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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

RESEARCH

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

RESEARCH

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

RESEARCH

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

RESEARCH HIGHLIGHT

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

RESEARCH

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

RESEARCH

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

RESEARCH

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

RESEARCH

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

RESEARCH

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

RESEARCH

 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

RESEARCH

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

RESEARCH

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

RESEARCH

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

RESEARCH

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

RESEARCH

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

RESEARCH HIGHLIGHT

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

RESEARCH HIGHLIGHT

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

RESEARCH

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