Genome Biology & Evolution



Genome Biology and Evolution (GBE) publishes leading original research at the interface between evolutionary biology and genomics. Papers considered for publication report novel evolutionary findings that concern natural genome diversity, population genomics, the structure, function, organisation and expression of genomes, comparative genomics, proteomics, and environmental genomic interactions. Major evolutionary insights from the fields of computational biology, structural biology, developmental biology, and cell biology are also considered, as are theoretical advances in the field of genome evolution. GBE’s scope embraces genome-wide evolutionary investigations at all taxonomic levels and for all forms of life — within populations or across domains. Its aims are to further the understanding of genomes in their evolutionary context and further the understanding of evolution from a genome-wide perspective.

GBE is owned by the Society for Molecular Biology and Evolution (SMBE). Motivated by the continued growth of the field, SMBE conducted a grass-roots survey in 2007 to investigate the needs of the field regarding new publication outlets. The survey elicited a resounding response from members of SMBE and other scientists in the fields of genomics and molecular evolution. The key findings from that survey were that the field wanted an on-line only journal that was devoted specifically to the areas of genome evolution and comparative genomics and that was published under an Open Access model. The response of SMBE was to launch GBE in order to serve those needs of the field. The SMBE meeting attracts about 800 participants each year. As a reflection of the rapid growth of genomic technologies, about half of the science presented at each SMBE meeting is about genomics. With the help of the evolutionary expertise that is gathered in SMBE, GBE is positioned and designed to set the highest standards for papers in the growing field of evolutionary genomics.

GBE is open access and does not require a SMBE membership for journal access.
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Molecular Biology and Evolution

2017-06-02

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From Chimps to Humans to Cold Sore Cousin Mixing Before Worldwide Spread

2017-05-11

Honing in on Culprit behind Fleece Variation in Domesticated Sheep

2017-05-08

2017-05-08

An Expanded History of Life on Earth at Your Fingertips

2017-05-08

Speciation and Genome Evolution in the Symbionts of Hominid Lice

2017-04-14

2017-04-13

2017-04-06

A Resource for Timelines, Timetrees, and Divergence Times

2017-04-06

2017-04-05

A Markov Clustering Approach to Study Population Genetic Structure

2017-04-05

2017-04-04

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2017-04-03

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2017-03-29

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2017-03-28

2017-03-27

2017-03-23

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2017-03-20

Eight Fast-Evolving Megacircles

2017-03-16

2017-03-15

New Insights from the Evolution of Human Chromosome 2 Ancestral Centromeric Region

2017-03-15

2017-03-13

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2017-03-01

the polycystine radiolarian Lithomelissa setosa (Nassellaria) and Sticholonche zanclea (Taxopodida). A phylogenomic approach using 255 genes finds Radiolaria and Foraminifera as separate monophyletic groups (together as Retaria), while Cercozoa is shown to be paraphyletic where Endomyxa is sister to Retaria. Analysis of the genetic components of the cytoskeleton and mapping of the evolution of these on the revised phylogeny of Rhizaria reveal lineage-specific gene duplications and neofunctionalization of α and β tubulin in Retaria, actin in Retaria and Endomyxa, and Arp2/3 complex genes in Chlorarachniophyta. We show how genetic innovations have shaped cytoskeletal structures in Rhizaria, and how single cell transcriptomics can be applied for resolving deep phylogenies and studying gene evolution in uncultured protist species.

GBE | Most Read

Genome Biology & Evolution

Extreme Mitogenomic Variation in Natural Populations of Chaetognaths

2017-06-14

Abstract
The extent of within-species genetic variation across the diversity of animal life is an underexplored problem in ecology and evolution. Although neutral genetic variation should scale positively with population size, mitochondrial diversity levels are believed to show little variation across animal species. Here, we report an unprecedented case of extreme mitochondrial diversity within natural populations of two morphospecies of chaetognaths (arrow worms). We determine that this diversity is composed of deep sympatric mitochondrial lineages, which are in some cases as divergent as human and platypus. Additionally, based on 54 complete mitogenomes, we observed mitochondrial gene order differences between several of these lineages. We examined nuclear divergence patterns (18S, 28S, and an intron) to determine the possible origin of these lineages, but did not find congruent patterns between mitochondrial and nuclear markers. We also show that extreme mitochondrial divergence in chaetognaths is not driven by positive selection. Hence, we propose that the extreme levels of mitochondrial variation could be the result of either a complex scenario of reproductive isolation, or a combination of large population size and accelerated mitochondrial mutation rate. These findings emphasize the importance of characterizing genome-wide levels of nuclear variation in these species and promote chaetognaths as a remarkable model to study mitochondrial evolution.

Unraveling the Population History of Indian Siddis

2017-06-14

Abstract
The Siddis are a unique Indian tribe of African, South Asian, and European ancestry. While previous investigations have traced their ancestral origins to the Bantu populations from subSaharan Africa, the geographic localization of their ancestry has remained elusive. Here, we performed biogeographical analysis to delineate the ancestral origin of the Siddis employing an admixture based algorithm, Geographical Population Structure (GPS). We evaluated the Siddi genomes in reference to five African populations from the 1000 Genomes project, two Bantu groups from the Human Genome Diversity Panel (HGDP) and five South Indian populations. The Geographic Population Structure analysis localized the ancestral Siddis to Botsawana and its present-day northeastern border with Zimbabwe, overlapping with one of the principal areas of secondary Bantu settlement in southeast Africa. Our results further indicated that while the Siddi genomes are significantly diverged from that of the Bantus, they manifested the highest genomic proximity to the North-East Bantus and the Luhyas from Kenya. Our findings resonate with evidences supporting secondary Bantu dispersal routes that progressed southward from the east African Bantu center, in the interlacustrine region and likely brought the ancestral Siddis to settlement sites in south and southeastern Africa from where they were disseminated to India, by the Portuguese. We evaluated our results in the light of existing historical, linguistic and genetic evidences, to glean an improved resolution into the reconstruction of the distinctive population history of the Siddis, and advance our knowledge of the demographic factors that likely contributed to the contemporary Siddi genomes.

The Genomic Impact of Gene Retrocopies: What Have We Learned from Comparative Genomics, Population Genomics, and Transcriptomic Analyses?

2017-06-14

Abstract
Gene duplication is a major driver of organismal evolution. Gene retroposition is a mechanism of gene duplication whereby a gene’s transcript is used as a template to generate retroposed gene copies, or retrocopies. Intriguingly, the formation of retrocopies depends upon the enzymatic machinery encoded by retrotransposable elements, genomic parasites occurring in the majority of eukaryotes. Most retrocopies are depleted of the regulatory regions found upstream of their parental genes; therefore, they were initially considered transcriptionally incompetent gene copies, or retropseudogenes. However, examples of functional retrocopies, or retrogenes, have accumulated since the 1980s. Here, we review what we have learned about retrocopies in animals, plants and other eukaryotic organisms, with a particular emphasis on comparative and population genomic analyses complemented with transcriptomic datasets. In addition, these data have provided information about the dynamics of the different “life cycle” stages of retrocopies (i.e., polymorphic retrocopy number variants, fixed retropseudogenes and retrogenes) and have provided key insights into the retroduplication mechanisms, the patterns and evolutionary forces at work during the fixation process and the biological function of retrogenes. Functional genomic and transcriptomic data have also revealed that many retropseudogenes are transcriptionally active and a biological role has been experimentally determined for many. Finally, we have learned that not only non-long terminal repeat retroelements but also long terminal repeat retroelements play a role in the emergence of retrocopies across eukaryotes. This body of work has shown that mRNA-mediated duplication represents a widespread phenomenon that produces an array of new genes that contribute to organismal diversity and adaptation.