Comparative phylogenomic analyses of teleost fish Hox gene clusters: lessons from the cichlid fish Astatotilapia burtoni: comment

SummaryThe alphaproteobacterial genus Bradyrhizobium has been best known as N2-fixing members that nodulate legumes, supported by the nif and nod gene clusters. Recent environmental surveys show that Bradyrhizobium represents one of the most abundant free-living bacterial lineages in the world’s soils. However, our understanding of Bradyrhizobium comes largely from symbiotic members, biasing the current knowledge of their ecology and evolution. Here, we report the genomes of 88 Bradyrhizobium strains derived from diverse soil samples, including both nif-carrying and non-nif-carrying free-living (nod free) members. Phylogenomic analyses of these and 252 publicly available Bradyrhizobium genomes indicate that nif-carrying free-living members independently evolved from symbiotic ancestors (carrying both nif and nod) multiple times. Intriguingly, the nif phylogeny shows that all nif-carrying free-living members comprise a cluster which branches off earlier than most symbiotic lineages. These results indicate that horizontal gene transfer (HGT) promotes nif expansion among the free-living Bradyrhizobium and that the free-living nif cluster represents a more ancestral version compared to that in symbiotic lineages. Further evidence for this rampant HGT is that the nif in free-living members consistently co-locate with several important genes involved in coping with oxygen tension which are missing from symbiotic members, and that while in free-living Bradyrhizobium nif and the co-locating genes show a highly conserved gene order, they each have distinct genomic context. Given the dominance of Bradyrhizobium in world’s soils, our findings have implications for global nitrogen cycles and agricultural research.

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Visual Information Alone Changes Behavior and Physiology during Social Interactions in a Cichlid Fish (Astatotilapia burtoni)

PLoS ONE ◽

10.1371/journal.pone.0020313 ◽

2011 ◽

Vol 6 (5) ◽

pp. e20313 ◽

Cited By ~ 32

Author(s):

Chun-Chun Chen ◽

Russell D. Fernald

Keyword(s):

Social Interactions ◽

Visual Information ◽

Cichlid Fish ◽

Astatotilapia Burtoni

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Heritability and adaptive significance of the number of egg-dummies in the cichlid fish Astatotilapia burtoni

Proceedings of The Royal Society B Biological Sciences ◽

10.1098/rspb.2010.2483 ◽

2011 ◽

Vol 278 (1716) ◽

pp. 2318-2324 ◽

Cited By ~ 7

Author(s):

Topi K. Lehtonen ◽

Axel Meyer

Keyword(s):

Species Recognition ◽

Cichlid Fish ◽

Fertilization Success ◽

Narrow Sense Heritability ◽

Key Innovation ◽

Bright Spots ◽

Spot Number ◽

Astatotilapia Burtoni ◽

Important Trait ◽

High Degree

Cichlid fishes are a textbook example of rapid speciation and exuberant diversity—this applies especially to haplochromines, a lineage with approximately 1800 species. Haplochromine males uniquely possess oval, bright spots on their anal fin, called ‘egg-spots’ or ‘egg-dummies’. These are presumed to be an evolutionary key innovation that contributed to the tribe's evolutionary success. Egg-spots have been proposed to mimic the ova of the mouthbrooding females of the corresponding species, contribute to fertilization success and even facilitate species recognition. Interestingly, egg-spot number varies extensively not only between species, but also within some populations. This high degree of intraspecific variation may appear to be counterintuitive since selection might be expected to act to stabilize traits that are correlated with fitness measures. We addressed this ‘paradox’ experimentally, and found that in the haplochromine cichlid Astatotilapia burtoni , the number of egg-spots was related to male age, body condition and dominance status. Intriguingly, the egg-spot number also had a high heritable component (narrow sense heritability of 0.5). These results suggest that the function of egg-spots might have less to do with fertilization success or species recognition, but rather relate to mate choice and/or male–male competition, helping to explain the high variability in this important trait.

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