Evolutionary Biology
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Publications

Some recent publications by subject (full list see here)

SPECIATION

Admixture mapping reveals the crow’s secret
Knief U, Bossu CM, Saino N et al. (2019) Epistatic mutations under divergent selection govern phenotypic variation in the crow hybrid zone. Nat Ecol Evol: 3: 570–576.

Genomic islands of differentiation in a multiple-population context
Vijay N*, Bossu CM*, Poelstra JW, Weissensteiner MH, Suh A, Kryukov AP, Wolf JBW (2016) Evolution of heterogenous genome differentiation across multiple contact zones in a crow species complex. Nat Commun, 7: 13195.

Interaction of socially transmitted hunting practice and population divergence
Foote A*, Vijay N*, Avila-Arcos M et al. (2016) Genome-culture coevolution promotes rapid divergence of killer whale ecotypes. Nat Commun, 7: 11693.

EVOLUTIONARY ECOLOGY

Long- and short-term measures of population size contain information on conservation status
Peart CP*, Tusso S*, Pophaly SD* et al. (2020) Determinants of genetic variation across eco-evolutionary scales in pinnipeds. Nat Ecol Evol, in press.

Rapid bio-diversification by shuffling genomes
Tusso S, Nieuwenhuis BPS, Sedlazeck FJ et al. (2019) Ancestral admixture is the main determinant of global biodiversity in fission yeast. Mol Biol Evol, 36: 1975–1989.

On the difficult decision of choosing the right configuration of your mating locus
Nieuwenhuis BPS*, Tusso S* et al. (2018) Repeated evolution of self-compatibility for reproductive assurance. Nat Commun, 9: 1639. 

MOLECULAR EVOLUTION

A large inventory of structural mutations and their relevance to speciation
Weissensteiner MH, Bunikis I, Catalán A et al. (2020) The population genomics of structural variation in a songbird genus, Nat Commun, in press.

Support for the central tenet of nearly-neutral evolutionary theory
Kutschera VE, Poelstra JW, Botero-Castro F et al. (2020) Purifying selection in corvids Is less efficient on islands. Mol Biol Evol, 37: 469–474.

The dark matter of the genome matters
Weissensteiner MH, Pang AWC, Bunikis I et al. (2017) Combination of short-read, long-read, and optical mapping assemblies reveals large-scale tandem repeat arrays with population genetic implications. Genome Res, 27: 697–708.

METHODOLOGY

Time dependency of dN/dS after speciation
M
ugal CF, Kutschera VE, Botero-Castro F et al. (2020) Polymorphism Data Assist Estimation of the Nonsynonymous over Synonymous Fixation Rate Ratio ω for Closely Related Species. Mol Biol Evol, 37: 260–279.

To what extent do bioinformatic pipelines bias biological reality?
Shafer ABA, Peart CR, Tusso S, Maayan I, Brelsford A, Wheat CW, Wolf JBW (2017) Bioinformatic processing of RAD-seq data dramatically impacts downstream population genetic inference. Methods Ecol Evol, 16: 940–950.

GBS goes ABC
Shafer ABA, Gattepaille LM, Stewart REA, Wolf JBW (2015) Demographic inferences using short-read genomic data in an approximate Bayesian computation framework: in silico evaluation of power, biases and proof of concept in Atlantic walrus. Mol Ecol, 24: 328–345.

REVIEW & OPINION

Relevance and empirical access to a central biological parameter
Peñalba JV & Wolf JBW (2020) From molecules to populations: appreciating and estimating recombination rate variation. Nat Rev Genet, in press

Study design and interpretation of speciation genomic studies
Wolf JBW & Ellegren H (2016) Making sense of genomic islands of differentiation in light of speciation. Nat Rev Genet, 18: 87-100.

What may happen if we join genomics with tracking technology?
Shafer ABA, Northrup JM, Wikelski M et al. (2016) Forecasting Ecological Genomics: High-Tech Animal Instrumentation Meets High-Throughput Sequencing. PLoS Biol, 14: e1002350.

OLDER KEY PUBLICATIONS

Insight from Wik slott near Uppsala - thank you all for a nice workshop
Shafer ABA, Wolf JBW, Alves PC et al. (2015) Genomics and the challenging translation into conservation practice. Trends Ecol Evol, 30: 78–87. 

A comprehensive speciation genomic study in European crows
Poelstra JW*, Vijay N*, Bossu C* et al. (2014) The genomic landscape underlying phenotypic integrity in the face of gene flow in crows. Science, 344: 1410-1414.

Pervasive isolation-by-ecology pattern is consistent with ecologcial speciation theory
Shafer A & Wolf JBW (2013) Widespread evidence for incipient ecological speciation: a meta-analysis of isolation-by-ecology. Ecol Lett, 16: 940-950.

The genomic landscape of speciation: an avian example
Ellegren H, Smeds L, Burri R et al. (2012) The genomic landscape of species divergence in Ficedula flycatchers. Nature, 491: 756-760.