scholarly journals Mapping epigenetic divergence in the massive radiation of Lake Malawi cichlid fishes

2021 ◽  
Vol 12 (1) ◽  
Author(s):  
Grégoire Vernaz ◽  
Milan Malinsky ◽  
Hannes Svardal ◽  
Mingliu Du ◽  
Alexandra M. Tyers ◽  
...  
Keyword(s):  
Phenotypic Diversity ◽  
Sequence Divergence ◽  
Lake Malawi ◽  
Cichlid Species ◽  
Adaptive Diversification ◽  
Cichlid Fishes ◽  
Muscle Tissues ◽  
Genome Wide ◽  
Dietary Ecology ◽  
Species Specific

AbstractEpigenetic variation modulates gene expression and can be heritable. However, knowledge of the contribution of epigenetic divergence to adaptive diversification in nature remains limited. The massive evolutionary radiation of Lake Malawi cichlid fishes displaying extensive phenotypic diversity despite extremely low sequence divergence is an excellent system to study the epigenomic contribution to adaptation. Here, we present a comparative genome-wide methylome and transcriptome study, focussing on liver and muscle tissues in phenotypically divergent cichlid species. In both tissues we find substantial methylome divergence among species. Differentially methylated regions (DMR), enriched in evolutionary young transposons, are associated with transcription changes of ecologically-relevant genes related to energy expenditure and lipid metabolism, pointing to a link between dietary ecology and methylome divergence. Unexpectedly, half of all species-specific DMRs are shared across tissues and are enriched in developmental genes, likely reflecting distinct epigenetic developmental programmes. Our study reveals substantial methylome divergence in closely-related cichlid fishes and represents a resource to study the role of epigenetics in species diversification.

scholarly journals The methylomes of Lake Malawi cichlids reveal epigenetic variation associated with phenotypic diversification

2020 ◽  
Author(s):  
Grégoire Vernaz ◽  
Milan Malinsky ◽  
Hannes Svardal ◽  
Mingliu Du ◽  
Alexandra M. Tyers ◽  
...  
Keyword(s):  
Dna Sequences ◽  
Lake Malawi ◽  
Early Embryogenesis ◽  
Epigenetic Variation ◽  
Cichlid Fishes ◽  
Muscle Tissues ◽  
Genome Wide ◽  
Evolutionary Radiation ◽  
Dietary Ecology ◽  
Phenotypic Diversification

ABSTRACTEpigenetic variation modulates gene expression and can be heritable. However, knowledge of the contribution of epigenetic variation to diversification and speciation in nature remains limited. Here, we present the first genome-wide methylome study in a large vertebrate evolutionary radiation, focussing on liver and muscle tissues in six genetically similar but eco-morphologically divergent cichlid fishes from Lake Malawi. In both tissues we find substantial methylome divergence in DNA sequences conserved between species and differentially methylated regions (DMR) are significantly enriched in recently active transposable elements. DMRs in the liver are associated with transcription changes of genes with hepatic functions, pointing to a link between dietary ecology and methylome divergence. Unexpectedly, DMRs shared across adult tissues are enriched in genes involved in embryonic and developmental processes, suggesting roles in early embryogenesis. Our study provides initial evidence for DNA methylation contributing to phenotypic diversification of cichlids, and represents an important resource for further work.

scholarly journals Astiotrema turneri n. sp. (Digenea: Plagiorchiidae) from cichlid fishes (Cichlidae: Perciformes) of Lake Malawi, south-eastern Africa

Zootaxa ◽  
2006 ◽  
Vol 1319 (1) ◽  
pp. 43 ◽  
Author(s):  
RODNEY A. BRAY ◽  
COCK VAN OOSTERHOUT ◽  
JONATAN BLAIS ◽  
JOANNE CABLE
Keyword(s):  
Ventral Sucker ◽  
Body Shape ◽  
Lake Malawi ◽  
Eastern Africa ◽  
Intestinal Bifurcation ◽  
Cichlid Species ◽  
Cichlid Fishes ◽  
South Eastern

Astiotrema turneri n. sp. is described from the cichlid species Pseudotropheus zebra, P. emmiltos, Labeotropheus trewavasae and Melanochromis vermivorus from Lake Malawi. It differs from Astiotrema reniferum (as described by Yeh & Fotedar 1958) in its distinctly broader body, the much smaller cirrus-sac, its oblique testes, the shorter ventral sucker to ovary distance, the vitellarium reaching into the forebody and the extracaecal uterus; from Astiotrema impletum in the sucker-ratio, the longer caeca, the smaller cirrus-sac and the extracaecal uterus; and from Glossidium pedatum (and its probable synonyms Astiotrema lazeri and Afromacroderoides lazerae) in its much broader body shape, in its distinct oesophagus, the intestinal bifurcation in the posterior forebody, in the distinctly oblique testes, the extracaecal uterus and the vitellarium reaching well into the forebody.

scholarly journals A Hybrid Genetic Linkage Map of Two Ecologically and Morphologically Divergent Midas Cichlid Fishes (Amphilophus spp.) Obtained by Massively Parallel DNA Sequencing (ddRADSeq)

2013 ◽  
Vol 3 (1) ◽  
pp. 65-74 ◽  
Author(s):  
Hans Recknagel ◽  
Kathryn R Elmer ◽  
Axel Meyer
Keyword(s):  
Dna Sequencing ◽  
Linkage Map ◽  
Phenotypic Diversity ◽  
Interspecific Cross ◽  
Comparative Genomic ◽  
Linkage Groups ◽  
Cichlid Species ◽  
Cichlid Fishes ◽  
A Genome ◽  
Adaptive Radiations

Abstract Cichlid fishes are an excellent model system for studying speciation and the formation of adaptive radiations because of their tremendous species richness and astonishing phenotypic diversity. Most research has focused on African rift lake fishes, although Neotropical cichlid species display much variability as well. Almost one dozen species of the Midas cichlid species complex (Amphilophus spp.) have been described so far and have formed repeated adaptive radiations in several Nicaraguan crater lakes. Here we apply double-digest restriction-site associated DNA sequencing to obtain a high-density linkage map of an interspecific cross between the benthic Amphilophus astorquii and the limnetic Amphilophus zaliosus, which are sympatric species endemic to Crater Lake Apoyo, Nicaragua. A total of 755 RAD markers were genotyped in 343 F2 hybrids. The map resolved 25 linkage groups and spans a total distance of 1427 cM with an average marker spacing distance of 1.95 cM, almost matching the total number of chromosomes (n = 24) in these species. Regions of segregation distortion were identified in five linkage groups. Based on the pedigree of parents to F2 offspring, we calculated a genome-wide mutation rate of 6.6 × 10−8 mutations per nucleotide per generation. This genetic map will facilitate the mapping of ecomorphologically relevant adaptive traits in the repeated phenotypes that evolved within the Midas cichlid lineage and, as the first linkage map of a Neotropical cichlid, facilitate comparative genomic analyses between African cichlids, Neotropical cichlids and other teleost fishes.

scholarly journals Gene coexpression networks reveal molecular interactions underlying cichlid jaw modularity

2021 ◽  
Vol 21 (1) ◽  
Author(s):  
Pooja Singh ◽  
Ehsan Pashay Ahi ◽  
Christian Sturmbauer
Keyword(s):  
In Silico ◽  
Regulatory Networks ◽  
Evolutionary Significance ◽  
Cichlid Species ◽  
Cichlid Fishes ◽  
Gene Coexpression ◽  
Modular Evolution ◽  
Jaw Apparatus ◽  
Coexpression Networks ◽  
Pharyngeal Jaw

Abstract Background The oral and pharyngeal jaw of cichlid fishes are a classic example of evolutionary modularity as their functional decoupling boosted trophic diversification and contributed to the success of cichlid adaptive radiations. Most studies until now have focused on the functional, morphological, or genetic aspects of cichlid jaw modularity. Here we extend this concept to include transcriptional modularity by sequencing whole transcriptomes of the two jaws and comparing their gene coexpression networks. Results We show that transcriptional decoupling of gene expression underlies the functional decoupling of cichlid oral and pharyngeal jaw apparatus and the two units are evolving independently in recently diverged cichlid species from Lake Tanganyika. Oral and pharyngeal jaw coexpression networks reflect the common origin of the jaw regulatory program as there is high preservation of gene coexpression modules between the two sets of jaws. However, there is substantial rewiring of genetic architecture within those modules. We define a global jaw coexpression network and highlight jaw-specific and species-specific modules within it. Furthermore, we annotate a comprehensive in silico gene regulatory network linking the Wnt and AHR signalling pathways to jaw morphogenesis and response to environmental cues, respectively. Components of these pathways are significantly differentially expressed between the oral and pharyngeal jaw apparatus. Conclusion This study describes the concerted expression of many genes in cichlid oral and pharyngeal jaw apparatus at the onset of the independent life of cichlid fishes. Our findings suggest that – on the basis of an ancestral gill arch network—transcriptional rewiring may have driven the modular evolution of the oral and pharyngeal jaws, highlighting the evolutionary significance of gene network reuse. The gene coexpression and in silico regulatory networks presented here are intended as resource for future studies on the genetics of vertebrate jaw morphogenesis and trophic adaptation.

scholarly journals The Tomato Interspecific NB-LRR Gene Arsenal and Its Impact on Breeding Strategies

Genes ◽  
2021 ◽  
Vol 12 (2) ◽  
pp. 184
Author(s):  
Giuseppe Andolfo ◽  
Nunzio D’Agostino ◽  
Luigi Frusciante ◽  
Maria Raffaella Ercolano
Keyword(s):  
Evolutionary Dynamics ◽  
Special Focus ◽  
Breeding Strategies ◽  
Adaptive Diversification ◽  
Solanum Lycopersicum L ◽  
Solanaceae Species ◽  
Specific Pathogen ◽  
Adaptive Processes ◽  
Species Specific ◽  
R Loci

Tomato (Solanum lycopersicum L.) is a model system for studying the molecular basis of resistance in plants. The investigation of evolutionary dynamics of tomato resistance (R)-loci provides unique opportunities for identifying factors that promote or constrain genome evolution. Nucleotide-binding domain and leucine-rich repeat (NB-LRR) receptors belong to one of the most plastic and diversified families. The vast amount of genomic data available for Solanaceae and wild tomato relatives provides unprecedented insights into the patterns and mechanisms of evolution of NB-LRR genes. Comparative analysis remarked a reshuffling of R-islands on chromosomes and a high degree of adaptive diversification in key R-loci induced by species-specific pathogen pressure. Unveiling NB-LRR natural variation in tomato and in other Solanaceae species offers the opportunity to effectively exploit genetic diversity in genomic-driven breeding programs with the aim of identifying and introducing new resistances in tomato cultivars. Within this motivating context, we reviewed the repertoire of NB-LRR genes available for tomato improvement with a special focus on signatures of adaptive processes. This issue is still relevant and not thoroughly investigated. We believe that the discovery of mechanisms involved in the generation of a gene with new resistance functions will bring great benefits to future breeding strategies.

scholarly journals Humans and other commonly used model organisms are resistant to cycloheximide-mediated biases in ribosome profiling experiments

2021 ◽  
Vol 12 (1) ◽  
Author(s):  
Puneet Sharma ◽  
Jie Wu ◽  
Benedikt S. Nilges ◽  
Sebastian A. Leidel
Keyword(s):  
Human Cells ◽  
Ribosome Profiling ◽  
Model Organisms ◽  
Treatment Conditions ◽  
Genome Wide ◽  
Optimized Protocol ◽  
Gene Level ◽  
Translation Inhibitor ◽  
Species Specific ◽  
Conformational Restrictions

AbstractRibosome profiling measures genome-wide translation dynamics at sub-codon resolution. Cycloheximide (CHX), a widely used translation inhibitor to arrest ribosomes in these experiments, has been shown to induce biases in yeast, questioning its use. However, whether such biases are present in datasets of other organisms including humans is unknown. Here we compare different CHX-treatment conditions in human cells and yeast in parallel experiments using an optimized protocol. We find that human ribosomes are not susceptible to conformational restrictions by CHX, nor does it distort gene-level measurements of ribosome occupancy, measured decoding speed or the translational ramp. Furthermore, CHX-induced codon-specific biases on ribosome occupancy are not detectable in human cells or other model organisms. This shows that reported biases of CHX are species-specific and that CHX does not affect the outcome of ribosome profiling experiments in most settings. Our findings provide a solid framework to conduct and analyze ribosome profiling experiments.

Extensive MHC variability in cichlid fishes of Lake Malawi

Nature ◽  
1993 ◽  
Vol 364 (6435) ◽  
pp. 330-334 ◽  
Author(s):  
Dagmar Klein ◽  
Hideki Ono ◽  
Colm O'hUigin ◽  
Vladimir Vincek ◽  
Tijs Goldschmidt ◽  
...  
Keyword(s):  
Lake Malawi ◽  
Cichlid Fishes

scholarly journals Behavior-dependent cis regulation reveals genes and pathways associated with bower building in cichlid fishes

2018 ◽  
Vol 115 (47) ◽  
pp. E11081-E11090 ◽  
Author(s):  
Ryan A. York ◽  
Chinar Patil ◽  
Kawther Abdilleh ◽  
Zachary V. Johnson ◽  
Matthew A. Conte ◽  
...  
Keyword(s):  
Gene Expression ◽  
Neural Plasticity ◽  
Genetic Basis ◽  
Specific Expression ◽  
Preferential Expression ◽  
Cichlid Fishes ◽  
Brain Gene Expression ◽  
Genome Wide ◽  
Allele Specific ◽  
Genomic Regions

Many behaviors are associated with heritable genetic variation [Kendler and Greenspan (2006) Am J Psychiatry 163:1683–1694]. Genetic mapping has revealed genomic regions or, in a few cases, specific genes explaining part of this variation [Bendesky and Bargmann (2011) Nat Rev Gen 12:809–820]. However, the genetic basis of behavioral evolution remains unclear. Here we investigate the evolution of an innate extended phenotype, bower building, among cichlid fishes of Lake Malawi. Males build bowers of two types, pits or castles, to attract females for mating. We performed comparative genome-wide analyses of 20 bower-building species and found that these phenotypes have evolved multiple times with thousands of genetic variants strongly associated with this behavior, suggesting a polygenic architecture. Remarkably, F1 hybrids of a pit-digging and a castle-building species perform sequential construction of first a pit and then a castle bower. Analysis of brain gene expression in these hybrids showed that genes near behavior-associated variants display behavior-dependent allele-specific expression with preferential expression of the pit-digging species allele during pit digging and of the castle-building species allele during castle building. These genes are highly enriched for functions related to neurodevelopment and neural plasticity. Our results suggest that natural behaviors are associated with complex genetic architectures that alter behavior via cis-regulatory differences whose effects on gene expression are specific to the behavior itself.

Social Status and Arginine Vasotocin Neuronal Phenotypes in a Cichlid Fish

2015 ◽  
Vol 85 (3) ◽  
pp. 203-213 ◽  
Author(s):  
Olinda Almeida ◽  
Rui F. Oliveira
Keyword(s):  
Social Status ◽  
Social Behaviour ◽  
Cichlid Fish ◽  
Brain Regions ◽  
Cell Number ◽  
Arginine Vasotocin ◽  
Cichlid Species ◽  
Neuronal Populations ◽  
Soma Size ◽  
Species Specific

The nonapeptide arginine vasotocin (AVT) and its mammalian homologue arginine vasopressin play a key role in the regulation of social behaviour across vertebrates. In teleost fishes, three AVT neuronal populations have been described in the preoptic area (POA): the parvocellular (pPOA), the magnocellular (mPOA) and the gigantocellular (gPOA). Neurons from each of these areas project both to the pituitary and to other brain regions, where AVT is supposed to regulate neural circuits underlying social behaviour. However, in the fish species studied so far, there is considerable variation in which AVT neuronal populations are involved in behavioural modulation and in the direction of the effect. In this study, the association between AVT neuronal phenotypes and social status was investigated in the Mozambique tilapia (Oreochromis mossambicus). This species is an African female mouth-brooding cichlid fish in which males form breeding aggregations in which dominant males establish territories and subordinate males to act as floaters. With respect to sex differences in AVT neuronal phenotypes, females have a larger number of AVT neurons in the pPOA and mPOA. Within males, AVT appeared associated with social subordination, as indicated by the larger cell body areas of AVT neurons in mPOA and gPOA nuclei of non-territorial males. There were also positive correlations between submissive behaviour and the soma size of AVT cells in all three nuclei and AVT cell number in the mPOA. In summary, the results provide evidence for an involvement of AVT in the modulation of social behaviour in tilapia, but it was not possible to identify specific roles for specific AVT neuronal populations. The results presented here also contrast with those previously published for another cichlid species with a similar mating system, which highlights the species-specific nature of the pattern of association between AVT and social behaviour even within the same taxonomic family.

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