We are interested in marine ecological and evolutionary processes in the tropics and their implications in the contexts of climate change, conservation and management. Such processes include notably productivity, dispersal, adaptation, speciation and adaptive radiation. Over the last two decades we have been using the hamlets, a group of reef fishes from the greater Caribbean, as a model system for our research. We are now in the process of developing other reef fish model species that are amenable to multi-generational experiments. From a methodological perspective we have a strong (but non-exclusive) focus on genetics.
Oscar Puebla
ZMT / ICBM
Research
Selected ongoing projects
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According to the genic view, species are characterized by the genes that underlie functional divergence. In this project, we take a phylogenomic approach to assess this view at the scale of a whole radiation. The results show that phenotypic diversification and reproductive isolation — two major attributes of species — may unfold in the near-absence of phylogenetic signal, both genome-wide and at the gene-tree level. Conducted by Martin Helmkampf, Floriane Coulmance, Melanie Heckwolf and twelve collaborators from Panama, Colombia, Mexico, the USA and the UK. Led by OP, funded by the DFG.
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Gills are commonly known as the organ through which fishes breathe, but they also play a critical role in waste excretion, osmoregulation and immunity. Like the gut and skin, the gills harbor a community of micro-organisms, the so-called microbiome. Yet due to the difficulty to culture it and the limits of metabarcoding, the fish gill microbiome is poorly known and its functional role poorly understood. Nevertheless, it is possible to sequence microbial genomes without culturing them. This is what we do in this project using > 300 gill samples from the hamlets, a group of Caribbean reef fishes. A high proportion of the DNA that we recovered belonged to the fish host, but we were nonetheless able to assemble 67 microbial genomes, most of which belong to new species. These genomes provide insights into the functional capabilities of the fish gill microbiome and point to intricate host-microbe and microbe-microbe interactions, with potential implications for fish homeostasis and health. They also provide potential for a biomarker-based approach to monitor the health of fish populations by analyzing the composition of their gill microbiomes. Conducted by Sabrin Abdelghany in collaboration with Matthew Schechter and Murat Eren. Led by OP, funded by the DAAD.
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Isolation by distance, whereby genetic distance between individuals or populations increases with geographic distance, is a fundamental population genetic pattern that is observed across a broad range of taxa and spatial scales. This pattern is driven by dispersal limitation and is therefore informative about dispersal rate (sigma), a parameter of both basic and applied interest. Yet isolation by distance is typically evidenced with classic genetic markers such as microsatellites or single nucleotide polymorphisms, which does neither allow to estimate sigma without an ad hoc estimate of effective population density (De) nor to distinguish the effect of recent dispersal from more ancestral processes. Blocks of identity by descent (IBD), continuous tracts of DNA that are co-inherited from a common ancestor, provide another lens through which isolation by distance may be viewed. This approach allows to jointly estimate recent sigma and De, and to distinguish recent dispersal from more ancestral processes by considering long and short IBD blocks, respectively. In this project, we apply this approach to the barred hamlet (Hypoplectrus puella), a reef fish from the wider Caribbean with a three-weeks planktonic larval phase, at both the local (200 km) and regional (>3500 km) scale. Conducted by Nina Tombers and Martin Helmkampf. Led by OP.
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Recent radiations provide rare windows into the early stages of diversification. With the advent of second and third-generation DNA sequencing technologies, it is now possible to study this process at the whole-genome level. Nevertheless, few studies have taken a similar comprehensive approach at the phenotypic level. This is what we do here using the hamlets (Hypoplectrus spp) as a model system.
These reef fishes from the greater Caribbean diversified rapidly into 19+ species that differ essentially in terms of colour pattern.
Using a recently developed workflow, we analysed in situ photographs of 571 fishes from 14 species at pixel resolution with a fully standardised and automated procedure. The results show that sympatric species form phenotypic clusters that differ significantly from each other, but nonetheless present substantial within-species variation and between-species overlap. At the scale of the greater Caribbean, geographic variation within species further contributes to this overlap, resulting in almost continuous variation across the whole radiation. A complementary dataset of 327 genomes from 20 species indicates that similar patterns are observed at the population genomic level. These results show that sympatric clusters are maintained by selection from a phenotypic and genomic substrate that is largely continuous and shared among species. conducted by Floriane Colmance. Led py OP, funded by the DFG.