Parallel and non-parallel changes of the gut microbiota during trophic diversification in repeated young adaptive radiations of sympatric cichlid fish

AbstractRecent increases in understanding the ecological and evolutionary roles of microbial communities has underscored their importance for their hosts’ biology. Yet, little is known about gut microbiota dynamics during early stages of ecological diversification and speciation. We studied the gut microbiota of extremely young adaptive radiations of Nicaraguan crater lake cichlid fish (Amphilophus cf. citrinellus) to test the hypothesis that parallel evolution in trophic ecology is associated with parallel changes of the gut microbiota. Bacterial communities of the water (eDNA) and guts were highly distinct, indicating that the gut microbiota is shaped by host-specific factors. Across individuals of the same crater lake, differentiation in trophic ecology was associated with gut microbiota differentiation, suggesting that diet affects the gut microbiota. However, differences in trophic ecology were much more pronounced across than within species whereas little evidence was found for similar patterns in taxonomic and functional changes of the gut microbiota. Across the two crater lakes, we could not detect evidence for parallel changes of the gut microbiota associated with trophic ecology. Similar cases of non-parallelism have been observed in other recently diverged fish species and might be explained by a lack of clearly differentiated niches during early stages of ecological diversification.

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Parallel and non-parallel changes of the gut microbiota during trophic diversification in repeated young adaptive radiations of sympatric cichlid fish

10.21203/rs.3.rs-20414/v3 ◽

2020 ◽

Author(s):

Andreas Härer ◽

Julián Torres-Dowdall ◽

Sina J. Rometsch ◽

Elizabeth Yohannes ◽

Gonzalo Machado-Schiaffino ◽

...

Keyword(s):

Gut Microbiota ◽

Microbial Communities ◽

Trophic Ecology ◽

Cichlid Fish ◽

Conclusive Evidence ◽

Rrna Gene ◽

Crater Lakes ◽

Ecological Diversification ◽

Early Stages ◽

Adaptive Radiations

Abstract Background: Recent increases in understanding the ecological and evolutionary roles of microbial communities has underscored the importance for their hosts’ biology. Yet, little is known about gut microbiota dynamics during early stages of ecological diversification and speciation. We sequenced the V4 region of the 16s rRNA gene to study the gut microbiota of Nicaraguan Midas cichlid fish (Amphilophus cf. citrinellus). Specifically, we tested the hypothesis that parallel divergence in trophic ecology in extremely young adaptive radiations from two crater lakes is associated with parallel changes of their gut microbiota. Results: Bacterial communities of fish guts and lake water were highly distinct, indicating that the gut microbiota is shaped by host-specific factors. Among individuals of the same crater lake, differentiation in trophic ecology was weakly associated with gut microbiota differentiation, suggesting that diet, to some extent, affects the gut microbiota. However, differences in trophic ecology were much more pronounced across than within species whereas similar patterns were not observed for taxonomic and functional differences of the gut microbiota. Across the two crater lakes, we could not detect conclusive evidence for parallel changes of the gut microbiota associated with trophic ecology. Conclusions: A lack of clearly differentiated niches during early stages of ecological diversification might result in non-parallel changes of gut microbial communities, as observed in our study system as well as in other recently diverged fish species.

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Parallel and non-parallel changes of the gut microbiota during trophic diversification in repeated young adaptive radiations of sympatric cichlid fish

10.21203/rs.3.rs-20414/v1 ◽

2020 ◽

Author(s):

Andreas Härer ◽

Julián Torres-Dowdall ◽

Sina J. Rometsch ◽

Elizabeth Yohannes ◽

Gonzalo Machado-Schiaffino ◽

...

Keyword(s):

Gut Microbiota ◽

Microbial Communities ◽

Trophic Ecology ◽

Cichlid Fish ◽

Conclusive Evidence ◽

Rrna Gene ◽

Crater Lakes ◽

Ecological Diversification ◽

Early Stages ◽

Adaptive Radiations

Abstract Background: Recent increases in understanding the ecological and evolutionary roles of microbial communities has underscored the importance for their hosts’ biology. Yet, little is known about gut microbiota dynamics during early stages of ecological diversification and speciation. We sequenced the V4 region of the 16s rRNA gene to study the gut microbiota of Nicaraguan Midas cichlid fish ( Amphilophus cf. citrinellus ). Specifically, we tested the hypothesis that parallel divergence in trophic ecology in extremely young adaptive radiations from two crater lakes is associated with parallel changes of their gut microbiota.Results: Bacterial communities of fish guts and lake water were highly distinct, indicating that the gut microbiota is shaped by host-specific factors. Among individuals of the same crater lake, differentiation in trophic ecology was weakly associated with gut microbiota differentiation, suggesting that diet, to some extent, affects the gut microbiota. However, differences in trophic ecology were much more pronounced across than within species whereas similar patterns were not observed for taxonomic and functional differences of the gut microbiota. Across the two crater lakes, we could not detect conclusive evidence for parallel changes of the gut microbiota associated with trophic ecology.Conclusions: A lack of clearly differentiated niches during early stages of ecological diversification might result in non-parallel changes of gut microbial communities, as observed in our study system as well as in other recently diverged fish species.

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Parallel and non-parallel changes of the gut microbiota during trophic diversification in repeated young adaptive radiations of sympatric cichlid fish

10.21203/rs.3.rs-20414/v2 ◽

2020 ◽

Author(s):

Andreas Härer ◽

Julián Torres-Dowdall ◽

Sina J. Rometsch ◽

Elizabeth Yohannes ◽

Gonzalo Machado-Schiaffino ◽

...

Keyword(s):

Gut Microbiota ◽

Microbial Communities ◽

Trophic Ecology ◽

Cichlid Fish ◽

Conclusive Evidence ◽

Rrna Gene ◽

Crater Lakes ◽

Ecological Diversification ◽

Early Stages ◽

Adaptive Radiations

Abstract Background: Recent increases in understanding the ecological and evolutionary roles of microbial communities has underscored the importance for their hosts’ biology. Yet, little is known about gut microbiota dynamics during early stages of ecological diversification and speciation. We sequenced the V4 region of the 16s rRNA gene to study the gut microbiota of Nicaraguan Midas cichlid fish ( Amphilophus cf. citrinellus ). Specifically, we tested the hypothesis that parallel divergence in trophic ecology in extremely young adaptive radiations from two crater lakes is associated with parallel changes of their gut microbiota. Results: Bacterial communities of fish guts and lake water were highly distinct, indicating that the gut microbiota is shaped by host-specific factors. Among individuals of the same crater lake, differentiation in trophic ecology was weakly associated with gut microbiota differentiation, suggesting that diet, to some extent, affects the gut microbiota. However, differences in trophic ecology were much more pronounced across than within species whereas similar patterns were not observed for taxonomic and functional differences of the gut microbiota. Across the two crater lakes, we could not detect conclusive evidence for parallel changes of the gut microbiota associated with trophic ecology. Conclusions: A lack of clearly differentiated niches during early stages of ecological diversification might result in non-parallel changes of gut microbial communities, as observed in our study system as well as in other recently diverged fish species.

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Parallel and non-parallel changes of the gut microbiota during trophic diversification in repeated young adaptive radiations of sympatric cichlid fish

Microbiome ◽

10.1186/s40168-020-00897-8 ◽

2020 ◽

Vol 8 (1) ◽

Author(s):

Andreas Härer ◽

Julián Torres-Dowdall ◽

Sina J. Rometsch ◽

Elizabeth Yohannes ◽

Gonzalo Machado-Schiaffino ◽

...

Keyword(s):

Gut Microbiota ◽

Microbial Communities ◽

Trophic Ecology ◽

Cichlid Fish ◽

Conclusive Evidence ◽

Rrna Gene ◽

Crater Lakes ◽

Ecological Diversification ◽

Early Stages ◽

Adaptive Radiations

Abstract Background Recent increases in understanding the ecological and evolutionary roles of microbial communities have underscored the importance of their hosts’ biology. Yet, little is known about gut microbiota dynamics during the early stages of ecological diversification and speciation. We sequenced the V4 region of the 16s rRNA gene to study the gut microbiota of Nicaraguan Midas cichlid fish (Amphilophus cf. citrinellus). Specifically, we tested the hypothesis that parallel divergence in trophic ecology in extremely young adaptive radiations from two crater lakes is associated with parallel changes of their gut microbiota. Results Bacterial communities of fish guts and lake water were highly distinct, indicating that the gut microbiota is shaped by host-specific factors. Among individuals of the same crater lake, differentiation in trophic ecology was weakly associated with gut microbiota differentiation, suggesting that diet, to some extent, affects the gut microbiota. However, differences in trophic ecology were much more pronounced across than within species whereas similar patterns were not observed for taxonomic and functional differences of the gut microbiota. Across the two crater lakes, we could not detect conclusive evidence for parallel changes of the gut microbiota associated with trophic ecology. Conclusions A lack of clearly differentiated niches during the early stages of ecological diversification might result in non-parallel changes of gut microbial communities, as observed in our study system as well as in other recently diverged fish species.

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Local variation and parallel evolution: morphological and genetic diversity across a species complex of neotropical crater lake cichlid fishes

Philosophical Transactions of the Royal Society B Biological Sciences ◽

10.1098/rstb.2009.0271 ◽

2010 ◽

Vol 365 (1547) ◽

pp. 1763-1782 ◽

Cited By ~ 108

Author(s):

Kathryn R. Elmer ◽

Henrik Kusche ◽

Topi K. Lehtonen ◽

Axel Meyer

Keyword(s):

Genetic Diversity ◽

Species Complex ◽

Body Shape ◽

Crater Lake ◽

Shape Change ◽

Parallel Evolution ◽

Cichlid Fish ◽

Shape Variation ◽

Body Depth ◽

Crater Lakes

The polychromatic and trophically polymorphic Midas cichlid fish species complex ( Amphilophus cf. citrinellus ) is an excellent model system for studying the mechanisms of speciation and patterns of phenotypic diversification in allopatry and in sympatry. Here, we first review research to date on the species complex and the geological history of its habitat. We analyse body shape variation from all currently described species in the complex, sampled from six crater lakes (maximally 1.2–23.9 kyr old) and both great lakes in Nicaragua. We find that Midas cichlid populations in each lake have their own characteristic body shape. In lakes with multiple sympatric species of Midas cichlid, each species has a distinct body shape. Across the species complex, most body shape change relates to body depth, head, snout and mouth shape and caudal peduncle length. There is independent parallel evolution of an elongate limnetic species in at least two crater lakes. Mitochondrial genetic diversity is higher in crater lakes with multiple species. Midas cichlid species richness increases with the size and age of the crater lakes, though no such relationship exists for the other syntopic fishes. We suggest that crater lake Midas cichlids follow the predicted pattern of an adaptive radiation, with early divergence of each crater lake colonization, followed by intralacustrine diversification and speciation by ecological adaptation and sexual selection.

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Parallel evolution in Ugandan crater lakes: repeated evolution of limnetic body shapes in haplochromine cichlid fish

BMC Evolutionary Biology ◽

10.1186/s12862-015-0287-3 ◽

2015 ◽

Vol 15 (1) ◽

pp. 9 ◽

Cited By ~ 18

Author(s):

Gonzalo Machado-Schiaffino ◽

Andreas F Kautt ◽

Henrik Kusche ◽

Axel Meyer

Keyword(s):

Parallel Evolution ◽

Cichlid Fish ◽

Crater Lakes ◽

Haplochromine Cichlid ◽

Repeated Evolution ◽

Body Shapes

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Epigenetic Divergence during Early Stages of Speciation in an African Crater Lake Cichlid Fish

10.1101/2021.07.30.435319 ◽

2021 ◽

Author(s):

Gregoire Vernaz ◽

Alan G. Hudson ◽

M. Emilia Santos ◽

Bettina Fischer ◽

Madeleine Carruthers ◽

...

Keyword(s):

Transcriptional Activity ◽

Crater Lake ◽

Cichlid Fish ◽

Common Garden ◽

Biological Processes ◽

Global Methylation ◽

Habitat Occupancy ◽

Early Stages ◽

Genome Wide ◽

Functional Relevance

Epigenetic variation can alter transcription and promote phenotypic divergence between populations facing different environmental challenges. Here we assess the epigenetic basis of diversification during the early stages of speciation. We focus on the extent and functional relevance of DNA methylome divergence between two Astatotilapia calliptera ecomorphs in crater Lake Masoko, southern Tanzania. We report extensive genome-wide methylome divergence between populations linked to key biological processes, including transcriptional activity of ecologically-relevant genes. These include genes involved in steroid metabolism, haemoglobin composition and erythropoiesis, consistent with divergent habitat occupancy of the ecomorphs. Using a common garden experiment, we found that global methylation profiles are rapidly remodelled across generations, but ecomorph-specific differences can be inherited. Collectively, our study suggests an epigenetic contribution to early stages of vertebrate speciation.

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Phylogenetic analysis of the Digenea (Platyhelminthes: Cercomeria) with comments on their adaptive radiation

Canadian Journal of Zoology ◽

10.1139/z85-062 ◽

1985 ◽

Vol 63 (2) ◽

pp. 411-443 ◽

Cited By ~ 103

Author(s):

Daniel R. Brooks ◽

Richard T. O'Grady ◽

David R. Glen

Keyword(s):

Phylogenetic Analysis ◽

Phylogenetic Tree ◽

Morphological Change ◽

Adaptive Radiation ◽

Parallel Evolution ◽

Morphological Diversification ◽

Ecological Diversification ◽

Low Degree ◽

Adaptive Radiations ◽

Low Levels

Phylogenetic analysis of 63 digenean family groups, based on 113 adult characters and 90 larval characters, produced a phylogenetic tree comprising nine orders. Adult characters alone resolved 76% of the phylogenetic tree, whereas larval characters alone resolved 74%. There was no disagreement in phylogenetic inferences drawn from only larval or only adult characters, and yet the larval forms of digeneans do not seem to be recapitulations of ancestral adult forms. The consistency index for the tree is 74%, indicating a low degree of parallel evolution in digenean morphology. Diversification in six sets of ecological characteristics combined resolves 26% of the phylogenetic tree. The combination of (i) larval and adult congruence in the absence of recapitulation, (ii) low levels of parallel evolution in morphology, and (iii) ecological diversification lagging far behind morphological change discounts traditional notions of adaptive radiations. Digeneans have experienced great morphological diversification constrained by their developmental programs and history, and have maintained their functional intergrity with few changes caused by extrinsic, "adaptive," forces.

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