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Evolutionary Genomics

Guest editors: Sarah Tishkoff and Hans Ellegren

© Credit: David Brossard, CC BY-SA 2

The study of evolution is being transformed by the use and integration of ‘big data’ with other well-established approaches, to advance our understanding of evolutionary processes. Genome Biology will highlight these advances in evolutionary genomics with a special issue showcasing important work in this area. 

Evolutionary Genomics

Genomic approaches for studying crop evolution
Understanding how crop plants evolved from their wild relatives and spread around the world can inform about the origins of agriculture. Here, we review how the rapid development of genomic resources and tools...
Mona Schreiber, Nils Stein and Martin Mascher
Genome Biology 2018 19:140
Published on: 21 September 2018

A new look at an old question: when did the second whole genome duplication occur in vertebrate evolution?
A recent study used 61 extant animal genomes to reconstruct the chromosomes of the hypothetical amniote ancestor. Comparison of this karyotype to the 17 chordate linkage groups previously inferred in the ances...
Linda Z. Holland and Daniel Ocampo Daza
Genome Biology 2018 19:209
Published on: 28 November 2018

The bird’s-eye view on chromosome evolution
The study of the evolution of chromosomal number and structure has long been of interest to evolutionary biologists. However, this research has been hindered by the lack of chromosome-level genome assemblies f...
Guojie Zhang
Genome Biology 2018 19:201
Published on: 23 November 2018

Adding resolution and dimensionality to comparative genomics: moving from reference genomes to clade genomics
The main goal and promise of comparative genomics has been to create a comprehensive catalog of genomic information and function across the phenomenal diversity of living systems. A recent study has demonstrat...
Jeffrey Rogers
Genome Biology 2018 19:115
Published on: 14 August 2018

Investigating enhancer evolution with massively parallel reporter assays
A recent study in Genome Biology has characterized the evolution of candidate hominoid-specific liver enhancers by using massively parallel reporter assays (MPRAs).
Soo Bin Kwon and Jason Ernst
Genome Biology 2018 19:114
Published on: 14 August 2018

A history of male migration in and out of the Green Sahara
The Sahara was once fertile; a recent study identifies ... human Y-chromosomal lineages that flourished in this Green Sahara and their relation to present-day populations.
Yali Xue
Genome Biology 2018 19:30
Published on: 13 March 2018

GC-biased gene conversion conceals the prediction of the nearly neutral theory in avian genomes
The nearly neutral theory of molecular evolution predicts that the efficacy of natural selection increases with the effective population size. This prediction has been verified by independent observations in d...
Paulina Bolívar, Laurent Guéguen, Laurent Duret, Hans Ellegren and Carina F. Mugal
Genome Biology 2019 20:5
Published on: 7 January 2019

Recombination of ecologically and evolutionarily significant loci maintains genetic cohesion in the Pseudomonas syringae species complex
Pseudomonas syringae is a highly diverse bacterial species complex capable of causing a wide range of serious diseases on numerous agronomically important crops. We examine the evolutionary relationships of 391 a...
Marcus M. Dillon, Shalabh Thakur, Renan N. D. Almeida, Pauline W. Wang, Bevan S. Weir and David S. Guttman
Genome Biology 2019 20:3
Published on: 3 January 2019

Genomes reveal marked differences in the adaptive evolution between orangutan species
Integrating demography and adaptive evolution is pivotal to understanding the evolutionary history and conservation of great apes. However, little is known about the adaptive evolution of our closest relatives...
Maja P. Mattle-Greminger, Tugce Bilgin Sonay, Alexander Nater, Marc Pybus, Tariq Desai, Guillem de Valles, Ferran Casals, Aylwyn Scally, Jaume Bertranpetit, Tomas Marques-Bonet, Carel P. van Schaik, Maria Anisimova and Michael Krützen
Genome Biology 2018 19:193
Published on: 15 November 2018

Comparative genomics reveals the distinct evolutionary trajectories of the robust and complex coral lineage
Despite the biological and economic significance of scleractinian reef-building corals, the lack of large molecular datasets for a representative range of species limits understanding of many aspects of their ...
Hua Ying, Ira Cooke, Susanne Sprungala, Weiwen Wang, David C. Hayward, Yurong Tang, Gavin Huttley, Eldon E. Ball, Sylvain Forêt and David J. Miller
Genome Biology 2018 19:175
Published on: 2 November 2018

Chromosome-level assembly reveals extensive rearrangement in saker falcon and budgerigar, but not ostrich, genomes
The number of de novo genome sequence assemblies is increasing exponentially; however, relatively few contain one scaffold/contig per chromosome. Such assemblies are essential for studies of genotype-to-phenot...
Rebecca E O’Connor, Marta Farré, Sunitha Joseph, Joana Damas, Lucas Kiazim, Rebecca Jennings, Sophie Bennett, Eden A Slack, Emily Allanson, Denis M Larkin and Darren K Griffin
Genome Biology 2018 19:171
Published on: 24 October 2018

Chromosome evolution at the origin of the ancestral vertebrate genome
It has been proposed that more than 450 million years ago, two successive whole genome duplications took place in a marine chordate lineage before leading to the common ancestor of vertebrates. A precise recon...
Christine Sacerdot, Alexandra Louis, Céline Bon, Camille Berthelot and Hugues Roest Crollius
Genome Biology 2018 19:166
Published on: 17 October 2018

A comparative study of endoderm differentiation in humans and chimpanzees
There is substantial interest in the evolutionary forces that shaped the regulatory framework in early human development. Progress in this area has been slow because it is difficult to obtain relevant biologic...
Lauren E. Blake, Samantha M. Thomas, John D. Blischak, Chiaowen Joyce Hsiao, Claudia Chavarria, Marsha Myrthil, Yoav Gilad and Bryan J. Pavlovic
Genome Biology 2018 19:162
Published on: 15 October 2018

Modularity of genes involved in local adaptation to climate despite physical linkage
Linkage among genes experiencing different selection pressures can make natural selection less efficient. Theory predicts that when local adaptation is driven by complex and non-covarying stresses, increased l...
Katie E Lotterhos, Sam Yeaman, Jon Degner, Sally Aitken and Kathryn A Hodgins
Genome Biology 2018 19:157
Published on: 5 October 2018

Reconstruction of avian ancestral karyotypes reveals differences in the evolutionary history of macro- and microchromosomes
Reconstruction of ancestral karyotypes is critical for our understanding of genome evolution, allowing for the identification of the gross changes that shaped extant genomes. The identification of such changes...
Joana Damas, Jaebum Kim, Marta Farré, Darren K Griffin and Denis M Larkin
Genome Biology 2018 19:155
Published on: 5 October 2018

Evolutionary and developmental dynamics of sex-biased gene expression in common frogs with proto-Y chromosomes
The patterns of gene expression on highly differentiated sex chromosomes differ drastically from those on autosomes, due to sex-specific patterns of selection and inheritance. As a result, X chromosomes are of...
Wen-Juan Ma, Paris Veltsos, Roberto Sermier, Darren J Parker and Nicolas Perrin
Genome Biology 2018 19:156
Published on: 5 October 2018

Ankyrin domain encoding genes from an ancient horizontal transfer are functionally integrated into Nasonia developmental gene regulatory networks
How regulatory networks incorporate additional components and how novel genes are functionally integrated into well-established developmental processes are two important and intertwined questions whose answers...
Daniel Pers and Jeremy A. Lynch
Genome Biology 2018 19:148
Published on: 28 September 2018

ABLE: blockwise site frequency spectra for inferring complex population histories and recombination
We introduce ABLE (Approximate Blockwise Likelihood Estimation), a novel simulation-based composite likelihood method that uses the blockwise site frequency spectrum to jointly infer past demography and recomb...
Champak R. Beeravolu, Michael J. Hickerson, Laurent A. F. Frantz and Konrad Lohse
Genome Biology 2018 19:145
Published on: 25 September 2018

Genes reveal traces of common recent demographic history for most of the Uralic-speaking populations
The genetic origins of Uralic speakers from across a vast territory in the temperate zone of North Eurasia have remained elusive. Previous studies have shown contrasting proportions of Eastern and Western Eura...
Kristiina Tambets, Bayazit Yunusbayev, Georgi Hudjashov, Anne-Mai Ilumäe, Siiri Rootsi, Terhi Honkola, Outi Vesakoski, Quentin Atkinson, Pontus Skoglund, Alena Kushniarevich, Sergey Litvinov, Maere Reidla, Ene Metspalu, Lehti Saag, Timo Rantanen, Monika Karmin
Genome Biology 2018 19:139
Published on: 21 September 2018

Origin of exon skipping-rich transcriptomes in animals driven by evolution of gene architecture
Alternative splicing, particularly through intron retention and exon skipping, is a major layer of pre-translational regulation in eukaryotes. While intron retention is believed to be the most prevalent mode a...
Xavier Grau-Bové, Iñaki Ruiz-Trillo and Manuel Irimia
Genome Biology 2018 19:135
Published on: 17 September 2018

Comparative transcriptomic analyses and single-cell RNA sequencing of the freshwater planarian Schmidtea mediterranea identify major cell types and pathway conservation
In the Lophotrochozoa/Spiralia superphylum, few organisms have as high a capacity for rapid testing of gene function and single-cell transcriptomics as the freshwater planaria. The species Schmidtea mediterranea ...
Lakshmipuram Seshadri Swapna, Alyssa M. Molinaro, Nicole Lindsay-Mosher, Bret J. Pearson and John Parkinson
Genome Biology 2018 19:124
Published on: 24 August 2018

A simple genetic basis of adaptation to a novel thermal environment results in complex metabolic rewiring in Drosophila
Population genetic theory predicts that rapid adaptation is largely driven by complex traits encoded by many loci of small effect. Because large-effect loci are quickly fixed in natural populations, they shoul...
François Mallard, Viola Nolte, Ray Tobler, Martin Kapun and Christian Schlötterer
Genome Biology 2018 19:119
Published on: 20 August 2018

Evolutionarily conserved partial gene duplication in the Triticeae tribe of grasses confers pathogen resistance
The large and highly repetitive genomes of the cultivated species Hordeum vulgare (barley), Triticum aestivum (wheat), and Secale cereale (rye) belonging to the Triticeae tribe of grasses appear to be particularl...
Jeyaraman Rajaraman, Dimitar Douchkov, Stefanie Lück, Götz Hensel, Daniela Nowara, Maria Pogoda, Twan Rutten, Tobias Meitzel, Jonathan Brassac, Caroline Höfle, Ralph Hückelhoven, Jörn Klinkenberg, Marco Trujillo, Eva Bauer, Thomas Schmutzer, Axel Himmelbach…
Genome Biology 2018 19:116
Published on: 15 August 2018

Selection-driven cost-efficiency optimization of transcripts modulates gene evolutionary rate in bacteria
Most amino acids are encoded by multiple synonymous codons. However, synonymous codons are not used equally, and this biased codon use varies between different organisms. It has previously been shown that both...
Emily A. Seward and Steven Kelly
Genome Biology 2018 19:102
Published on: 31 July 2018

The genomic impact of historical hybridization with massive mitochondrial DNA introgression
The extent to which selection determines interspecific patterns of genetic exchange enlightens the role of adaptation in evolution and speciation. Often reported extensive interspecific introgression could be ...
Fernando A. Seixas, Pierre Boursot and José Melo-Ferreira
Genome Biology 2018 19:91
Published on: 30 July 2018

Functional characterization of enhancer evolution in the primate lineage
Enhancers play an important role in morphological evolution and speciation by controlling the spatiotemporal expression of genes. Previous efforts to understand the evolution of enhancers in primates have typi...
Jason C. Klein, Aidan Keith, Vikram Agarwal, Timothy Durham and Jay Shendure
Genome Biology 2018 19:99
Published on: 25 July 2018

Wnt evolution and function shuffling in liberal and conservative chordate genomes
What impact gene loss has on the evolution of developmental processes, and how function shuffling has affected retained genes driving essential biological processes, remain open questions in the fields of geno...
Ildikó M. L. Somorjai, Josep Martí-Solans, Miriam Diaz-Gracia, Hiroki Nishida, Kaoru S. Imai, Hector Escrivà, Cristian Cañestro and Ricard Albalat
Genome Biology 2018 19:98
Published on: 25 July 2018

Epistasis analysis uncovers hidden antibiotic resistance-associated fitness costs hampering the evolution of MRSA
Fitness costs imposed on bacteria by antibiotic resistance mechanisms are believed to hamper their dissemination. The scale of these costs is highly variable. Some, including resistance of Staphylococcus aureus t...
Maho Yokoyama, Emily Stevens, Maisem Laabei, Leann Bacon, Kate Heesom, Sion Bayliss, Nicola Ooi, Alex J. O’Neill, Ewan Murray, Paul Williams, Anneke Lubben, Shaun Reeksting, Guillaume Meric, Ben Pascoe, Samuel K. Sheppard, Mario Recker…
Genome Biology 2018 19:94
Published on: 18 July 2018

Horizontal transfer of BovB and L1 retrotransposons in eukaryotes
Transposable elements (TEs) are mobile DNA sequences, colloquially known as jumping genes because of their ability to replicate to new genomic locations. TEs can jump between organisms or species when given a ...
Atma M. Ivancevic, R. Daniel Kortschak, Terry Bertozzi and David L. Adelson
Genome Biology 2018 19:85
Published on: 9 July 2018

Post-translational buffering leads to convergent protein expression levels between primates
Differences in gene regulation between human and closely related species influence phenotypes that are distinctly human. While gene regulation is a multi-step process, the majority of research concerning diver...
Sidney H. Wang, Chiaowen Joyce Hsiao, Zia Khan and Jonathan K. Pritchard
Genome Biology 2018 19:83
Published on: 27 June 2018

Hundreds of novel composite genes and chimeric genes with bacterial origins contributed to haloarchaeal evolution
Haloarchaea, a major group of archaea, are able to metabolize sugars and to live in oxygenated salty environments. Their physiology and lifestyle strongly contrast with that of their archaeal ancestors. Amino ...
Raphaël Méheust, Andrew K. Watson, François-Joseph Lapointe, R. Thane Papke, Philippe Lopez and Eric Bapteste
Genome Biology 2018 19:75
Published on: 7 June 2018

A major locus controls local adaptation and adaptive life history variation in a perennial plant
The initiation of growth cessation and dormancy represent critical life-history trade-offs between survival and growth and have important fitness effects in perennial plants. Such adaptive life-history traits ...
Jing Wang, Jihua Ding, Biyue Tan, Kathryn M. Robinson, Ingrid H. Michelson, Anna Johansson, Björn Nystedt, Douglas G. Scofield, Ove Nilsson, Stefan Jansson, Nathaniel R. Street and Pär K. Ingvarsson
Genome Biology 2018 19:72
Published on: 4 June 2018

Developmental transcriptomics of the brittle star Amphiura filiformis reveals gene regulatory network rewiring in echinoderm larval skeleton evolution
Amongst the echinoderms the class Ophiuroidea is of particular interest for its phylogenetic position, ecological importance and developmental and regenerative biology. However, compared to other echinoderms, ...
David V. Dylus, Anna Czarkwiani, Liisa M. Blowes, Maurice R. Elphick and Paola Oliveri
Genome Biology 2018 19:26
Published on: 28 February 2018

The peopling of the last Green Sahara revealed by high-coverage resequencing of trans-Saharan patrilineages
In order to investigate the role of the last Green Sahara in the peopling of Africa, we deep-sequence the whole non-repetitive portion of the Y chromosome in 104 males selected as representative of haplogroups wh...
Eugenia D’Atanasio, Beniamino Trombetta, Maria Bonito, Andrea Finocchio, Genny Di Vito, Mara Seghizzi, Rita Romano, Gianluca Russo, Giacomo Maria Paganotti, Elizabeth Watson, Alfredo Coppa, Paolo Anagnostou, Jean-Michel Dugoujon, Pedro Moral, Daniele Sellitto, Andrea Novelletto…
Genome Biology 2018 19:20
Published on: 12 February 2018

Adaptation of Arabidopsis thaliana to the Yangtze River basin
Organisms need to adapt to keep pace with a changing environment. Examining recent range expansion aids our understanding of how organisms evolve to overcome environmental constraints. However, how organisms a...
Yu-Pan Zou, Xing-Hui Hou, Qiong Wu, Jia-Fu Chen, Zi-Wen Li, Ting-Shen Han, Xiao-Min Niu, Li Yang, Yong-Chao Xu, Jie Zhang, Fu-Min Zhang, Dunyan Tan, Zhixi Tian, Hongya Gu and Ya-Long Guo
Genome Biology 2017 18:239
Published on: 28 December 2017