The great tit HapMap project: a continental-scale analysis of genomic variation in a songbird

October 11, 2024

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The great tit HapMap project: a continental-scale analysis of genomic variation in a songbird

Publicated to: Molecular Ecology Resources. 24 (5): e13969- - 2024-01-01 24(5), DOI: 10.1111/1755-0998.13969

Authors:

Spurgin, L.G.; Bosse, M.; Adriaensen, Frank; Albayrak, T; Barboutis, C.; Belda, EJ ; Bushuev,A.; Cecere, J.G.; Charmantier, Anne; Cichon, M.; Dingemanse, N. J.; Doliglez, Blandine; Eeva, Tapio; Erikstad, K.E.; Fedorov, V.

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Affiliations

Anglia Ruskin Univ, Dept Life Sci, Behav Ecol Grp, Cambridge - Author

Babes Bolyai Univ, Hungarian Dept Biol & Ecol, Evolutionary Ecol Grp - Author

Bulgarian Acad Sci, Inst Biodivers & Ecosyst Res, Bulgarian Ornithol Ctr - Author

Dokuz Eylul Univ, Buca Fac Educ Math & Sci Educ, Biol Educ - Author

Eotvos Lorand Univ, Dept Systemat Zool & Ecol, Behav Ecol Grp - Author

FRAM High North Res Ctr Climate & Environm, Norwegian Inst Nat Res - Author

Hasselt Univ, Interuniv Inst Biostat & Stat Bioinformat - Author

Hellenic Ornithol Soc, BirdLife Greece - Author

Ist Super Protez & Ric Ambientale ISPRA, Area Avifauna Migratrice - Author

Jagiellonian Univ, Inst Environm Sci - Author

LMU Munchen, Fac Biol, Behav Ecol - Author

Lomonosov Moscow State Univ, Fac Biol - Author

Lomonosov Moscow State Univ, Fac Biol, Zvenigorod Biol Stn - Author

Max Planck Inst Biol Intelligence, Dept Ornithol - Author

Netherlands Inst Ecol NIOO KNAW, Dept Anim Ecol - Author

Palacky Univ, Fac Sci, Dept Zool - Author

Univ Antwerp, Dept Biol, Evolutionary Ecol Grp - Author

Univ Bern, Inst Ecol & Evolut, Evolutionary Ecol Lab - Author

Univ Coimbra, Fac Sci & Technol, Dept Life Sci, MARE Marine & Environm Sci Ctr - Author

Univ Exeter, Ctr Ecol & Conservat - Author

Univ Glasgow, Sch Biodivers One Hlth & Vet Med - Author

Univ Groningen, Groningen Inst Evolutionary Life Sci GELIFES - Author

Univ Helsinki, Zool Unit, Finnish Museum Nat Hist - Author

Univ Milan, Dipartimento Sci & Polit Ambientali - Author

Univ Montpellier, CNRS, IRD, CEFE,EPHE - Author

Univ Nat Resources & Life Sci, Inst Wildlife Biol & Game Management - Author

Univ Nevada - Author

Univ Oslo, Ctr Ecol & Evolutionary Synth CEES, Dept Biosci - Author

Univ Oulu, Dept Ecol & Genet - Author

Univ Oxford, Edward Grey Inst, Dept Biol - Author

Univ Padua, Dept Biol - Author

Univ Politecn Valencia, Inst Invest Gestio Integrada Zones Costaneres, Campus Gandia - Author

Univ Sheffield, Sch Biosci - Author

Univ Tartu, Dept Zool - Author

Univ Turku, Dept Biol - Author

Uppsala Univ, Anim Ecol Evolutionary Biol Ctr, Dept Ecol & Evolut - Author

Vrije Univ Amsterdam, Anim Ecol Grp, Dept Ecol Sci - Author

Wageningen Univ & Res, Anim Breeding & Genom - Author

Yamashina Inst Ornithol - Author

Abstract

A major aim of evolutionary biology is to understand why patterns of genomic diversity vary within taxa and space. Large-scale genomic studies of widespread species are useful for studying how environment and demography shape patterns of genomic divergence. Here, we describe one of the most geographically comprehensive surveys of genomic variation in a wild vertebrate to date; the great tit (Parus major) HapMap project. We screened ca 500,000 SNP markers across 647 individuals from 29 populations, spanning similar to 30 degrees of latitude and 40 degrees of longitude - almost the entire geographical range of the European subspecies. Genome-wide variation was consistent with a recent colonisation across Europe from a South-East European refugium, with bottlenecks and reduced genetic diversity in island populations. Differentiation across the genome was highly heterogeneous, with clear 'islands of differentiation', even among populations with very low levels of genome-wide differentiation. Low local recombination rates were a strong predictor of high local genomic differentiation (FST), especially in island and peripheral mainland populations, suggesting that the interplay between genetic drift and recombination causes highly heterogeneous differentiation landscapes. We also detected genomic outlier regions that were confined to one or more peripheral great tit populations, probably as a result of recent directional selection at the species' range edges. Haplotype-based measures of selection were related to recombination rate, albeit less strongly, and highlighted population-specific sweeps that likely resulted from positive selection. Our study highlights how comprehensive screens of genomic variation in wild organisms can provide unique insights into spatio-temporal evolutionary dynamics.

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Keywords

AdaptationBirdsClimate-changeDifferentiationDivergenceEcological geneticsEvolutionGene flowGenomics/proteomicsIslandsLandscapeLife below waterMolecular evolutionNatural-populationsPopulation geneticsPopulation genetics - empiricalSelectionSpeciation

Quality index

Bibliometric impact. Analysis of the contribution and dissemination channel

The work has been published in the journal Molecular Ecology Resources due to its progression and the good impact it has achieved in recent years, according to the agency WoS (JCR), it has become a reference in its field. In the year of publication of the work, 2024 there are still no calculated indicators, but in 2023, it was in position 21/200, thus managing to position itself as a Q1 (Primer Cuartil), in the category Ecology. Notably, the journal is positioned above the 90th percentile.

Independientemente del impacto esperado determinado por el canal de difusión, es importante destacar el impacto real observado de la propia aportación.

Según las diferentes agencias de indexación, el número de citas acumuladas por esta publicación hasta la fecha 2026-04-02:

WoS: 5
Scopus: 5

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Impact and social visibility

From the perspective of influence or social adoption, and based on metrics associated with mentions and interactions provided by agencies specializing in calculating the so-called "Alternative or Social Metrics," we can highlight as of 2026-04-02:

The use, from an academic perspective evidenced by the Altmetric agency indicator referring to aggregations made by the personal bibliographic manager Mendeley, gives us a total of: 60.
The use of this contribution in bookmarks, code forks, additions to favorite lists for recurrent reading, as well as general views, indicates that someone is using the publication as a basis for their current work. This may be a notable indicator of future more formal and academic citations. This claim is supported by the result of the "Capture" indicator, which yields a total of: 59 (PlumX).

With a more dissemination-oriented intent and targeting more general audiences, we can observe other more global scores such as:

The Total Score from Altmetric: 12.
The number of mentions on the social network X (formerly Twitter): 5 (Altmetric).
The number of mentions in news outlets: 1 (Altmetric).

It is essential to present evidence supporting full alignment with institutional principles and guidelines on Open Science and the Conservation and Dissemination of Intellectual Heritage. A clear example of this is:

The work has been submitted to a journal whose editorial policy allows open Open Access publication.
Assignment of a Handle/URN as an identifier within the deposit in the Institutional Repository: http://hdl.handle.net/1871.1/9524b356-a665-46f0-a650-207baf85eaf5

Continuing with the social impact of the work, it is important to emphasize that, due to its content, it can be assigned to the area of interest of ODS 14 - Conserve and sustainably use the oceans, seas and marine resources for sustainable development, with a probability of 66% according to the mBERT algorithm developed by Aurora University.

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Leadership analysis of institutional authors

This work has been carried out with international collaboration, specifically with researchers from: Austria; Belgium; Bulgaria; Czech Republic; Estonia; Finland; France; Germany; Greece; Hungary; Italy; Japan; Netherlands; Norway; Oman; Poland; Portugal; Russia; Sweden; Switzerland; Turkey; United Kingdom; United States of America.

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The great tit HapMap project: a continental-scale analysis of genomic variation in a songbird

Affiliations

Abstract

Keywords

Quality index

Bibliometric impact. Analysis of the contribution and dissemination channel

Leadership analysis of institutional authors