Periodic Reporting for period 1 - ANEMONE (Evolving a Home for Nemo: Genomic Consequences and Convergence in a Model Marine Mutualism)
Período documentado: 2020-08-01 hasta 2022-07-31
The complexity of mutualistic interactions have attracted a great deal of scientific attention, and although general evolutionary expectations exist, no unifying evolutionary theory of mutualism has been established. Largely impeding the development of a synthetic framework for mutualism are misunderstandings, or incomplete understandings, of individual case studies. No mutualism is perhaps more representative of this than the iconic clownfish-sea anemone symbioses, a model mutualism regularly used for exploring fundamental biological processes, but one in which our understanding remains wildly incomplete due to a lack of research into the evolution and genomics of the host anemones. The goals of this project are to conduct full genome sequencing of the clownfish-hosting sea anemones to test general evolutionary expectations of mutualism. Specifically, I will test:
1) Whether the mutualistic benefits of hosting clownfishes has led to multiple adaptive radiations in host sea anemones
2) Whether the mutualistic benefits of hosting clownfishes led to significant ecological opportunity for host anemones, and thus, signatures of demographic population expansion, that coincide with the onset of the symbiosis.
3) Whether mutualism with clownfishes has generated similar selective pressure and convergent genome evolution and architecture among host anemones.
4) The Red King Hypothesis, which states that the balance of mutually exploitative symbioses should lead constituent mutualistic lineages to have slower rates of molecular evolution than their free-living relatives.
This project will be the first genomic investigation into the mutualism of the clownfish-hosting sea anemones, provide novel insight into this charismatic symbiosis that will bear on the interpretation of dozens of prior studies that span scientific disciplines, and generate valuable community resources for future research. The proposed research is timely and necessary as the recently published genomes of 10 clownfish species have already led to a number of publications on the genomic evolution of clownfishes. Generating genomic data for the clownfish-hosting anemones is critical to provide proper perspective on how the entire symbiosis has evolved and place future papers into a proper mutualistic context. Further, much of the general expectations of how biodiversity evolves within mutualisms come from terrestrial examples. Adding thoroughly disentangled marine examples is thus critical for providing comparative data in order to evaluate the generalities of mutualism across ecosystems.
1) Whether the mutualistic benefits of hosting clownfishes has led to multiple adaptive radiations in host sea anemones
2) Whether the mutualistic benefits of hosting clownfishes led to significant ecological opportunity for host anemones, and thus, signatures of demographic population expansion, that coincide with the onset of the symbiosis.
3) Whether mutualism with clownfishes has generated similar selective pressure and convergent genome evolution and architecture among host anemones.
4) The Red King Hypothesis, which states that the balance of mutually exploitative symbioses should lead constituent mutualistic lineages to have slower rates of molecular evolution than their free-living relatives.
This project will be the first genomic investigation into the mutualism of the clownfish-hosting sea anemones, provide novel insight into this charismatic symbiosis that will bear on the interpretation of dozens of prior studies that span scientific disciplines, and generate valuable community resources for future research. The proposed research is timely and necessary as the recently published genomes of 10 clownfish species have already led to a number of publications on the genomic evolution of clownfishes. Generating genomic data for the clownfish-hosting anemones is critical to provide proper perspective on how the entire symbiosis has evolved and place future papers into a proper mutualistic context. Further, much of the general expectations of how biodiversity evolves within mutualisms come from terrestrial examples. Adding thoroughly disentangled marine examples is thus critical for providing comparative data in order to evaluate the generalities of mutualism across ecosystems.
Work performed during this project resulted in the first major revision of clownfish-sea anemone host associations in over 30 years, the identification of cryptic host sea anemone species from previously generated population genomic datasets, and the generation of full genome sequence data for 40 individuals from 11 nominal species- none of which had previously been sequenced.
Updated host association data resulted in the documentation of over 24 new sea anemone host associations across 10 different clownfish species. When simplified to focus on only the anemones that serve as hosts to reproductive adult clownfishes we discovered that these reproductive adult host association frequencies are significantly linked to clownfish color and pattern. Ultimately, these updated patterns of host association allowed us to disentangle the adaptive radiation of clownfishes and explains convergent color pattern evolution in this enigmatic group.
Cryptic species of host sea anemones were delimited using previously generated genomic data (reduced representation and bait-capture sequencing approaches). Data were analyzed for three species of anemones with sufficient samples sizes: Entacmaea quadricolor, Heteractis crispa, and H. magnifica. Using population genetic clustering analyses, I identified five highly differentiated cryptic lineages of E. quadricolor, two cryptic lineages of H. crispa, and at least three cryptic lineages of H. magnifica.
The delimitation of new cryptic lineages informed downstream sample selection for full genome sequencing. We sequenced at least one individual from 8 of the 10 nominal clownfish-hosting sea anemone species. We also generated full genome data for all five cryptic E. quadricolor species and both cryptic H. crispa species. In total we generated full genome sequence data for 40 individuals from 11 nominal species and 7 undescribed cryptic species.
Genome assembly, annotation, and comparative analyses are ongoing. Data generated updating host associations is currently being written up for peer reviewed publication. The dataset I analysed to identify cryptic host anemone species is currently being expanded to include more samples and geographic locations.
Updated host association data resulted in the documentation of over 24 new sea anemone host associations across 10 different clownfish species. When simplified to focus on only the anemones that serve as hosts to reproductive adult clownfishes we discovered that these reproductive adult host association frequencies are significantly linked to clownfish color and pattern. Ultimately, these updated patterns of host association allowed us to disentangle the adaptive radiation of clownfishes and explains convergent color pattern evolution in this enigmatic group.
Cryptic species of host sea anemones were delimited using previously generated genomic data (reduced representation and bait-capture sequencing approaches). Data were analyzed for three species of anemones with sufficient samples sizes: Entacmaea quadricolor, Heteractis crispa, and H. magnifica. Using population genetic clustering analyses, I identified five highly differentiated cryptic lineages of E. quadricolor, two cryptic lineages of H. crispa, and at least three cryptic lineages of H. magnifica.
The delimitation of new cryptic lineages informed downstream sample selection for full genome sequencing. We sequenced at least one individual from 8 of the 10 nominal clownfish-hosting sea anemone species. We also generated full genome data for all five cryptic E. quadricolor species and both cryptic H. crispa species. In total we generated full genome sequence data for 40 individuals from 11 nominal species and 7 undescribed cryptic species.
Genome assembly, annotation, and comparative analyses are ongoing. Data generated updating host associations is currently being written up for peer reviewed publication. The dataset I analysed to identify cryptic host anemone species is currently being expanded to include more samples and geographic locations.
The clownfish-sea anemone symbiosis has long been an evolutionary enigma- mutualisms with sea anemones having previously been identified as the key innovation that sparked the subsequent radiation of clownfishes. However, no ecological variable has ever been identified that can explain species level diversity or color pattern variation. Our updated host associations, along with our new approach to treat host-use in an evolutionarily significant way, links clownfish color pattern evolution to the sea anemone hosts used at the reproductive adult life stage. This discovery largely solves the mystery of clownfish color pattern evolution and identifies the sea anemone host as the key to understanding patterns of diversification. An entire new field focused on understanding the adaptive function of clownfish color pattern, and the ecological processes behind how the sea anemone host has driven these convergent patterns is now open.
Cryptic species delimitation analyses have revealed co-occurring cryptic Entacmaea quadricolor lineages on coral reefs throughout the Japanese Archipelago. These occur on the same reefs at the same depths and are morphologically indistinguishable. However, each cryptic species hosts a different clownfish symbiont, with on anemone species hosting Amphiprion clarki and the other hosting Amphiprion frenatus. This 100% ecological host partitioning clearly demonstrates that the clownfish symbionts are able to differentiate between closely related cryptic species and hints that there may be far more host specialization and co-evolution between host anemone and fish symbiont than previously realized. Interestingly, the cryptic lineage that hosts A. clarkii is more closely related to a separate E. quadricolor lineage from the Maldives that also host A. clarkii than it is to the co-occurring E. quadricolor lineage that hosts A. frenatus.
Full genome data assembly is ongoing, and we do not yet have results from this aspect of the project.
All data generated from this project will be analzyed, written up for publication, and made fully open access. Data generated from this project will be presented at major international conferences in 2023. Ultimately, the results generated from this project to date suggest that it will revolutionize our understanding of this iconic mutualism. We anticipate these findings and data to be broadly useful ranging from basic scientific studies of mutualism to highly applied conservation biology initiatives, as well as for the ornamental aquarium trade, which heavily targets these species and is a financially lucrative enterprise.
Cryptic species delimitation analyses have revealed co-occurring cryptic Entacmaea quadricolor lineages on coral reefs throughout the Japanese Archipelago. These occur on the same reefs at the same depths and are morphologically indistinguishable. However, each cryptic species hosts a different clownfish symbiont, with on anemone species hosting Amphiprion clarki and the other hosting Amphiprion frenatus. This 100% ecological host partitioning clearly demonstrates that the clownfish symbionts are able to differentiate between closely related cryptic species and hints that there may be far more host specialization and co-evolution between host anemone and fish symbiont than previously realized. Interestingly, the cryptic lineage that hosts A. clarkii is more closely related to a separate E. quadricolor lineage from the Maldives that also host A. clarkii than it is to the co-occurring E. quadricolor lineage that hosts A. frenatus.
Full genome data assembly is ongoing, and we do not yet have results from this aspect of the project.
All data generated from this project will be analzyed, written up for publication, and made fully open access. Data generated from this project will be presented at major international conferences in 2023. Ultimately, the results generated from this project to date suggest that it will revolutionize our understanding of this iconic mutualism. We anticipate these findings and data to be broadly useful ranging from basic scientific studies of mutualism to highly applied conservation biology initiatives, as well as for the ornamental aquarium trade, which heavily targets these species and is a financially lucrative enterprise.