10.1111/2041-210X.14010</a>

DOI - Digital Object Identifier

<a href="http://dx.doi.org/10.1111/2041-210X.14010" target="_blank" >10.1111/2041-210X.14010</a>

Result language

angličtina

Original language name

Genome polarisation for detecting barriers to geneflow

Original language description

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.

Czech name

—

Czech description

—

Type

J_imp - Article in a specialist periodical, which is included in the Web of Science database

CEP classification

—

OECD FORD branch

10603 - Genetics and heredity (medical genetics to be 3)

Project

Result was created during the realization of more than one project. More information in the Projects tab.

Continuities

I - Institucionalni podpora na dlouhodoby koncepcni rozvoj vyzkumne organizace

Publication year

2023

Confidentiality

S - Úplné a pravdivé údaje o projektu nepodléhají ochraně podle zvláštních právních předpisů

Name of the periodical

Methods in Ecology and Evolution

ISSN

2041-210X

e-ISSN

2041-2096

Volume of the periodical

14

Issue of the periodical within the volume

2

Country of publishing house

GB - UNITED KINGDOM

Number of pages

17

Pages from-to

512-528

UT code for WoS article

000888764100001

EID of the result in the Scopus database

2-s2.0-85142369024