Rapid speciation in Cichlids apart from neodarwiniam


The article "Epigenetic divergence during early stages of speciation in an African crater lake cichlid fish" by Vernaz et al. (2022) investigates the role of epigenetics in the early stages of speciation in the cichlid fish Astatotilapia calliptera. Cichlid fishes are a diverse group of fish that are found in freshwater habitats in Africa. They are known for their rapid speciation, and have been used as a model system for studying the genetic and environmental factors that drive speciation. NeoDarwinism fails to provide mechanisms for rapid speciation due to the slow accumulation of mutations.

The study by Vernaz et al. focused on two lake ecomorphs of A. calliptera that diverged approximately 1,000 years ago. These ecomorphs, which are called benthic and pelagic, live in different habitats in Lake Masoko, Tanzania. The benthic ecomorph lives in the deeper, anoxic waters of the lake, while the pelagic ecomorph lives in the shallower, oxygenated waters.

The study found that the two ecomorphs showed extensive genome-wide methylome divergence, which is the modification of DNA that can affect gene expression without changing the underlying DNA sequence. This methylome divergence was associated with altered transcriptional activity of genes involved in a variety of biological processes, including erythropoiesis (the production of red blood cells), hemoglobin composition, and steroid metabolism. NeoDarwinism on the other hand is "gene centric."

The authors suggest that epigenetic divergence may be playing a role in the early stages of speciation in A. calliptera. They hypothesize that the different environmental conditions in the benthic and pelagic habitats of Lake Masoko have selected for different epigenetic profiles in the two ecomorphs. This epigenetic divergence may be helping to drive the evolution of new traits and adaptations that allow the two ecomorphs to survive and reproduce in their respective habitats.

This study provides new insights into the role of epigenetics in speciation. It suggests that epigenetic divergence can occur early in the speciation process, and that it can play a role in the evolution of new traits and adaptations. This research could have implications for our understanding of speciation in other organisms, and it could also lead to new insights into the mechanisms of epigenetic inheritance.

The extended evolutionary synthesis (EES) model argues that speciation can be driven by a combination of genetic and epigenetic changes. The EES model is more comprehensive than the neodarwinian model, and it better accounts for the complexity of speciation.

The study of epigenetics in speciation is still in its early stages, but it has the potential to revolutionize our understanding of how new species form. Epigenetic variation may be a more important driver of speciation than previously thought. This could have implications for our understanding of the evolution of biodiversity, as well as the conservation of endangered species.

Article snippets:

Epigenetic variation can alter transcription and promote phenotypic divergence between populations facing different environmental challenges

we assess the epigenetic basis of diversification during the early stages of speciation

Our study focuses on two lake ecomorphs that diverged approximately 1,000 years ago and a population in the nearby river from which they separated approximately 10,000 years ago.

Collectively, our study suggests an epigenetic contribution to the early stages of vertebrate speciation.

The genomic basis of adaptive phenotypic diversification and speciation has been extensively studied but many questions remain

Recent studies in plants and animals provided initial evidence for a contribution of heritable epigenetic divergence to functional phenotypic

We next examined the genomic localization of DMRs among populations and found promoter regions to be highly enriched in DMRs in all comparisons (greater than twofold enrichment), consistent with their cis-regulatory function

This suggests high methylome conservation between gene bodies of the most closely related populations.

We first noted that genes involved in transcription regulation were highly enriched in DMRs and then identified three further sets of biological processes for the genes enriched in methylome divergence

Notably, methylome divergence in developmental genes was shown previously to account for close to half of all species-specific epigenetic differences among three species part of the Lake Malawi cichlid radiation9

Additionally, regions showing benthic-specific methylome patterns and located in promoters, gene body and intergenic regions were significantly enriched for specific transcription factor binding motifs

This suggests cis-regulatory functions for such population-specific DMRs in development, hematopoiesis and metabolism, possibly correlated with acclimation to the benthic habitat. It is well established that differential methylation in promoter regions might impact the activity of methyl-sensitive transcription factors, therefore resulting in an altered transcriptional landscape21

suggesting an altered transcription factor activity landscape arising from population-specific methylome divergence, further work is needed to decipher the underlying mechanisms.

the role of epigenetics in facilitating rapid transcriptional divergence in the context of the early stages of speciation is currently unknown

methylation levels at promoter regions were significantly negatively correlated with transcriptional activity overall (

Critically, significant changes in transcriptional activity were strongly associated with methylome divergence at promoter regions (

these results suggest significant divergence in epigenetic and transcriptional landscapes affecting erythropoiesis and hemoglobin composition in benthic fish, which may facilitate occupation of anoxic conditions of the benthic habitat.

suggests that epigenetic divergence may have facilitated differences in dietary resource use patterns during colonization of Lake Masoko habitats.

Indeed, tissue-independent methylome divergence could reflect distinct core developmental processes between the populations, participating in early-life phenotypic differences, although methylome analysis of other somatic or embryonic tissues would be needed to further investigate their functions.

These results suggest that although methylome landscapes are highly environment-specific, showing high plasticity and significant association with altered transcriptional activity of functional genes, some methylome divergence has become fixed and may be inherited in populations of Lake Masoko (fixed DMRs

Our study lays the groundwork to investigate further the extent of the inheritance of epigenetic patterns in East African cichlids and assess any adaptive roles associated with methylome divergence

Our results provide direct and new evidence for functional and heritable methylome divergence associated with the early stages of speciation in the very young radiation (approximately 1,000 years ago) of Astatotilapia ecomorphs in Lake Masoko

In principle, therefore, epigenetic processes may provide the capacity for rapid occupation and competitive dominance in new ecological niches before fixation of epigenetic and genomic variation.

To our knowledge, our study demonstrates for the first time substantial methylome divergence, in part inherited, and associated with altered transcription in a very young vertebrate radiation at an unprecedented whole-genome resolution

Additionally, other epigenetic processes might be at play in parallel to DNA methylation in facilitating phenotypic diversification in teleost fish radiation, such as microRNAs1,1

A key challenge now is to determine the mechanisms and rates of fixation of heritable epigenetic variation within populations6,7,44, including epigenetic inheritance and reprograming, the extent of the adaptive advantage associated with methylome divergence, and how this associates with the genomic fixation observed during the later stages of speciation.


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